[mlpack] branch master updated (f2d5b83 -> 76b8849)
Barak A. Pearlmutter
barak+git at pearlmutter.net
Mon Jan 18 11:19:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
bap pushed a change to branch master
in repository mlpack.
from f2d5b83 correct diferent spelling
new f15744f upstream development repo moved from svn to git on github
new 5a7b54f create
new 75ce990 Added basic directories.
new 1df3ef6 library in
new 6726d3c hi
new 24ee655 hi
new 1ed6760 hi
new abd33ba added comments so doxygen will pick up trees
new aec0026 hi
new 64ab67b hi
new 7a00654 Updated to support external tree
new 6f8792c hi
new 3de2182 hi
new 078b62c hi
new 56f45d2 hi
new 022a90f hi
new fc0d935 hi
new 683f6cf hi
new edb213a latex help for matrices
new 50f6472 hi
new cd18391 hi
new f0bedcb use curl instead of wget
new 1b248be hi
new 8055c17 hi
new 736a77d works with spaces
new 5d903d9 hi
new cf06bc2 fixed help for fx-cleanup
new 9c08670 hi
new 8447807 hi
new 0ef8f31 hi
new 8c651ff hi
new 8ffa2d3 hi
new 83c95e2 linear svm seems to be working
new 2931114 hi
new d109b27 hi
new d945422 hi
new d611f08 Fixed the damn bug
new 213aef3 hi
new da73f0e looks like superpar will be taking life soon
new 92b3b64 hi
new dbc24ee hi
new c0bfb52 hi
new d35268d hi
new 4ae6bf2 hi
new 0a18417 hi
new e57876d hi
new 8bfe12e tkde expressed in GNP-preduce -- yay
new 3863ada hi
new dcb3173 fixed a build system problem
new 8ac4398 hi
new 2676d95 hi
new 323bbfb hi
new 1b77d60 hi
new 834ebf4 hi
new 65bf5ec hi
new 6fcec94 first scheck in
new a5b60ac added some more files
new dad6f0a hi
new 7d06d09 hi
new d922914 hi
new 0da2d15 removed some files
new 36e3835
new 166630e Working on it still
new d2813d9 HyperRectangle unit passed unit test
new 0be0ccd hi
new 0583dfd added a new file
new 1ed6d1b still working on it
new 0a3a0dc still working on
new 733abe3 node test compiled
new 3c57098 still working on it
new 26bc4b7 node_test passed
new b1ab722 still working
new 6fd1a1e hi
new e422ef6 hi
new 360b91a Switching from TYPELISTs to stucts
new d17acb6 hi
new 122b44a Still working
new f81dd10 Holy Object Traversal BATMAN!
new 402dca5 close to compiling
new f97bd9d compiled
new 74ea09d finished binary dataset iterator
new d0a8c1b Building trees seems to work
new bd029d7 hi
new f4f92a6 Tree building works
new 3e2a077 Single tree methods are running
new 04b7862 Possibly AllRangeNearest is running but unit test doesn't We need to modify it
new f785f69 Unit tests are passing with success
new 835915a Added timit
new 29c5d4b Added some files
new 5c19e85 Removed backup files
new 4cde7d1 hi
new 14850bb TKDE WORKS!
new 4afdad9 hi
new e032560 hi
new fdf132e hi
new ffc0f8c first check in seems to work
new 180b043 first check in
new bf98e82 added to the repository
new 5cd4bc3 Close to compile
new da13787 Find out how to compile sigsegv
new 569b306 Ready for debugging
new 4cc07dd Fixed some bugs
new 5a11dc6 Partially runs but the paging doesn't work properly
new c74231b hi
new b8098e4 hi
new 2223d6a Unit test seems to pass correctly
new 4ade6ae Initial version of n-point. Contains code for matchers, metrics and naive n-point plus a few handy datasets for testing.
new 6ecea27 removed some printfs
new 5b657a2 put everything under a namespace
new c4176e0 Added namespaces in the allocators
new 63c3a20 Minor improvements to the metric and matcher plus new utilities for the general multi-matcher problem
new ca4ebc8 fixed it so ti can link better with fastlib
new 4f9feed Fixed some incompatibilities
new 3a76fad Added a build file
new 306b6e3 Improved build file
new d7dcc0c First check in
new e08ac40 Added a build file Added a null type
new d2e21b6 Fixed build file
new 3784714 Trying to use both engines
new 567296b first check in of jiang's directory
new 007bb55 hi
new 91c5e47 Making it compatible with both memory managers
new 64fb89c hi
new f003f88 hi
new 2d49ec6 Removed datasets
new 90aac22 fixed my bugs
new 90fca9d fixed the test, it is running properly
new bbc690b the test is running properly
new 361d251 All unit tests are running properly
new 5978734 Everything is running smoothly
new 7e81af6 Now all the tests are running fixed some major problems in the tpiemm
new 02cb563 hi
new 5e5a83c I had forgotten the build file
new de95c2a first check in
new 17e813d hi
new 44eb496 hi
new 6c9ade2 hi
new 8caf9fb hi
new b5964b0 hi
new 9f923ce hi
new 3cb0654 hi
new e8cd932 hi
new 5e272c0 Fixed a bug for all nn
new 789b4e3 more bugs fixed
new 7b590af doing some optimizations
new 7a49da6 fixed some bugs for the tpie memory manager, still the overhead from the access is very high
new 02655aa I am trying to build a balanced tree
new 39f0f1b hi
new afeb627 hi
new 0cec193 hi
new b3b3c64 hi
new a5f29cc hi
new 4e1fa4c hi
new 323294f hi
new 5fe59ba hi
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new c311464 hi
new 17f28b1 hi
new 0f892aa hi
new 3420ec2 hi
new d8c791e hi
new cd2b346 hi
new 2796fd9 hi
new 8953c3f hi
new 5194e58 hi
new 268c1cb hi
new 8f4dabd hi
new b2e9aca hi
new bee3c06 hi
new 78cc5f3 hrect_test and node_test are passing with the new lock method
new db6e058 trees are running very welllllll, passing tests
new 14ba541 hi
new 9f64aa2 64-bit building
new 8154213 fixed a few bugs
new edbc0af hi
new e8e95d2 hi
new b82b7a2 hi
new 6fd54b3 fixed mahor bugs that woudl stall the system,
new 4a935d6 fixed the bug for SIGSEGV
new 4d2adc4 hi
new 1a2c6e5 Major revisions, I added the knn_node , trying to figure out whether or not storing knns on the leafs helps locality
new f9b5207 Compiled
new 3a80bd5 Made major changes so that it can accomodate for different nodes, node and knnnode
new 75e16d2 Seems to be running
new 972cb19 There was a fucking bug that took me 5 hours to find
new 1d488ef Removed memory locking from memory manager, because it creates problems during tree build
new 4d8eeca Changed so that we can input big integers from the input long long int fx_param_int(struct datanode *module, const char *name, long)
new 90d2a77 minor changes
new 069e34f fixed bug in fastexec with integer reading
new 6bdf02f build system slight update
new 364383c fixed a minor bug in collect newarest neighbors
new bd7b5d6 Trying to make the balanced case work
new ddd96b0
new 3cc0f9c Made speed up in memory_manager_with_tpie
new 4b07250 hi
new c22635b hi
new 4acef57 hi
new 25a91e1 finished GNP section
new f8e5b91 finished GNP section
new 797e2e7 hi
new ec9d19d Improvement in the TPIE MM now it works faster I put some advising as well
new 04509d5 hi
new f0c70b6 hi
new 2e1ed96 hi
new 8bece88 associative memory
new ac29e2b hi
new f0f8d00 A bug in collecting the neighbors was fixed
new c7565ff hi
new 856183f hi
new a428f8d hi
new eb39099 section 4 added
new bc6247a Added affinity and other algorithms
new 34961ce proof of all-nn
new 875f14a hi
new 2ba9732 all-nn and nbc proofs
new 9e14fe9 Haven't tested yet whether the balanced tree works but at least compiles
new aff6b63 Added utils directory
new d7ea999 hi
new 06c97e9 Collecting results in test files Application for TIMIT
new c7c0b49 Minor bug
new 521bac7 Forgot to add build file
new 4ec1ef6 proofs, theorm format
new 2fc8b33 Added a section 2
new 9e0fd27 Added a section 2
new 53e4ab6 Added a section 2
new 8a4a12d docked intro
new 805ab63 starting affinity revision
new 8aa43a0 starting affinity revision
new d69bee2 hi
new b05038d further affinity
new 3df493e further affinity
new 3738bce hi
new cc2bdb4 hi
new ec6eaa7 forgot to add it
new 76aa51f Garry changed the the Vector alias, temporarily not working
new 8f8c72b most of affinity
new ab8bd54 Added documentation
new 5d27483 cutting nbc
new 2d01b15 Something is wrong on heater
new 8a71f20 Printing the command line arguments
new 23677ed minor
new 85f1990 hi
new 0a29a27 affinity damping
new 6a5e4d1 We have to set Knns=0 in the reference tree
new 9e8d7cd hi
new 2a6eed4 mention of trees
new 7a4a548 mention of trees
new 7c08366 mention of trees
new bf94586 made stuff smaller, added aff
new 38efcaf mention of trees
new f7c65b7 hi
new a7ec8e2 hi
new da89696 hi
new 500ff01 Updated AP
new 04ba853 pictures, bib
new 62411d0 Made figure 1 work
new 9a50eeb hi
new b8c3742 hi
new 9cf0842 hi
new 0a47a15 hi
new b503511 intro
new eb2301e hi
new 50ec68f hi
new 08bebd8 hi
new 15b7b99 reverted
new 7f47ee6 working on GNA
new 9af008b working on 2pt
new 267193c working on 2pt
new b86dbbf hi
new aff489a hi
new 73bf608 working on 2pt
new 16b434d hi
new 11432f2 working on allnn
new fa87454 hi
new f6772d3 hi
new 8924113 refreshing proofs
new ff33730 refreshing proofs
new b51d13a hi
new 5119cd1 hi
new 37957f0 refreshing proofs
new e8ae909 refreshing proofs
new 6eb14da refreshing proofs
new ce894e4 hi
new 851c99e hi
new 7454b3a extra info
new 91f3adb hi
new 6b138c3 hi
new 84e8109 hi
new 6f66d43 hi
new 807d2da hi
new 8034779 hi
new 711a346 hi
new af3b580 hi
new 02e02b7 hi
new 9493928 hi
new fbf9aa2
new 3e99cdf
new 4841686
new 016699c
new 734594d
new e0a324e
new de3c55d Compiled
new 5120ad3 better
new a86bd06
new fd14355
new 37d9382 Fully functional weighted and unweighted naive npoint.
new 57c7737 added auton npt
new b720d92
new ddec7af
new 2e318b8
new f8e4296 hi
new b270014 hi
new 1f3b3b3 hi
new 3646097 latest debugging version of auton npt
new 4643c84 hi
new 9854ec3 hi
new 4ae53b9
new e604e35
new 2db3a51 partially debugged npoint
new 1e8dc23 hi
new bba14f4 hi
new 33920e9 hi
new 6ebf33f hi
new 909f71d hi
new aef9565 hi
new 3be6b5c added intmap
new 7b7c2f4 hi
new 9df9bc4
new ce4ac2c okay, finding minor design problems, i'll check back in later
new 79e3ea2 hi
new 9e849f0 Adding beginning stub code for parallel EM
new 9b15bbe
new 65d887c hi
new db77f65 hi
new 7deca9b hi
new 2a0d5b0
new ede806f hi
new 05fc253 hi
new f908e28 hi
new dc1bce8 woot, parallel works on one machine
new 297959c hi
new c0085d4 hi
new 6a97374 hi
new cf58966
new 09d9a5d hi
new ecda67f hi
new 016b627 hi
new 545a3ca hi
new 42a4610 first checking of the proposal
new b3ea0a7 hi
new a2d54b6 hi
new 358af3b hi
new 0e02cbe hi
new 35a9b78 hi
new f11bbf9 hi
new d8aaa00 hi
new fce1846 hi
new 9cd175c hi
new dbdf541 moved over Auton KDE distribution here, but it has to be ported. I'll do this later
new 126c96e hi
new 7bb5c5c hi
new 8b92df6 hi
new 81a070f hi
new 73cddd6 hi
new d121f60 hi
new 6be072e hi
new 9b593b3 hi
new edfae28 hi
new a35cb2b hi
new 7fb1ff5 some revs regarding reviews
new 7ec0a98 hi
new 92b8a74 ITS ALIVE!!!!!
new 4d3ac0f hi
new 249d701 hi
new d7c3c12 hi
new 21aaf30 hi
new 322377d hi
new d5f6719 hi
new 55a9772 hi
new 48c7883 hi
new f1d9f11 hi
new 182a2d9 hi
new 533b0b4 close to working now
new 83164b3 hi
new 02624b7
new bb0f6cd
new 9e478c5 hi
new af364bd added intro
new e800d32 hi
new 408c73b added the paper on bandwidth tuning
new 8f86d75 more corrections
new 6047fff working nbr
new a751810 more
new 93b1b3d hi
new 956729b hi
new b32540e added some figures
new 2800ed4 hi
new 010fae7 hi
new 7ac2f5e started adding figures
new 24ebba6 getting closer
new 7080cf9 have to write more on work remaining to be done
new f661bc9 hi
new 739f35a hi
new 913a3a3 This will be used for proposals.
new e824a36 Added brinson proposal
new 2525644
new 9270f46 wrote more on semidefinite
new 6e03d4d one more section to finish
new 1ed2b54 hi
new d3b6e34 hi
new f20d27e hi
new 5a0cf12 hi
new a614cae hi
new 6b72a14 remove some temp files
new 66178d3 close to first draft, Speech recognition is left for last
new 4164231 hi
new eb97ff8 thor moved into the main line -- tree code experiences radical changes
new 11ff57c hi
new 7c16ce1 added bib file
new cb9ea93 improved alignment issues
new c2f81cb Please do not add temporary files to Subversion
new 7ec93ab added allnn
new 410de49 hi
new adda3b0 references added in the manuscript
new 82ab365 getting there
new 6308d04 tables added on cache performance
new f7ca7e9 hi
new e85d5c5 more thor stuff
new b1db32f several changes, fixed images, changed title. Looks more like a document. Ready for proof reading
new d63875c one step before submission for revision to Alex
new 0cb6ba1 hi
new df12bd5 hi
new e99663a hi
new 68d903a almost ready
new ec58bfc more updates to thor -- sorry
new ff3ddec some more edits
new 6d8241a separated out interface from implementation
new b629c57 hi
new 1487909 cleaning up documentation
new b5b645b documentation fixes
new 43c7d7e hi
new 41548f2 fixed a compile issue with thor
new cfc1163 Added Alex's comments. Ready for the final review
new 58c998d before the final review I need to fix some references
new bda7f76 parallel works again
new 069ca3c made affinity converge better
new f5c34c3 affinity converges again
new 6406b4a affinity converges again
new 60a3f87 hi
new 7b65660 initial nbc: upto Algorithm
new f119d89 after Kelly's corrections
new 815ec81 Submitted
new 7083fad oops, fixed a bug
new 0a67173 moment expansion works, apparently
new 4c852e3 first pass nbc
new 71fb735 nbc compiles
new e1d3c55 hi
new e9a9959 hi
new 2f8cd39 added index to thor
new 1ee6c15 hi
new ec2e789 hi
new 1b1b718 hi
new 501948a hi
new a149f38 hi
new bea1bb2 made some fixes to thor's file access
new 6efb432 hi
new 8f533d4 hi
new c9a1d94 fixed a bug
new fa9835e added the proposal presentation, still draft
new ca16423 non-portable mutex initializers no longer used
new 75cb14a getting closer
new f5b7b3e first stab at bichromatic/LOO
new f1e6015 numerical problem fix: clamp positive
new 1f18b9c incorporated some of Alex's comments
new 65849c0 This should be the final number of slides
new 301b701 some problem with too small ubs
new b047bd0 hi
new 39614f5 hi
new 222c09d hi
new da86619 hi
new 85a8105 hi
new 628a190 separated dfs.h into dfs_impl.h
new a2d3c32 hi
new aac8518 hi
new 8651119 hi
new 3f59680 bug fixed; appears operational
new 7340b4b hi
new 1a6092d hi
new 1d80f49 hi
new 9a22cce hi
new 8716ce3 hi
new 81755ea hi
new ebbbe43 hi
new 04e8727 hi
new ef74b26 hi
new 1fbc072 added some metrics to thor, fixed my kde to allow gaussian convolution
new fc135d8 fx-rpc now works with fx
new dc47954 after second alex's comments
new 0df2570 breadth-first seems operational
new 8c6c744 gdb support for fx-rpc
new 604eb93 slightly improved breadth-first
new 679781b hi
new c36191b Initial checkin of the series expansion stuff in a library form
new ef5a465 Update to the series expansion library
new 33216a0 hi
new 3d92999 hi
new 528fe6b hi
new 19d9760 hi
new 154e2f1 More unit test for series expansion
new 5cad560 something wrong with not labeling stuff, maybe
new 417a609 Partially templatized series expansion class, still need to implement for Epanechnikov Kernel
new 11a9cfc Cleanup in progress for expansion stuff
new aa03d9a hi
new f67053f hi
new 981a626 Made SeriesExpansionAux object with SeriesExpansion class as a pointer
new 99f0042 Added BinomialCoefficient method under discrete.cc/discrete.h
new f1cc8f8 Small bug fix in TransFarToFar: the order of the approximation was set to 0, but it really should have been set to the order of the translated expansion
new c2e1455
new d35da42 hi
new 8449a34 hi
new fc7aa45 Added a new member variable under SeriesExpansionAux for speeding up convolution sum
new 58d5b8f Added acceleration for TransFarToFar operator
new 1aa4306 Added acceleration for TransLocalToLocal
new a37b232 added the flash animations
new 9131426 Added the method for computing the required order of approximation for H2L operator
new 402865f hi
new b2d75d0 added more flash
new 08421b5 converging
new 6f12363 Initial checkin of derivative computer
new a991631 Templatized kernel derivative computer
new ce66a74 Added in derivative computation for Epanechnikov kernel, but needs to be tested
new 24fb0a3 almost done
new dd4ee19 paper modifications
new d7f3001 hi
new a41c042 hi
new 906ea61 hi
new c0a49c3 nearly ready
new f994a7f corrections before the first dry run
new 028cb16 more corrections after the first dry run
new c10db0e Now supports Epanechinkov transform using the generalized FMM framework. Need to workout some cancellation error issue
new 0cd3b0b Some fixes for cancellation error that might pop up for complex cases
new 98fc958 Going to break up SeriesExpansion class into FarFieldExpansion and LocalExpansion classes (objectifying)
new 3cc66ad Added LocalExpansion class (to be ported over from SeriesExpansion class)
new a7d06af before alex
new 9377645 integrated Alex's comments
new 2a8ffbd Objectification complete, need to fill out error bound functions
new 6db7973 Epanechinkov expansion bug finally caught
new 81918e8 Removed series_expansion.h since it was split into FarFieldExpansion and LocalExpansion
new 99259a9 Ported over error bound computation for Gaussian expansions
new cb4caf6
new d788019 Initial checkin of multibody code
new 44d5b9e Porting in progress, added in basic skeleton of the code
new c79d8f2 more corrections
new 763bf02 before dry run in fastlab
new 1c843f2 Added the basic finite difference scheme, now debugging and unit testing remains
new 97f1dc1 Exhaustive multibody coded in for three-body Gaussian
new ffaa9c0 after the dry run
new 8f15abd multibody porting completed, now have to add in expansion stuff
new 2761ff3 Pruning rule with error reclamation
new 23b975d more code restructuring, with MultibodyKernel defined
new 58d7b98 more code restructuring, with MultibodyKernel defined
new 2acbf36 before the official presentation
new 1e128e5 minor updates
new 307b88f more code cleanup
new 60a4dbb Basic form of 3-way convolution added for series expansion
new 3837fbe Convolution form of three-body summation added, but needs debugging
new 29ea120 All bugs fixed for three-way convolution
new d2a4268 Test case added for Three way convolution of Gaussian sums
new 0ea9900 Added in three-way convolution for Gaussian in multibody code
new 3de611a More compilation fixes, still need to add in error bound computation for convolution and more fancier approximation methods
new 29fb878 some minor changes, regarding generalization beyond 3-body
new 6745f1a More memory bug fix for seriesexpansion class
new 1f8d94a final bug fix on three-way convolution - fixed the bug that made the centroid of each node as zero vector
new 6499060 Added in combination enumerator, now ready to transition to hybrid algorithm
new 25a9ac2 Initial check in of LHC stuff
new 9fbe5d1 restructuring
new b147e46 main driver added
new e5b0507 Now compilable, still need to port the rest
new bbee077 made my home directory
new e867f7f Added allknn directory (initial checkin)
new a25ecde Fully ported tree-based orthogonal range search
new c038883 All bugs fixed for single-tree orthogonal range queries
new 83ef1ed Starting implementation of dual-tree based orthogonal range queries
new f1795a4 Now the timing comparison between the two is fair
new e1cfe90 restructuring for batch experiment
new 494efdc Added combination to rank function
new 916ff47 Version before adding in bidirectional optimization
new 0dc30cf hi
new b721d06 hi
new d81fa7b Now records speedup factor over naive
new a867af6 Initial version of bidirectional, needs improvement
new 0612c58 still needs improvement
new 29a8ef7 Implemented a second cheaper convolution of two multipole moments mixed in with exhaustive computation
new 7a74df1 Tried out both types of series expansion, but does not work, will be focusing on bidirectional version
new e8e13ab hi
new cbc4ae5 Another version
new dde475f Bug fix
new 2c67386 Checkin before the porting
new dc21560 started kde header file
new 298fe5b first check in
new 119dd2f Axilrod-Teller ported
new e310216 Started series expansion based KDE class
new 67b02e4 hi
new 428b134 before antonios results
new b0f8e0d Added naive KDE
new 2a0fe97 Basic skeleton of KDE ported
new fb59a5d Added proximity project directory, now starting on FFT version of KDE
new 5b8920c fixed commutative -> reflexive for distance metric def
new 60bec86 fixed e.g. -> i.e. (my bad)
new 4494dd5 Spill kd-tree implemented
new d627e18 Added main.cc
new 6f15efa basic finite difference KDE ported, now need to plug in series expansion
new cd2a598 Finite difference debugged
new 271a7a9 mean shift directory added, enhanced pruning rule for kde in effect
new c9ef829 hi
new 69a7a57 final?
new f37da7a Basic skeleton of series expansion stuff added, but needs to add in the core part
new 8e30fbb Took debugging part
new b36721e hi
new 5d14c70 hi
new 2e1d44d Single bandwidth KDE with series-based acceleration has been ported
new 7922309 PCA tree in progress
new 6e91c9b almost done
new c58cbd5 hi
new 72e0252 hi
new 0f242db hi
new eed6b63 started fft version of KDE
new cdcb526 hi
new 2fd0e8f
new 5a8b084
new 8fdcdd5 Ported more of fft KDE
new 01f4f2f Miscellaenous cleanup
new 9f46e23 FFT KDE compiles now, now need to debug
new a0e402b Combined error bound computation and derivative computations into a single class
new 45b884b now supports KDE with Epanechnikov kernel series-expansion
new e218841
new 2550bc9 initial checkin of allknn
new 5c56026 final
new 648ef6b Initial directory checkin of local polynomial regression
new 35412b5 siam added
new 24b7019 single and multi versions
new 84a6162 Bill's code
new faa923a a small bug fix for far field evaluation - the function really needed to take the approximation order but it evaluated up to the full order
new 06a94c8 p^D expansion stuff
new 53f0bf2 updated the build file for the series expansion library
new 8b095cb small bug fix on multiplicative kernel expansion
new a770c61 another bug fix
new eb7f0e7
new 16838b6 more bug fix on translation operators for multiplicative kernel
new 3c93fbf generalized plug-in series-expansion framework completed
new bed80b2 needs fixing for fft KDE
new 99b4489 FFT KDE fully debugged.
new 126fcf8 Started LPR
new 1a0dc6a Naive local polynomial regression completed
new 64802c2 Small fix for checking against exhaustive result
new 40273aa Fixed so that scaling is done before the tree construction
new b2c37d9 some adjustment in p^D expansion
new cb5acfb added dir niche
new 1507625 FGT KDE being ported
new a2c6725 Change to multibody code due to SeriesExpansion library change
new 07bc532 Adding NSF proposal
new 87da5d3 Simplified error bound for D^p expansion
new 04442c9 Updated drafts
new 7aa1555 stuff
new b95de20 stuff
new 9d42317 FGT KDE debugged
new 082035f some minor changes in timing for FGT KDE
new 068ef7e updated proposal
new 1e9e26f
new b36beb5 more draft
new 6c0ded9 changes in .../u/niche
new f517e44 changes in .../u/niche
new 3760c2f added .../u/niche/entropy
new 1355624 Initial commit for experimental setup of IFGT
new 9d767ce more NSF
new 407f84a DataAdaptive IFGT bug fix
new 7d68a79 Experimental setup fix for IFGT
new 463ce16 nsf drafts
new eefff02 draft revisions
new 7421a38 moved some stuff, nishant
new 4b96a24 moved some stuff, nishant
new 50971f9 drafts again
new 79d87fa updated .../u/niche/tree
new 95468c0 minor
new 80f1c12 drafts drafts drafts
new b06dac4 I am sick of drafts
new e9c4363 blah
new ec826b1 created for my tex files
new 0f431bf first checkin max trace doesn't work fails
new 6790f88 working on wedgeHF
new 8f7bf2a Some bug fixes for KDE
new 7119fac memory bug has been fixed
new 8612150 currently tweaked KDE for p^D expansion for experiments
new f24a96e compilation fix for multibody
new 030f32e this version of max trace is running. We actually needed to scale the objective function with something small (a*Trace(X)) a~10^-4 so that the dual becomes feasible.
new 35be276 added ball tree bounding structure
new 0076eae fixed tree bug
new 0659833 updated strategy.pdf
new 854b6df added bi_fdkde.cc
new 4f76471 minor
new c2e8a7e minor
new 7d9e085 updated niche/tree/bi_fdkde.cc
new 53d78bc minor
new 27bd7c5 changed strategy.tex to entropy_l2e.tex - nishant
new 2041201 rolled back Doxyfile
new 11919a6 hi
new 8f07be8 del
new d1edb58 added tree -niche
new dd1cd3c cleaned up stuff - nishant
new 9af6e82 added more spacing entropy estimators
new 446b313 updated jackknifed_m_spacing.m
new 62781e8 nishant, added efficient jackknifed m spacing estimator
new 9e58b49 added spectral project - nishant
new bc5bb1c added nn_cube.cc -nishant
new 0ca6c53 nishant
new f8e4d43 nishant
new 3a4ec03 added functional_ica.tex -nishant
new 3171bf9 added .../entropy/scratch -nishant
new 4a08a5c Checkpoint1 contains the pointer based implementation of tree creation without storing the tree in the database. The tests seem to show correctness. The Euclidean distance functions have not been tested.
new 0cbb1ab This is check point1.
new 066980a nishant
new 907e368 updated functional_ica.tex -nishant
new 62ae0e2 nbc changes to THOR - breaks things
new dec7567 small fix in the upper bound change computation in Prunable
new 05422ed another fix for UpdateBounds
new 7b9d3a9 restructuring of the build file
new ed60b5d modified post processing function to fully update lower and upper bounds for each query point
new f1ac910 This checkpoint introduces median computation into the system.
new 7fdb4a4 updated functional dir - nishant
new 55bdbc6 nishant
new 0c9492f nishant
new cfa051a nishant
new 4aa89e7 nishant
new 0457112 nishant
new d7b5ce2 Redefined function sets for SeriesExpansion classes, and fixed compilation errors due to this change
new 887c0a2 Changes:
new 9b6aab5 working
new d5aa198 removed binaries
new 2f65bb6 hierarhicical pca almost completed
new 20b3efd hierarchical pca debugging
new 856ad72 hierarchical pca fixed!
new 9ed840f pca tree final commit
new a3e09da This is the first working version of dual tree nn. It also includes the master sql table and things like that. dual is working and seems to be giving correct answers for a few random tests. it needs to be optimized for its taking about 1.5 secs for 5000 queries :(.
new 48d4822 generalized kd-tree with plug-in split rules
new 9748b8b added swf and wmf
new 309e1b4
new 6402142 checkin of thor kde (initial)
new 4c7fc71 skeleton thor KDE compiles, but needs to fill in function
new 3427a92 adding skeleton thor KDE
new 13ed82e marched through the initialization and tree construction phase of thor
new 911d6b2 minor change to series expansion
new 7267671 Thor KDE does not crash any more, but stub functions need to be filled in
new 7f6ea90
new 7df1abb Filled out a portion of the skeleton of THOR KDE
new 74df495 first check in
new fdb74f1
new cffa63f First check in
new 7c84d77 finite difference KDE without optimization written, debugging left
new d5aab3d checkin of what i have now
new ef10bd0 regression bugs still not fixed
new c906a97 removed main
new 2f9b211 THOR KDE with pure finite difference works
new 8035c2d all bugs in thor kde finite difference ironed out, need to add in further optimizations
new a02e82d decided to add sparse vector
new b3d2900 This is the tested correct Parallel KD tree construction.
new c016277 Added Garry's optimized pruning rule, just need to integrate series expansion stuffs now
new ab55b33 close to write tests
new 4183b18 getting closer
new 04e7b2e quick fix on the timer stuff for timing naive
new d2c0327 cleaned up the template mess in series expansion class and fixed compilation errors due to the template cleanup
new 438aec0 not compiling yet
new 9837800 This is the tested correct Parallel dual tree as well as parallel KD Tree construction. Now only code cleanup and commenting is left. Also implement the file write and read option.
new 3c297a7 new formulation of KDE using THOR semantic
new d43f17f compiles but doesn't link
new e0e8997 Converted KDE to use THOR grammar
new 9f816e4 Made separate mains for fgt and fft
new f35c114 THOR-style DFS series-expansion based KDE implemented
new 52bfa5b sparse vector unit tests running
new c3a6312 buggy partial regression code
new b5d11dc Pointer based Dual NN. Is working correctly for single tree. Runtime for 400k points is about 16 seconds.
new 60d7cd7 Small compilation change in multiplicative expansion
new 4571161 :
new 62872ef compiles but it doesn't link, there are some undefined links
new 4af5bb0 compiled !!!!!!!!!!
new cdc3b4c critical performance bug fix
new 9702aaa This is the final. All file functions have been tested. They are good. Now just clean up a little.
new 6220521 factorial functions in auxilary series expansion object converted to const functions
new 22a4a00 Does cutoff of singular value based on its value compared to the maximum
new 3126cfd Fix on generalized kd-tree implementation
new 1a88c99 added two options for expansion pattern for THOR-based KDE
new 37d5ba7 This code is working fine. It does B^T WY usin kd treesregression.h
new ff3b74c This code is working fine. It does B^T WY usin kd trees. Made just a minor change wrt the previous version
new 0421469 Code is working, but is still not gold standard
new ddd4e1f sparse matrix works now, unit tests compile
new 7430f18 added einvalues but it is not 100% functional yet
new 77f6807 Separated naive kde implementation into separate file
new 4b34c2d added fMRI sign SGER
new 1f50d17 This is the first check in of the trilinos package
new 2e7ff67 removed a binary file that was accidently checked in
new c762db1 This code is buggy. Looks like the inversion is not happening properly
new 63a563e This one is perfectly running
new 0cb0a6d updated fmri sign sger
new d6ced80 Still buggy. Transformation is no working in regression.h
new 62c4d85 DO NOT CHECK IN LARGE FILES
new b01837d
new 12938ca
new fe34bc3
new be4bc6a
new 28a2fe0
new 7d9a134
new 75b919b This checkpoint introduces median computation into the system.
new f4d2bd0 Changes:
new 658f038
new cb34625 Perfectly working code
new 24dbf55 Buggy code. Trying to incoporate the order of permutation of the regression estimates
new d0cb2ea regression code. slightly buggy
new 2baf6ca buggy regression code. Segfaults during tree formation
new 5c775fe regression code sligtly buggy. faults at tree construction
new 4a6c952 buggy regression code. faults at tree construction
new 42ddcc0 working code
new 9b1aaa7 build file
new beb7923
new b533a52 fully working regression code. TRake care of permutations of regression values now
new ad86872 added more functionality I have to fix some errors for eigenvalues
new 6a2cc23 Compiles but it doesn't link because our blas library is missing complex functionality
new 35f3e1a some minor corrections to the headers
new 1300e42 added the clapack and cblas definitions in the la namespace so that they do not conflict with trilinos
new 86769da implemented the rest of the multiplication. I also need to implement cholesky and LU factorization
new 23c7b63 added ifpack that does the factorizations that are going to be implemented later
new e7a69d9 Added complex routines for blas lapack but they compile as a separate library so that it doesn't slow down applications that do not need complex routines
new 5bc67c5 now it links with comples blaslapack so that everything works perfeclty with trilinos
new 8c150b8 changed Epetra_ConfigDefs so it looks for Epetra_config.h in the same directory
new 9620dad Eventually working, links with all blas libraries and the headers have been corrected
new 089f88c eigensolver works
new 0bb26f0 allmost running, most of the test except for basic operations are running
new 6075f88 fixed the copy constructor but basic operations still now running
new 127485f all running, a small correction in the copy constructor needed
new 9802252 everything is running !!!
new 39019fb This package works
new dffbf8b added all the neccessary files with the appropriate modifications
new 5adec19
new 36750e4 tree saving/loading supported
new e066709 currently saves the permuted matrix dataset, but need to figure out how apply permutation
new c947e37 range search with serialization finished
new 3aebcbd quick fix to account for dataset permutation
new 5fbb43e added niche/fastica
new 0d33de9 added stuff to niche/fastica
new f0ae13a updated niche/fastica
new 516f374 updated niche/fastica
new f70393b updated niche/fastica
new de440ed updated niche/fastica
new b60f573 updated funcica.m -nishant
new 6a56334 corrected funcica.m -nishant
new 842363d added s1s2.mat -nishant
new 5341389 allow use of gfortran
new bd40783 updated niche/fastica
new 699c327 committed
new 5b1c636 updated niche/fastica
new ea5f1b3 moved stuff from u/niche/functional to my local matlab toolbox -nishant
new 4403215 updated niche/fastica
new dbeade0 added niche/fastica/TODO.txt
new af69cfa niche/fastica now has symmetric and deflation versions using logcosh, gauss, and kurtosis contrast functions
new b044515 regression code. Perfectly working about to incorpate NWR stuff
new dc2468f regression code. Perfectly working about to incorpate NWR stuff
new 6b4a355 added Union-Find data structure
new a95d42f updated niche/functional
new 1ff0f73 added incomplete Cholesky factorization
new 53480f7 fixed ifpack_ConfigDefs.h so that it compiles
new 0b3f394 updated niche/functional
new e6600e1 updated niche/functional
new d6b9055 Trying to make things compile
new 2be33fa compiles
new 4514a7c major overhaul of base directory
new f582c6c updated niche/functional
new cd591b8 minor style changes in base
new 0562ad3 removed cursed using namespace std
new a548b51 These files are perfectly working. Will now incorporate code to run executable multiple times
new 3718999 forgot base.h
new 18db27c reverted changes to success_t
new 3bcd23d DEBUG_SAME_INT -> DEBUG_SAME_SIZE
new fd487ec major bug the sparse_matrix.h was linking to the incorrect version of sparse_matrix_impl.h
new 7852a0b removed a few Makefiles
new bc8f702 updated emst
new 2b2a08a It's working
new 3b20e17 Made the autotuning for eigenvalues
new 63c4b15 Added a simple bandwidth estimation routine
new 770b623 updated niche/functional
new 7e5ed8f Multiclass SVM classifiers, using SMO.
new a21625f added fastica_full.cc -nishant
new 0487c3a Added LLE but not debugged it
new da6ddd3 updated niche/fastica
new ff26a59 adding platonic allnn
new ebdcbd7 cleaning up
new 89391c6 guide added
new f1da02e updated comments
new 4f45f0f Fully working files
new d3751fa finished coding fastica -nishant
new 02068a8 updated niche/fastica
new 6fdf4f1 deleted unnecessary files - nishant
new 66627dc updated example
new 75f36f6 updated niche/fmri_sign
new 30310cc delete stuff from niche/fmri_sign
new bf5d69f delete more stuff from niche/ASL_sign
new 1339446 changed assert to DEBUG_ASSERT in textfile.cc
new ca9032f small updates
new 734675b a few more changes
new 874658f updated niche/functional
new f6897ce niche/functional - changed names, added test script -nishant
new c13818a updated niche/functional
new 76130c8 updated niche/functional
new 3ca11a1 Compilation fixes before the code freeze
new b61c6be updated niche/functional
new d251788 minor changes to base
new 9c87116 updated niche/functional
new f64250a updated niche/functional
new b525a6a added centering function to niche/functional
new e0ca413 added get_scores.m to niche/functional
new c38121e niche
new 4b9f54f Slightly buggy
new e2bff9a the partial main file for the new regression code
new c1e526d updated niche/functional
new 422cf3c updated niche/functional
new dd4e418 added s1s2_10.mat to niche/functional
new 76bdb05 allnn_main.cc documented
new 7640242 allnn.h minor module fix
new 6ac6725 changed the style
new 7776bc0 changed the style we need to fix the eignetest
new 6121b80 added smoothing.m to niche/functional
new b3e3dcc updated niche/functional
new 06094c5 Added the allknn so that I am compliant with fasltib
new 33a995e it is running
new 78ac134 added the test set
new 95c9964 platonic allnn complete
new 30e38e0 correction to ot::print comment
new 38e95ff added Init checks; bug fix
new 3ec4860 updated niche/fastica
new 2438aa8 updated niche/fastica
new c18ef48
new 44d80ef polished niche/fastica
new 2b7a80a Working. Will now add B^TWY code
new 5c7d9ad updated niche/fastica
new 05b703f OT_DEF comment, removed dumb DEBUG test
new 3676964 fx_get_result functions
new 48e6604 added some tests
new fa472f3 HMM codes
new fe36be2 HMM codes
new b0b8467 HMM codes
new 89f6ee8 Took out the parts that are currently under development
new 37def8b first upload of nbc
new eaa8d8f added niche/RADICAL
new d791fad removed the small error and added again
new 7ae55f7 Working B^TWB code
new 2f3f608 close to run LLE
new 915c1af updated niche/RADICAL
new 002f359 updated niche/fastica
new f599542 1st commit of kalman
new 03004fc mem past-tense names now present
new aff91b5 this is the first version of EM uploaded
new 58d5020 this is the first upload of the mog_l2e, the file l2_error.h still needs some modifications
new 3b2c7b3 these files are cleaned up a little bit but still to be commented
new 604173e data file
new d10c761
new 7c4dfb7 data file
new abdeb42 Multicalss SVM classifier
new 710716f build file
new 2839a8b HMM codes
new e56ca9c add a readme file to multiclass svm classifier
new b1607d1 last minute changes
new 80d71f2 runs but there is an instability in ComputeLLE
new 6ebd422
new 24fedb5
new 81d6872 corrected so that MultiplyT returns a symmetric matrix
new 5a3c5db minor edit
new 3f726e3 minor edit
new 91e77e3 updated niche/RADICAL
new 987cba6 nnsvm1118
new 1d6c9b2 Add two functions: Dataset::n_labels Dataset::GetLabels
new e0f781e Optimizing the eigensolver
new 82fb9ff Swapped the thor-style KDE with the current stable version
new c71f9e0 First upload of molecular dynamics code
new e72532a Seems to work although LLE gives a singular matrix
new 55f6e39 Added a function to export to a test file
new 962d437 updated niche/radical
new 5fe779a updated niche/radical
new 535e9f2
new 5f87550
new 95ed1ba working cde with comments
new e0fa404
new b111c20 updated fmri SGER
new 4b75c0d The files have been commented and a README file has been included for assistance
new a957fcf old version of KDE is bugged, so I'm checking in the thor-style KDE which works
new 4332e50 Took out dataset reading from algorithm core
new 7eea0b6 Added dataset scaler
new eb1d3f6 formatting, dos2unix
new 28dd077 looser mem::BitCopy typing
new caaf0db fixed dir example -> wwong
new b240dbd svm appears to have moved to u/houyang
new a1b2580 Comments added properly to all the files except phi.h and math_functions.h
new e2f0fc0 fixed build.py deplibs
new 44f1a3b the commented files as well as a README file
new 79659f9 the README file
new bca971a added deprecated includes
new 8d8027e
new fb1a963 Renamed main.cc to kde_main.cc
new d37d418 cleaned it up
new 6d93cb4 added author name
new 2427311 Required changes made and author name added
new 684f836 build.py modified. minor bug fix in svm.h
new 820321d infomax ica code
new f4bb761 added niche/fastica/fastica_stylish.cc
new 4ee8579 program changed as per ryan's review and author names added
new 0f0eef7 Fast KDE is now using submodule for organizing parameters
new b4e0da9
new f4c6c19 restored example
new 7c51fef Extensive commenting and instructions on how to run fast kde is completed
new 797cf0c the set functions added to mog.h
new 1cc5e10 sed tabs to spaces
new 58dcabb fixed Nick's weird tabbing
new c114e51 FFT based KDE fully documented
new e7d01c7 adding the proper set functions in mog.h
new 4772dce exclude trilinos in Doxygen
new 27a9c67 updated niche/fastica
new c520303 Basic documentation for running FGT based KDE completed
new c1ced13 the program will now spit out the likelihood value of the model chosen and the model parameters too
new 782ceb2
new 0e0e137
new 80940aa
new 5cfd127
new 06fac56 These are the files that have been thoroughly commented, for code review
new d486e2f adding test data
new abf6df8 deleted old file
new 5bed3e4 updated niche/fastica
new d3e20cd deleted old fastica -nishant
new 8c9ecbb updated fastica
new adeef2a update fix for the change to SetDiagonal
new 36ed21a minor changes
new 0b32184 Bug fix in FGT based KDE
new b8ea03d updated niche/fastica
new 5ad20a5 General commenting updates
new c3660ff updated niche/fastica
new de55a27 more doxygen stuff
new 2896bf9 removed thor style KDE (backup version)
new f047395 updated niche/fastica
new 310e45f updated documentation for niche/fastica
new a856e44 updated niche/fastica
new f5e986c updated niche/fastica
new a3181b3 Destructors removed
new 5f557ed
new 0c9b157
new 9af1b79 Another pass in doxygen-style documentations
new 7abd0c8 Fully commented oh i meant
new 0ee227b Fully Commented and refurbished
new 7805b27 DEBUG_SAME_DBL -> DEBUG_SAME_DOUBLE
new a8e5560 updates to align with style preferences
new bbb33f7 edits to align with style preferences
new 76a9f38 fixed some style
new fc1a58a fixed UnionFind unit tests
new 10d8e4d Checking in more documented stuffs
new 9944abe nnsvm0122
new 9968615 edits for aligning with style preferences, convergence threshold stopping feature
new 5cc07d1 Very early draft of a document that should eventually become the FASTlib Manual.
new bb1bc19 HMM codes
new 358b818 nnsvm-0123
new 887dac4 fix bugs on model file loading
new 31f015d add toy data
new 28c4e0f updated niche/fastica
new 9fef1a0 removed compiled manual
new 33db2f3 nnsvm0122_deprecated_function_removed
new b24ec3b Added the original IFGT, took out the bugged IFGT
new 8c31f37 HMM codes
new bfe661b Minor commenting correction
new 01382ef Renamed the main driver file
new fb58983 deleting old things
new 1915599 deleting old things
new cd5818b deleting old things
new 2467e96 time invariant kf dated jan 23
new 851ce0e edited as per ravi's comments and added fastexec magic
new fd64b28 revised introduction
new be56dfb changes made as per ravi's suggestion and added fastexec magic
new 4572ad4 README modified as per parameters changed in the previous commit
new 823f3ae README modified as per parameters changed in the previous commit
new 890b4f6 minor modifications made regarding results and fixing the D param in the submodule
new 0026657 required changes made, optimizer class defiined and used, fx magic included, math_functions.h removed, 01/23 at 4:42
new c44548e Fixed up user-level functions for better interfacing
new 0756d74 Another quick fix under debug mode
new b276326
new 950b276
new 34e9a4e doxygen is working now
new 6f5cae4 bug fix for sv_indicators
new bbb4c47 M md/build.py M md/AtomTree.h M md/LennardJones.h M md/LennardJones_main.cc
new f088809 more unit tests are running now
new 2bef21d add/modify docs, add 2 and 3 classes toy datasets
new 248105d More extensive commenting on the FGT code
new 7199ee1 updated fmri sger -nishant
new 4100290
new db75dfb final draft
new 6755fde 1)Fixed bugs of addition and subtraction 2)Introduced local indices
new 1e313fa I changed the way get works after fill complete It uses copies instead of views, It is slower but it keeps the indexes and the size of the original matrix
new 482c57e Added more documentation but I haven't fixed the code after changing sparse
new 3cd73e7 DOS's CRLF-> UNIX's LF
new 6adc077 more revision
new 33d58a6 major bug with set fixed
new b86ee66 fixed major bug in makesymmetric
new 96d0260 math_functions.h indented properly
new b57f116 phi.h documented properly
new 332b3a8 phi.h documented properly
new 102b353 doc modify
new 7cf4f36 phi.h documented properly and README.txt changed slightly
new fdb452f Added automatic parameter tuning for the original IFGT
new ef12543 Minor print statement taken out from IFGT
new 2ac038f author name added
new 607f8d8 author name added
new a619944 Made sure that the pencil has called EndLoading
new d954347 Added least square fit with the unit test. It is just a simple application of lapack
new 6957335
new 3c4af70 nnsvm1124
new 1d6d0a4 minor comment mod
new cc39d81 minor comment mod
new a7d5ad7 minor comment mod
new b013254 HMM codes
new 7bd2bdd HMM codes
new 1069dbe nnsvm1124-2
new 0bdadc9 nnsvm1124-3
new 25b2fd3 slight chance made
new 3be301c updated niche/fastica
new d51ce95 updated niche/fastica
new 55798ef updated niche/fastica
new f0381ce updated niche/fastica
new d4df76b test class header file deleted
new df8a731 optimizer added to svn, forgot it earlier
new f82993b Working version of allknn
new 32fb218 l2_error.h removed
new b60e4e0 Made it a little simpler
new 914461a changed it so that it links to the allknn library
new b682b4f updated niche/fastica
new 36acad8 Finished doxygen-style commenting
new c0fd0b5 HMM codes
new d667ee3 fixed documentation and doxygen
new 674b330 small dateset added
new 60c865d README file edited for date file
new 028e8a4 small dateset included and README changed accordingly
new a058359 Minor doxygen comment fix
new c19f566 Minor doxygen comment correction
new 34cb4e9 finalized code for fastica -nishant
new c886f25 final version
new 315089b
new 3244f27 really finalized fastica -nishant
new b4d779f final doc modify before freezing
new ebcb5d4 deleted old_fastica.cc
new 1cc18bf removed Doxyfile in fastica
new 4f105e2
new 85bdf9a deleted test_lin_alg.h
new bd99c4f
new a431428
new fa0d5cb Updated documentation
new 75112c0 These are fully functional files. Now I am about to change the code for component wise bounding
new 5674d3a Fixed some bugs in Copy constructor Now Sparsem operations work even for Filled matrices
new e3af141
new 2915ab9 copying revised, formatting
new c83dc0e optimizer added separately
new 90cdc62 optimizers.h moved to opt and removed from here and README edited accordingly
new aa28875 test file removed
new c73b5af test file corrected and added
new 679786a changed chapter 1
new 607a144 THOR updated
new 7421df3 updated directory structure
new ca9e1ec documentation for fx modules
new 2715ae9 A brand new repository with the new directory structure.
new f4a7dfa removed a useless file
new 658f4c3
new e2d6f7a A brand new repository for the new directory structure.
new 3357ce9
new c09df32
new 29bdd93
new 414886b s_min value increased to remove floating point underflow
new 1eee834 polytope had a sign mistake which was removed and corrected
new a01d2ca optimizers.h updated
new 9c9c726 mog.h updated
new 36d55b3 added a verbose message to indicate what IC we are on during deflation approach
new 06bb488 A fix for OrthoRangeSearch objects to support multiple usages for a single object
new 91625c5 using the new repository as of now
new 613f9e9 Initial checkin of the multibody code
new 9d652bb declared OrthoRangeSearch class to be non-copiable
new ed8cfcd
new 8a74f4d
new 25ffce3
new cc6b464 HMM README
new 4c1ae6a Minor documentation changes
new a2e1444 fixed some bugs added more tests Fixed basically the problem of unsorted indices that was giving an error
new c037406 changed the documentation a little bit
new 757c8ec fixed some potential bugs now that sparse matrix has changed
new beb2fc0 fixed copy constructor now set also break the indices_sorted_ command
new bec878a Partially completed diles
new 741ec40 Added the original vanilla dual-tree KDE
new bcfbf17 Added error reclamation trick for the dualtree KDE
new 5a27f99 memory consumption fix
new dfde9ed updated fastica_main.cc
new 94e3453 this code is to be optimized and made faster
new 94fc6d2 the code is to be optimized
new 0a64f21 fixed unit tests include
new a1bb516 Partially complete codes
new f6ef287 Added the vanilla dual-tree KDE
new 02392cf hartree-fock code
new d3d2558 This code is buggy and incomplete though it works for tau=0 case
new 6f0a3f7 Initial checkin of the regression package to be released
new a4c2f79 unit tests for Ryan
new fd4029f removed Makefile; limits.h; ccmem out-of-memory messages
new 6f57661 Complete code. Calculates BTWB and BTWY component wise. But still buggy
new bf12122 Outlined the basic form of the algorithm
new 159c491 Implementation header initial checkin
new d62071a Changed the build file
new aa2dee9 These files are perfectly working
new f144ca5 Base case of the phase 1 algorithm flashed out
new 2abc12f Skeleton 4-way recursion code added in
new 80527d1 first check in
new 59fd0c0 Finished the pruning rule
new dc998a8 Added preprocessing for the reference tree
new 9abf9e1
new 876dc3a
new 2c9ea06
new 230ff60 Some file renaming, added the header for post processing
new 0c36d52 Finished the postprocessing for the first phase of the algorithm
new c7f8530 Restructuring of the files
new fd3db6b Changed the field variable names of Stat class to be more general
new 09c0b23 Basically ready to start the Krylov phase of the algorithm
new 48edb52 more structuring
new 8ca2c18 updated fmri
new 40fe1f4 updated fmri
new 2b11e1c updated fmri
new 42040c4 updated fmri
new e175e1b
new 866c110 updated fmri
new e953ef8 updated fmri
new 0571adf updated fmri
new e2f98f3 minor edit on the build file
new ed983bb More initialization routines completed
new eae5dc8 added tbi to fmri -nishant
new ad11dbe compiled
new bf99008 updated tbi -nishant
new ed2383f it is running but the optimization error is increasing instead of decreasing
new 892129d Ready to start the skeleton dual-tree code for the 2nd phase
new 80913b0 Base case for the second phase completed...
new 860957e Finished the rough structure except for the main Krylov subspace solver
new bc24336 Fixed the postprocessing function for the 2nd phase
new 8c32cfb updated temporal ica -nishant
new 5bd4e4c updated temporal ica -nishant
new 8beff85 updated temporal ica -niche
new a927190 SVD Code incoprorated. Will go on to write the frobenius norm pruning now
new 36769a2 SYMMLQ function finished. Debuggin in process
new 8102757 Currently debugging
new feaa56e Middle of debugging
new f5fee10 Phase 1 debugged
new 9d766c7 Added the test file for phase 1
new 1e5a974 The first working version of the matrix-free Krylov subspace local linear regression
new c1bc1ef Completely debugged locally linear regression
new 348e0a9 Changed the scaling
new 2c383c3 Added a new scaling function
new 0d7dc02 Added the naive method
new add5522 Fixed the local linear naive code
new 204b3a7 Fixed the local linear naive code
new c9d0201 Fixed a crucial bug in naive local linear
new a169165 updated functional ica -nishant
new dae9239 updated functional ica -nishant
new 45bb168 Fixed a small performance bug
new e98c520 Need to replace SYMMLQ method with Lanczos tridiagonalizer
new 7d19797 Perfectly working pieces of code. They do both component wise and frobenius norm pruning. Will add SVD now
new f1c1bcd Now phase 2 does relative error
new 7d3d559 Took out the test routine
new 8ec624c Performance enhancement
new 3be8cfc Krylov subspace version of local linear regression completed
new 98177bf SVD code incorporated. Fully working
new fc7aacb This is the function which caclulates the pseudo inverse of a matrix by SVD
new becb06a
new 13d31e9
new 0eb4cdd
new 5e2f6b2
new 108cd92
new 0186d3a
new f1f0868
new d55165f major revision added armijo's method it is not running properly yet
new 51cfc12 updated niche/functional
new 151a985 seems to run although it needs to be cross tested with a swiss roll example to verify it. We are a little bit worried that the nearest neighbors might be wrong and we have to check on that, because the optimum solution is 9% off the deasible set. Need also to inser the constraint that the data are centered around zero.
new 85aa103 I had forgotten to add the test
new 47fd5fa Renamed the naive algorithm to handle locally constant regression
new bffbbdf Buggy. Couldnt debug it
new fb4be89 updated niche/functional
new b22f4e5 updated niche/functional
new 2c3479c initial check in of the dense version of local polynomial regression
new 30080ce Restructuring the utility class
new a8ccafa Added the implementation file for the dense version of LPR
new ae5bb27 Added utility class for matrix
new 68cfc55 Base case finished
new 2592646 Finished the query tree initialization phase for dense version of LPR
new 38a1070 it seems to me it is working, it is just a matter of tuning the parameters
new 542794a updated niche/functional
new 0788216 updated niche/functional
new 5e3a004 Algorithm reformulation
new f13a95e More fixes
new 59b86b4 it seems to work comments The armijo rule is really slow The statistical update of sigmas is good We need to stay sometime in low sigmas otherwise we do not optimize the trace Next setp is BFGS method
new aa010ab Finished implementing the dense formulation of LPR
new 63aaf1d Fixed the compilation error
new 1eee6fe Fixed the compilation error
new d8ef8d2 Debuggin in process
new 1e81b47 More fixes
new be5037c Bug fix
new 7f5a9d8 Fixed the compilation error
new 963f9be More fix
new ca90907 updated niche/functional
new 1a1986b Fix for NWR
new 17db223 updated niche/functional
new c0a1108 changed stuff
new 13c84e3 Bug fix in naive local polynomial
new 0c1982b updated niche/functional
new e9a4d22 updated niche/functional
new b790743 Minor fix to dense LPR code
new 641dbb0 Another fix to the naive lpr code
new 8415f14 updated niche/functional
new 4df60ae Fix in the matrix util
new e4a140f Minor fixes to output module
new 32ad6d7 updated niche/functional
new ea3b948 Added Deng and Moore's pruning rule, but needs to be filled in
new 27ef380 More utility functions for testing correctness
new eb062b2 Confirmed the correctness of the pruning
new 2eb33b7 Fixed parameter module
new d62ed51 updated niche/functional
new 9a1c07c updated niche/functional;
new d44ef1a updated niche/functional
new 0129c89 updated niche/functional
new 3496ca6 updated niche/functional
new 91bff55 added 2 utilities to access the trees and made the tyupedef publicwq
new 97fa603 Huijings code for getting the centroids and nearest neighbors
new 0dc8e7d delete accidental insertion of a binary file
new 89fe436 finished the BFGS now I have to debug
new a8c3e1d ScaleRows works with a matrix too
new d12ab9b Fixing the naive algorithm to compute confidence bands
new f4b7ddb Naive algorithm now outputs confidence bands
new 5612968 BFGS is not running properly but we are getting there possibly the initial steps are not good
new b867b7c Verified the naive algorithm
new 104e4ad Took out the template argument that specified the local polynomial order
new 9846258 Variable bandwidth for naive algorithm implemented
new e809c27 Fixed the query=reference case
new 449e7c7 Minior fix to the do LOO nn search
new 7bce493 Naive LPR confidence band fix
new 5c42e89 Minor addition to the driver file
new ac83f3b LOO by index, not dist
new d3ba206 Modified the tree-based code to do train/prediction phase separately
new ff573bc Little fix on the parameter
new 90ac681 Need to fix the correctness of dense LPR
new c441f3e it is running all bugsfixed
new 3dbdd1d it is terminating now
new 0fd58ea updated nmf -niche
new 5b8fb08 updated nmf -niche
new 3c35106 it doesn't give the expected results on the swiss roll
new 56a601f Some bug fix
new 2e9e51b No bug - just a misuse of the kernel function in two algorithms during comparison
new bbee8be Fast code now computes confidence bands
new fb6175c updated niche/functional
new f745abd updated niche/functional
new 799ff2a updated niche/functional
new 77928d2 updated niche/functional
new 6d6f66f It works suspiciously I am not sure it is right yet
new 99c6e39 Epanechnikov series expansion added for code
new 63e4207 updated niche/functional
new 75eb0e3 updated niche/functional
new 65bf7b1 Minor variable name fix
new 4de9e71 Some performance tuning
new e4adc8a Added the lower bound optimization for the dense formulation
new 994a960 Dense LPR cannot run beyond linear order
new dc10577 updated niche/functional
new ebadacf Change in bound computing function
new dde0dd0 Faster Epanechnikov pruning added
new 8ac34d0 Now does proper pruning based on the B^T W(q)^2 B component, with Epanechnikov kernel acceleration
new d3de9a1 Final performance tuning on the dense version of the algorithm
new b8ca6ba updated niche/functional
new c26f42d this one seems to work Unfortunatelly if we start randomly then we get nonsense
new c8a16a9 updated niche/functional
new 6e2a04c updated niche/functional
new 09fd227
new 3abe70e Added variable bandwidth support
new a7b3597 Methods added to the main driver
new 3eac432 Single tree mode added
new ac0831b Naive algorithm now uses much less memory
new a68ae84 updated niche/functional
new 09a5d16 Some compiling error fix for the matrix-free driver
new 296aeff Took out EpanKernel moment out and made it a separate header
new f6c20f0 corrected stuff working
new 1d79230 corrected version updated
new 9dfad1f faster folders removed
new 08c67b3 gradient descent added
new 6cf67f1 changed from armijo to wolfe and now it works it is much more stable We are ready to go to 10000 now
new 0671be4 KNN Based regression. Confidence Intervals are still being added
new 529e4a5 SGD and SMD_single step implemented but some problem with SMDSS
new a8d8fae Renamed and restructured the matrix-free version
new 19cbfb8 Second round of going through and fixing compilation errors
new c51e54c Almost done reviving the matrix-free version of LPR
new 872e7b4
new 7deebec Minor bug fix
new 2026282 A minor fix
new 57e2ccf Fix in the bug in pruning
new b616334 Added a maximum cap for the infeasibility Added another mode where we maximize the furthest neighbors
new 0d0ca19 Went through up to the phase 1 part of the matrix free algorithm
new 0f24fcf Started debugging the krylov solver part
new 534c8b5 Added a utility function for LPR
new 6e58cc1 Separated out heuristic function for node expansion into a separate file
new ab629b8 More fix to come for krylov_lpr_solver_impl.h
new c684ed2 different terminating conditions included
new 3ec5a95 Got it to compile
new d00254f Last generation of the bugs have been caught for krylov LPR
new 4ffa694 More crashes caught
new c046904
new 49dddb2
new c54699d optimizers added with more terminating conditions although none seem to work, and main deleted accidentally
new d2f1418 Bug in Phase 2 detected. need to fix now
new 41474a5 Phase 1 has Epanechnikov acceleration added
new 710db82 optimizers tried with mu > 1 but exploded so reduced it so i dont know exactly whats the change in optimizers.h, but the main.cc is added to the svn
new dd37ca6 Last attempt on krylov-based method
new 879be53 fixed non-BLAS LengthEuclidean
new 43bc106 Fully working without adaptive BW
new d66e8a0
new 648ff4a After a major reorganization that didn't necessarily give better code we have SPE converging, need more on fixing the gain Things to add: Linearly updating in SPE Inequality constraints on the furthest neighbors Hessian Update based n the links
new 4e2228c Epanechnikov acceleration added to Krylov method
new 8d87d60 Sparse version now stores dense far-field moments
new aff1938 Finally done with matrix-free version
new be92268 Memory consumption cut in half
new 71f2f6c updated niche/functional
new 6ce1bc7 Need to fix matrix-free version now
new edc7236 Fix for variable bandwidth
new 1eb548f Initial check in of dense version
new 0f0c837 Added the naive version
new f384336 Added the multiindex expansion tool
new 9bdc54c updated niche/functional
new 4e35eb3 added results_gene to niche/functional
new 0737de0 Fixed the bug on the knn bandwidth
new 9252a73 compiled
new 363de2e uo and running
new 2b5b4a2 Fix to the variable bandwidth case
new fb5adf5 Removed the custom-built Krylov solver, now going to replace it with Epetra solver
new 449c2cc updated niche/functional
new f33bc01 added k_fold_fpc_cv* to niche/functional
new 533d3a5 Looks like working.Havent tested it completely
new 6bb0d28 Got Epetra stuff to compile
new 8dcae4a Compiled the iterative method... Now debugging
new 3a22e17 Still does not work - possibly misuse or a bug in AztecOO
new 67fd4fd Everything is fixed, and it works now
new 445c11a changes in the cap
new 306aef2 A bug in the matrix-vector multiplier. Need to fix now
new 83a4a21 There was a problem in reference-side initialization - needed to clear out the Epanechnikov moments, but didn't. Now the reference stats are reset everytime the dual-tree multiplier call is made
new e19a0bb Initial check in of the Multi Conjugate-Gradient algorithm
new 996d016 updated niche/functional
new 442be9e updated niche/functional
new 4f86df6 Some more tweaks
new f2c60c4 A minor bug fix in CG method - needed to subtract off the number of queries at one point
new 147691a Added the optimization for letting converged queries exit the Krylov loop.
new a8de9f0 Added the Krylov solver file
new ffd2a11 Added a solver file to the build file description
new c9d5eb1 Fix in the parameter retrieval in the matrix-free method
new b53b670
new ea8ed12 Edited the status message a bit in the CG loop
new c237ae1 Need to optimize more by sharing stratification results
new e917e96 updated niche/functional
new 38987f4 updated niche/functional
new fd2db28
new f982e08 Optimized the performance of the CG-based LPR algorithm
new 5b3ab78 Now saves the first column of the linear operators for the matrix-free version, but this is still linear in the number of unknowns
new 4bf3d47 Looks to be fine
new ae84199
new 8e85eb7
new 3fb8bdd
new 9afb15d Revived the proximity project under new CVS
new 29bec45 Added the ball-tree
new df78dbf A little optimization in the stratified computation, but did not help much - going to save distance computations as well
new a655b1f
new 0b09d01
new 31f08c2 Added Modified Gram Schmidt and batch point mutivariate expansion utilities
new 58d7642 One bug in multi-cg loop caught - needed to maintain separate r dot z (old) values, but the previous one shared a global one
new 08e82ab Added a utility for computing the coordinate of the point that is farthest away from a given point inside a given bounding ball
new 7c57aaf
new b52a138
new 6de282c Added the leave-one-out regression estimates for the reference set training stage
new e5e724a Now precomputes query point expansions before finalizing regression estimates, since they are needed in computing the confidence intervals (need to be passed to the Krylov solver). The Krylov solver needs to be modified, plus one final dual-tree pass over the computed solution vectors need to be implemented
new 8017936
new 4939ad1
new fe05acf Fixed the compilation error for general kd-tree code
new 28e2e2b Now computes the influence values for each reference point, need to add in the final dual-tree pass for computing the magnitude of each weight diagram vector for each reference point to construct the confidence interval
new f6dba35 Fixed a bug in the dense version of the algorithm which did not shuffle the computed magnitude of weight diagrams and influence values accordingly due to the query tree construction; also there was a logic mistake in the design of the code which assumed that under variable-bandwidth case, the epanechnikov moment computed for the denominator matrix could be used for the weight diagram matrix, but this is not true since the effective normalization constant for weight d [...]
new c7122cb Caught a serious bug in non-shuffling of the weight diagram magnitude and influence values in the dense version of the algorithm
new b8f8db9 Now shuffles the values for weight diagram and influence values for Krylov version
new f39afd4 Fix in the compute function for naive code which contained erroneous extra argument
new bb0441f Fix in the compute function for naive code which contained erroneous extra argument
new 289f65b Partially complete code
new 026a85e partially complete
new d315ca8 Krylov subspace based LPR now computes full information required for crossvalidation: confidence bands, regression estimate, leave-one-out regression estimate, influence value, and magnitude of its weight diagram vector in the hat matrix
new c69e48e Some work for setting up the experiment for the dense version of the algorithm has been completed. I now need to look at the krylov subspace version for correctness since I do some fancy stuff for the normalization constants
new dc356ba Complete. Will need to do a small final check
new 6a2a91e Minor fixes in the user-level function Compute
new 93fdb3c The naive code had a bug in computing the influence value of a point; it should have computed t(q)^T (B^T W(q) B)^{-1} t(q) W(0), instead of t(q)^T (B^T W(q) B)^{-1} t(q)
new 221c1ce Bug fix in the dense version: same problem with the naive version since I forgot to divided by the normalization constant for the influence values
new bd9dfdc Last generation of the Krylov subspace based method has been caught - the bug was due to reusing the same dual-tree computation function across three different phases (some phases were required to use squared kernel values, rather than the regular values)
new dc9cea5 Another fix to the Compute function
new 255dfce Tweaked the termination condition in the CG algorithm
new 5b1d0cb Edited the krylov-based regression code for numerical stability
new 89b57d0 I need to fix the Krylov loop to make sure all three system solutions have converged before a query exists the Krylov loop.
new d639f48 Fixed the normalization constant handling for query influence values
new 1e64b08 More parameter tweaking in the CG loop
new d05803c indentation fix in multi_conjugate_gradient.h
new 0d6b734 Bug fix in the Krylov loop - changed a break statement in the for-loop that iterated over each query to a continue statement
new f703694 More fixes in CG loop regarding the updating the solutions
new 2aace70 Numerical stability fix
new bb43bb7 code hooray
new d918575 some memory optimizations
new 7991f3a templatized matrices
new cd564b8 Fully working. However there are mem leaks
new 46f9df9 Slightly modified. Still workingb but with mem leaks
new 2ddadcc Separated out the naive algorithm into a separate file. Now algorithms are templatized for different primitive types
new 900ca48 Fastlib tree now is OT-compliant, meaning it can be serialized/unserialized. However, it still does not admit a bounding box of general primitive type (for example, a short-int based bounding box rather than a double-based bounding box), which would involve making changes to bounds.h, math/math.h:DRange class.
new 7a7445d Fully functional. No leaks
new e55c93e stuff
new 4566179 fixed test suite, fixed arraylist ambiguity
new d02458f The driver application now reads in a dataset of short ints for demonstration.
new 2cc2d27 Fixed the compilation error
new cddb821 Compiling
new cade017 Remove some binary files tha accidently were added
new 3b80096 test seems to pass, we have to check for the validity of the results
new eb82302 It is working
new ec015dc some minor modifications, tests seem to run ok
new acc3b2b several bugs fixed
new a8f82fc
new 15d9bef
new d89b20d fisrt check in
new 3901a8d Some minor repairs
new 5970355 Implemented the member functions
new 57fdd2d Added some extra files
new 077762e more
new cd55143
new ef98e66
new c3698de Added a recorder for the final results Main function for mvu
new 00cd177 compiles
new 2d59fb7 I need to get rid of some warnings, it is running
new c576fb2 There was a bug with the num_iterations that wasn't initialized
new 9751f60 Trying to solve the submodule issue
new 27d858a Eventually it worked without warnings
new 45d581b Now the submodule works better
new 367f5ef
new f849e3f fixed a couple of bugs in the max furthest
new e0436b7
new bee57f8
new a2e31dd
new dc9aefc close to automatic tuning
new bfee4c9 auto tuning seems to work at least for swiss roll
new 128a8e9 beta revised ot, ArrayList
new 365c3e8 Log the lower bound for optimization
new 29dfeb2 modified bounds code to accomodate coordinate offset jwaters 3/25/2008
new e702a05 auto tuning on
new 79eb0f3 fixed a minor bug
new f439886 fixed another bug
new c392ac8 fixed the initialization of LOOCV
new e30b14f fixed the same bug
new e122850 updated
new 7f6cdcd
new 6c3e22a
new 4998695 added pca preprocessing
new 90fdbe2 Add a general cross validation class, which can be used for classification, regression and density estimation. Alpha Version. Still under construction.
new bf8a7b5 SVM regression
new a32ffc6 Add a statistics module. More functions to contribute.
new dee61ae Relevance Vector Machine (RVM)
new 383c962
new 0ec68c6
new 7d8c6c5
new 408cef9
new 480e9bc
new f8930f2 rvm classification
new 776b00d
new 11cce66 added pica
new 5db55d7
new bb2f0d8
new 12c6115
new 87fd9a6 first check in
new 2cc9c75 few corrections
new 321a060 added the example for memory_manager
new e67da2d rectified missing ccmem.cc
new 4d01e0e added deprecated debug macros
new 3ecfc50
new 35f25d1
new ed1c99b
new 357b233
new d9be94c
new a97f78f
new 6f963af
new 8060ee1
new 1ee16ae
new 671f4d0
new 222d506
new 4c48dfc
new 0eaa94b
new 17a212a
new 2db477b
new d8d10e0
new fb47312
new 725ca46
new c176edb
new a91fe8f
new 14f88f9
new 160e485
new 0358d20
new 1a857f3
new 7656b80
new a883762
new 12b2ca8
new 1198b51
new 456a5b4
new c49ed3f Fixed some bugs and passed a simple test
new 81205a0
new d905702
new 4f2e346
new f5c3a28
new a1170af
new 26ef36a
new fec6fd2 Metric tree had a bug, and now it is fixed...
new 9bc02c8 Still working on the dual manifold
new 1abcd3c Adding general typed ranges.
new c2c933c Separated the global variable declarations into a separate cc file
new c568308 Separated the global variable declarations into a separate cc file
new 1e5dcf1 Now uses static allocation for matrices (Nick's memory manager)
new 8809198 Added Static versions of the Init/Own/Copy function that allocates using Nick's memory mapped files.
new 5679851 Minor editing of the build file
new 96dc73c Added Static Init function for the general bound type.
new 60e8db5 Seems to compile , I have to remove from svn at some point th dual_manifold_objective{_impl}.h
new a9a0416 Added a directory for testing variants of PCA
new 18e1267 Test seems to converge.
new 80f65e9 Renamed the class name to make it a static class supporting different modes of PCA computation.
new 0e9327b Compilation error fix.
new bc529e4
new 1203f49
new 72b6fc0
new fb24c64
new 0b15bc6
new 7a13cf8
new 9b7fa53 More compilation fix. Now starting the fix-point algorithm.
new a67d885 Completed the fixed-point algorithm for PCA
new 3aae471 created an application for working with the movielens
new 0aa6101 Removed these files that were redundant
new ba5599e
new ca108d9 Making it more natural
new 438cca8 covertrees folder added
new 3a42324 fix bug in getlabels, delete (int)
new 062aed1
new f0b49fa Addback -> Addbackitem
new c1abb88 results seem promissing
new 776d0ba some minor fixes
new 36a1d0c hf stuff
new 35d157f
new 2894dff bug fix in crossvalidation.h
new b0fe649 Fix to the pruning rule in dualtree_kde.h
new 94878bc Fixed a potential performance bug in the KDE code that resulted in a stricter pruning criterion.
new 2ee9dcd Now uses median split KD-tree
new 0c9e4d6 Fixed a bug in median split kd-tree that resulted in infinite recursion.
new dc7b81a fkdnfl general
new 15b9aed Still need to fix the stitching problem in pca_tree.h
new cdd6a99 Updated a potential bug in the ball tree that could attempt to split even if the radius is very close to zero. Changed DBL_MIN to DBL_EPSILON as a result.
new 294a820 Cover tree files uploaded, tree building coded up, not working, still waiting on dependencies of ArrayList
new 6a6b321 SVD Tree has numerical stability issue when applied to high-dimensional matrices. Going to fix this using orthogonal iteration.
new 1523c59 Fixed the SeriesExpansion module so that it is up to date with the current library. Changed const ArrayList to const ArrayList references.
new a5e6e06 Minor change to the dualtree_kde.h to use InitCopy instead of Copy, a deprecated function.
new 47ccf11 Renamed pca_tree.h to subspace_stat.h. This file will be templatized for different ways of stitching up two different subspaces.
new 42b1f70 Fixed the compilation errors. Plus added the module to compute principal angles between two subspaces.
new d846b55
new 22169f8 fixed
new f7fb517 error testing stuff
new dfd10bc testing files added to svn
new 802468d
new 27f49df
new b36cd68
new 9c494f5
new a7c6468
new cfccd85
new 443db69
new 7b30316
new 82d0e0c
new 5226486
new e2e7d89
new 919d80a I have done some development on L-BFGS-B
new ec9137c
new 2054175
new a763d68
new 4f2a5b6
new 94606e8
new 037815e
new db7dc1f
new 05dbd30 Needs to be debugged.
new fd97806
new c6f028e fixed some issues with svd fixed l_bfgs and now it works again!!! projection whould come after wolfe step
new 610e763 In GetLabels(), all the input parameters are required to init beforehand. GeneralCrossValidator() is modified accordingly.
new c030200 New SMO implementation. Support vector machine for regression now functional.
new 7d92c33 minor bug fixed in SMO
new 17f7e97
new 5801a76 Memory leak error for ball-tree has been fixed...
new 70b9fee changed stuff
new b0ea040
new ee5d80d
new 868fae0
new 5364237
new 8da0c62
new 065913e
new 42e38e8
new 83b2874
new 2811f78
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new 22d4437
new 04723d3
new 817fe4f
new 1ca215e
new 0d563f1
new 54e2a28
new 4d34c17
new a6db2d1 Added the function for making kdtrees out of hyperrectangles.
new 16b213d Compilation error fix
new f258d1a
new 0be3de5
new 9513eb4
new 94c2f98
new 10d4bf2
new 01545e1
new 45e52e5
new 9f6287f
new ea50c09
new 5ca1131
new dbd833c
new 78ab53a fixed things
new f79502d Shrinking, Caching added
new 2d8028c minor bug fixed
new e212790 Added splitting functions for making trees out of hyperrectangles.
new f67c6a9 files added but not compiled as yet
new 9f464ac nearest neighbor preliminary code complete and working on a small test dataset
new 3a95d81 nearest neighbor preliminary code complete and working on a small test dataset and output decent
new 9411072 fixed lower bound problem
new 24a2b03
new 37860e8 added readme
new 5e9af06 the build file helps
new 3db190c Fixed the tree constructor for hyperrectangles.
new f09e868 Orthogonal range code now supports multiple orthogonal range queries. Need to be debugged.
new b333962 Small bug in warning message corrected, no functionality changed
new 1d04944
new c67c33e Fixed memory leak error
new 27890d4
new 68406f6 Fixed a bug in partitioning function for constructing trees out of hyperrectnalges.
new 1e26e4f A little change to the main test driver for range search code.
new 5f46740
new d1efe26 CalcKernelValue_ updated
new f2ec861
new 88b1e85
new 35e75f8
new d798c5c
new 5adf510
new 2945575 tried to make it faster, but didn't help too much
new 79b09dc
new ffb6e3b
new 94b5a13
new e725fcd hasn't compiled yet
new 4b10269 changing recursion to include square trees
new e2496bc Debugging is done... Now need to optimize...
new ef2cda3 Add statistics module, more functions to contribute.
new d246528 Add GeneralCrossValidator class which support k-fold cross-validation for classification, regression, density estimation and user-defined learners. Alpha version.
new 7ed70bf Move everything in my folder(houyang) from fastlib to fastlib2
new 3cb7432 Replace deprecated functions in crossvalidation.h and dataset.cc. Update svm code under mlpack with the updated version. It now supports support vector regression.
new fd33702
new fa61eb5
new 29ea650
new 705b52b
new 479cdf1
new 3acb8f4
new a0105ab
new 1a2646a
new 1824385
new 1f85f7d
new 9abfd50 it is running
new 0654587 changes the way midpoint is computed.Added a function that overwrites on an initialized vector
new 2178dd0 Replace deprecated functions in RVM with new ones.
new 5c2266a
new 2a75e69
new 443b502
new 56ba329
new a276d29
new 72a3a96 development done, now it is time to compile
new 8809a88 compiles
new 90a9b59 some trivial parts are running
new 7cae0e6 Restarted the hierarchical pca algorithm, now replaced with Vempala's fast SVD algorithm. Need to finish the subspace combining part...
new 2f2b6e4 doing better
new 35148cc Replaced EigenvectorsInit call which did not return eigenvalues in sorted order with SVDInit call which does.
new a05a472
new 58c3519 Completed the base fast SVD case for which the number of points is less than the dimension...
new 95924e6 Finished the base case, now have to work on the merging phase...
new 506456d
new 938696a trying a new thing so saving stuff in the svn
new 174dcf6
new 094ff68 Replaced unstable SVD merging step with regular Monte Carlo algorithm. Now going to try out a possibly more stable approach.
new 42b7ea6
new 3715d33 Finished the hierarchical PCA algorithm. Now need to work on high dimensional FMM.
new 8eff23a
new 9103af2
new a0bcaf2 Eliminated the storage space for the right singular vectors.
new 799a41a added niche/spam
new f25b317 Modified dataset scaler to avoid division by zero.
new 6f5c6b5 Added the function for computing maximum l2 norm reconstructoin error
new 14894db
new 2931879 still is not faster
new 5c5ca2c
new 2ef65ca Loop fusion on Accumulate function mult_local_expansion.h
new a17a2d8
new 134e8df Implemented the core functions estimating the computational cost for evaluating a far field expansion, far-to-local translation operator, and direct local accumulation.
new a8cd843 Now the code uses the implemented cost functions in series expansion library.
new a7b7eab More fixes to const reference problems for ArrayList
new 9708d16 Getting closer
new ea740bd
new e295045
new d30c44f
new ac82433
new 87a3e82 updated fnmf
new 72eb96d
new 7ed4d31
new 1542eb6
new 6226405
new e703702
new fdd7410
new 9ad038b Added some skeletons for Monte Carlo evaluation and prototypes for doing in O(D^p) expansion.
new c2b55e6
new d307f01 Fixed the ball-tree to be compatible with the fastlib tree interface, fixed subspace_stat class to have the correct mean vector in the case of the node owning only one point.
new 5f2768f Templatized the series expansion to accept arbitrary bound types.
new ecb2bc0
new fb28d1d
new 8a37f99 Added the cut-off criterion for pre-determining how many order of coefficients to precompute.
new daeb43d
new 508bccf
new 6032991 Separated the far-field expansion into an implementation file to shorten the file lengths.
new 6e27f4e Separated out the implementations of series expansion into separate impl files
new 5d9ea0e Fixed the build file so that it compiles.
new ff12146
new d709286
new 8b153f4
new d744130 Added the linear-time CUR decomposition algorithm.
new 1b6363f
new c339e0d
new 261055f Bug fix in CUR decomposition computation.
new cd140d6
new 27e1f00
new 74dae90
new afb4817
new ccc3506 Added matrix factorization formulation of far-field and local expansions.
new d6e2740 Took out Monte Carlo evaluation for D^p expansion. Fixed a bug in CUR decomposition that caused NaNs for matrices close to zero matrix.
new 03f5ecd
new 6a2882a Changed the prototype for the training function for the kernel-independent fmm
new f00112b Edited the CUR decomposition such that it returns the decomposition with sorted column numbers and row numbers.
new 6af0811 removed loads of test results
new 6bd58c7 major fx update
new e9175e2 general overhaul for fx update
new 5e4c556 added kda
new 0084d74 store -> output for compatibility
new d50b3e1 Finished the far-field moment computation for the kernel-independent fmm
new ecd4077 Bug fix in the CUR decomposition that did not initialize the R matrix in the right size. Implemented the far-to-far translation operator for the matrix factorization FMM.
new ec17e35 better matching by --help
new ed48eeb Added the far-field to local translation operator for the matrix factorization fmm
new 56d8bde
new b6ae9bc Added the local-to-local translation operator.
new cc8a692 Added the basis training for the local expansion of the leaf nodes.
new a443a79 Initial checkin of the matrix factorized version of FMM.
new 21ace2e Moved matrix-factorization FMM test implementation to contrib directory.
new bf53e2b Initial checkin of the matrix-factorized FMM
new bddffe7 Added the empty driver for the matrix factorized FMM.
new e017fe7 Fixed the compilation error.
new 368328b Added the wrapper kernel class for the matrix-factorized FMM.
new 294f6dc
new 1d2c20a More compilation error fix.
new 6015ec3 More compilation error fix.
new bec053e Forgot to initialize the local moments - now wrote the code for doing so.
new a1cc3ae
new 9d0046a
new 6989db8
new 9185b5d
new b5ec42b Implemented the evaluation method for matrix-factorized local expansion.
new 561c985
new f0d1921 Need to implement the canonical dual-tree recursion and debug...
new 4d65a5c first commit
new 6b59a6d added more files
new 388453d close to compiling
new cd55332
new 40867b4
new 071064e
new 50acdc0 compiled but doesn't run properly yet
new df18fbd It works sort of - I need to figure out how to do automatic error control at least probabilistically.
new afe908b Some minor fixes to the matrix factorized series expansion.
new 5fec2cb fixed the error in the gradient now minimizes
new 0079c3a it seems to work , needs to add an svd on the results, svd on matlab showed positive eigen_vector
new c48abf6 it is running now!!!!!
new 4d6942b fixed symmetry and hybrid error
new 5b2c49e Updated the matrix-factorized fmm to use exact cur decomposition with pivotting qr.
new 90e4d29 A minor fix to the matrix-factorized FMM. Still need to figure out how to do error bounds.
new d9ae0ec it seems to run very well for rank one only although I haven't checked the results
new 0cd9faa A segmentation fault fix.
new 4976c5e Put the code in order, and ready to play with the original formulation
new 0a75b43 Reverted back to the old CUR version... Now need to debug...
new 6dffee9 Bug fix in forming the outgoing representation - incorrect matrix-vector multiplication has been fixed.
new 031150b A little tweak in the number of samples to take in CUR decomposition - this needs to be automated!
new a10d665 A minor change to the code that involves how to compute the ending index of the points owned by the node.
new b5b15f1 It turns out SDP with rank one gives the same error with just simple NMF
new 985f0b6 changes name
new e0e859b todo at top of allnn.h
new a2e5f90 Revised kdtree & bounds updates to merge changes
new c46a49b Changed kdtree_impl functions to pass by reference (when applicable)
new e510a16 Our last attempt to make sdp nmf work
new 167af93 addded more files
new b779c59 distances changed and exptl folder added
new 0a1cc53 SMD multi step added with fast Hv product in main
new 68c7449 updating main and optimizers_reloaded.h
new c42b64e compiled
new 44ebad5 gradient gets nan, probably because somethins is unitialized
new b5ba2d5 now it looks more stable but doesn't converge yet i will better check it with a smaller matrix Probably the gradient is wrong
new e7c208d Works reasonable well - now need to enforce that the local moments are actually pushed downwards whenever the query tree is recursed so that we get a tighter lower bound.
new f058da9 Minor bug fix plus now the far-field expansion of the matrix-factorized version stores the maximum incurred error in approximation.
new 70b4c58 it is running for a small matrix with 31% error and it seems to me something is wrong, LBFGS keeps failing, while it shouldn't
new e5227ed Fixed the bug that caused FurthestColumnIndex column to return -1 as the index.
new 89bdb6f extended copy for matrices
new f660925 the convex mvu is sort of working not sure yet, the results are poor
new 322e57a some problems resolved, the barrier is not working properly, there is the problem
new 41ad633
new ce471f9 Current stable version.
new ef2fdfb the bug in the gradient was found now it is working but it seems to me that the minimum has a lot of points
new 73e1896 Some tweaking in the number of row/column samples taken in CUR decomposition.
new d38c689 ctree.h corrected, self_first added and Is_leaf function added
new 2c35c1f Documentation stuff added for the dual-tree based KDE code.
new 7144fa3
new dea43b3 Added the code for standardizing the dataset.
new 584b1c8 depth first and brute added
new 3cf7b59
new 176bbc5
new d761f60 Initial check in of the Monte Carlo version of FMM.
new b56de15 Finished prototype. Now need to optimize.
new 2eb8dcd Added periodic max distance
new 31bed1e Reasonably behaves well - now need to put in probability recycling mechanism.
new 1293d80 Added probability recycling mechanism.
new c8edcea Bug fix in probability reclaiming trick.
new 758311b
new a542c6a comments added and files made shorter and hence more files added
new 410c5e9 Now the code does finite-difference pruning for hard-to-sample cases.
new 85e8d0b Parameter tweaking to achieve more speedup.
new 5575dd7 small changes made
new 0eb5d8d Additional parameter tweaking for performance enhancement.
new 309b766 Additional parameter tweaking for performance enhancement.
new 8fb3a6f
new 0a90364 fx-param stuff put in to get rid of the warnings regarding documentation
new 978dadb minor changes in allknn_impl.h and distances.h
new 606d009 Separated the dualtree implementation of KDE into separate files.
new 5a4a741 Removed the THOR-style KDE.
new c7612f4 fixed Copy -> InitCopy change
new b2bcb0e
new c97cb93 Added Monte Carlo style pruning.
new 5de3f25 Fixed the Monte Carlo sampling to be per-query basis.
new cead166 Tweaked the performace by handling the probability redistribution in a smarter way.
new 314d985 Bug fix.
new dca7448 Fixed the probability allocation phase not to do so when the exact answers are required (p = 1)
new 6df6760
new 85ed48e
new 4ab707e
new d17d101 scf working
new 4a6642d added benchmark_ica.m
new dd64a0d fixed bug in DEBUG_APPROX_DOUBLE
new d65b225 added benchmark ica scripts
new b947e5c
new 86206a8 working, but slow
new 121f52a
new b9f6206
new 02d0618 Incorporated probability recycling mechanism.
new a34c626
new d6bd240
new e3a6006
new 9de263d Bug fix for not clearing out postponed extra probability in the base case.
new 5ab33e3 gonzalez file added and other files commented
new cc524a5 Another bug fix in BestNodePartners_ which sometimes made nonsensical probability distribution (over 100 %)
new 1bbb1cb
new 5360d2d
new 83e4f2b
new 3b0e9a0 Latest stable version - need to put in PCA tree trick.
new 9440dd0 More performance tweak in Monte Carlo sampling.
new c969571
new 05fade1
new dba861c
new b729322 all gonzalez stuff uploaded for trying to fix gonzalez, make it fast and accurate
new aba4543 stuff removed
new 2a2e273
new 96764f6
new a8769ef
new a9b8e75
new 06cc2c0
new 1d1cdaa
new 9f9d428
new e10c155 Initial import
new d96f523 Removed .mlpack files, which can be auto-generated by bin/mlpack
new f0f4435 Fixed a typo in the comments
new 11d5b25 renamed module Syntax to Ast & updated test.ml to reflect this
new ab1450a
new b5e0fbb
new 4fe941f
new cad2d30
new ceed8eb update mlpack script to ignore .svn dirs
new baa29d4 minor revisions to AST
new 92b4a2c
new 330a94c
new 5950377 added freeVars stuff
new eb7000c sparsepca and lle added so as to get ready for the fastlib 0.2 release
new 161b04e conflicts resolved
new 62c60ad
new 23eb8a7
new b8b3c79
new 07cfba6 commented out portions of interfaces, updated _tags
new f9838c1
new e60c1f7
new db297fe more updates and fixes
new 27bdf95
new db8f0db simplified everything to more closely match the thesis
new fb0fc67
new 3343053 final simplification pass
new ee273f0 The current stable version without PCA tree trick.
new ad22986
new 0808b90 extended nonconvex nmf
new 954ad32 Squared error optimization for Monte Carlo FMM series expansion.
new 91275de Bug fix on using series expansion with probabilistic error bound.
new 3fa2dd0 Corrected the code to be const correct.
new 13c40be
new aab06b7
new 32ff878 added CNF stuff
new 1b5bb7f refactored and cleaned up a bit
new f4e6cd8 toying with interval stuff...
new 70a833c I hate electrons.
new cc611f2 added the first of compilation transformations
new a2c978d Bandwidth cross-validation by least squares criterion added.
new e8f47f8
new 753503a
new 621aeb9
new 5abfec3
new a85447e before DIIS
new 95701e7
new e2d5534
new a4a54f1 added almost all compiler transforms; added an EDSL
new 465eccd Removed an initial implementation of Monte Carlo FMM since it has been integrated to the main KDE code.
new 9fc0f82 Added the demonstration of Chebyshev economization in Mathematica code.
new d60d60d Renamed the main driver file name
new fb6b309
new 5a961aa Added the force vector derivation for Axilrod-Teller potential.
new 09403ae Added and corrected stuff on latex writeup.
new 2e48074 in progress changes...
new a27dd77
new 3ef29b0 all done except compiling disjunctive propositions
new a702359
new 9829df2
new d9fdc96 Code upgrade to compute force vectors due to Axilrod-Teller potential in progress.
new 6d01fe4 Removed a bidirectional version of multibody.
new acc6d62 Debugged up to base case computation.
new f198029
new e222f10
new ee0c162 started on pretty printing
new 5814b0b
new e1cf908
new 2375168 moved files to 'mp'
new c5029a6
new 5afb588 finished moving stuff around; everything builds
new 470fd77 fixed _tags to be less promiscuous
new 69c648a
new a8ee858 added examples
new 00d77f7 Corrected some depreciations
new ed4b0cd Fixed some depreciations
new 4eedf23 Fixed some depreciations
new 822f370 fixed a bug in isProp
new c5f2e34 hacky damping, woo
new ad40331 started on the disjuction compiler
new 86021f8 the hack works better
new 562ec55
new 6dfe6de
new 40e6bd7 finished chapters 4 & 5!
new 173c0b4
new 898c1e8 fixed minor big in scalee
new 5329318 Added geometric nmf implementation too
new c3de0aa little cleanup
new decb634 last minute
new 15953c0 missing file
new 1d36da7 fixed Doxygen error in fx_submodule
new 7dd581b fixed timers
new d06f1de fixed fx problems
new c5e4497 Ryan can't spell, and cylces don't exist
new a2611a0 made sure absolute prunes are impossible when lower bound is zero
new 7ea8a54 quick fixes
new 2853ae5 added a disjunctive example
new 9915999 added a directory for disk allnn
new 942bf50 added better multi-tree timing infrastructure
new 10ce73b added another timer
new 74b9d6a Introducing disk trees and advicing
new 66d5e15 The code compiles, but long hours of debugging to come.
new cc39929 Finished coding simple finite difference version. Monte Carlo version forth-coming and debugging to be initiated.
new ec9a4b7 Naive Axilrod-Teller force vector computation added.
new 912fc7c Not much pruning happening. Debugging in progress.
new d5ce7c2 This version works and records correctly the memory_usage
new 9291dc6 Fixed some bugs in the memory manager Advice and I fixed some bugs on the trees
new 6bcee5c Added support for large datasets, it loads them with StaticInit that maps to mmap file
new 38175e6 Put it under fx_module
new 733622a some debug checks
new 94565aa We needed a code for allnn
new ecaaa8c Added the test file in the repository
new 38c733f Traditional allnn
new afd44d3 Minor update
new 6c84db4 moved from the old fastlib repository
new a346dae
new 594c69c Simulated kdB-trees in THOR experiment
new 9b978b5 Further changes in the tree
new 2809872 Median splits seem to work
new 3fdffab
new 3812e33 Updated to the latest fx.h
new 5460625 Fixed some warnings
new 7fb13ef Fixed a minor warning
new 8b290ae There was a problem with kdtree_mmap_impl.h in general this part of fastlib is not well developed, kind of hacky, it works now
new fa0166e Debuggin in progress. Now prunes a little bit, but slower than naive.
new 8754538 Added the new directory to start a new version of local polynomial regression using batch SVD
new 9e3585f Making q_mutables slightly better.
new f779db2 added naive timing stuff
new 4d62426 Added two more files - driver and the user level function implementation.
new 4b7273f Additions for Nadeem's requirment made, they haven't been tested yet though
new 3ef6c44 Removed local polynomial regression using SVD factorization, since it might not be a good idea to store dense factorizations for all points. Going back to the Krylov subspace method idea.
new cc7a0cf It seems to work although I think the file is not a good one
new 22ec106
new 8b54ef6
new de6e189
new 7a74e66
new 8e9714d Some bug fix.
new 29c29ef More bug fix - Eval function for 3 three nodes should have computed node-bound distances before concluding that the min distance was zero.
new 56a5e1d Fully debugged up to force computation, now need to incorporate Monte Carlo pruning.
new b565604 Added the golbal optimization nmf files
new 9d9f59b
new a120143 Close to compiling without errors but still a lot of debugging is waiting for me in the logic part
new 3f445ba Close to compiling without errors but still a lot of debugging is waiting for me in the logic part
new 2b7d517
new ff9e67d
new 7a3ce17
new de4373f
new 4395dc2
new 8948706
new 454168c Need to put some extra progress notifications and we are ready to test
new 9b31d8f The algorithm iterates, doesn't crash, we need some more work though
new 2ec37c4 A quick bug fix that overestimated the number of (n - 1) tuples.
new 61e8777 We have the first demo running, we need to improve on the initial boundaries, as it seems to me they affect
new 5055367 Some minor modifications on the progress reporting so that it is really silent when the silent_ flag is on
new c33311a In progress to use Monte Carlo pruning.
new 2bde27f Modularized the Axilrod Teller kernel code (multibody_kernel.h). Now need to finish Monte Carlo scheme.
new e6abdf6 Finished Monte Carlo version. Now need to carefully go through and verify the code...
new 28468c1 Kind of working. Need to go through and verify the code.
new d132d11
new ff88ab2 fixed mac error
new 1264b97 Attempt to make it mac compliant
new aec5065 Attempt to make it mac compliant
new 6e47860 A little bug fix and changed lower/upper bounds to use Monte Carlo estimate and to influence the contribution estimation.
new 9e9eb73 quick typo fix
new 0bf02f9
new e77d677 A major overhaul on the Monte Carlo sampling for KDE algorithm. Now uses sample variance for the pruning rule and does it in a true dual-tree fashion.
new cfb2ed7 Fixed a critical bug that did not push down estimated mass in the Monte Carlo case.
new e2c75ce Minor comestic repair in the comments.
new 79b995c Another minor cosmetic surgery in the comments.
new 586e2ac Another minor cosmetic change.
new ddd02f6
new 4fda741 Added some documentation for the annoying warnings
new 6c89182 revert back to using the central-limit theorem-based Monte Carlo approximation. Putting confidence band on extreme order statistics is not a practical idea.
new 07a93ad Need to think about optimizing the right hand side of the pruning rule, not the left-hand side. Minor fixes checked in.
new fc94b49 Bug fix for math::BinomialCoefficient(n, k); the previous implementation returned 1 for negative k values, which is not correct (should be zero.
new d0f8c45 I tried several things but it is still slow
new 2909f90
new aa86d3c
new 03ef8dd
new 13604f2
new 571e685
new 180d6eb Incorporated the rudimentary probability recycling scheme.
new 9a61a2f Incorporated the rudimentary probability recycling scheme.
new 7234788 Separated the statistics class object from DualtreeKde class for shortening the file length.
new cb331aa Corrected the writeup derivation.
new 4450bab Critical bug-fix in Monte Carlo sampling code. Now need to confirm that the rank order statistics is a good idea.
new 4a4b287 Error reclaiming implemented.
new fdcec48 testing basis energies
new eb0ea7c Dummy
new 8a932fb Fixed the Monte Carlo approximation.
new 9ee0a23 A little tweak for probability reclaiming.
new b03f5c8 initial checkin of RV writeup
new 6fb2ac3
new 7762a3b Added in the coverage percentile as a tweak parameter.
new 23b64b8 Compiles
new 4378732
new 38298b9 Tighten bounds almost works, we need to take advantage of the fact that non-convex case gives a good lower estimate
new 7f47a5b Tightening works but doesn't give any better bounds
new c004a28 Added nonuniform nonnegative weight support.
new 34eea59
new 33c24fc
new ea62c77
new 82dd2fa Added the routine for outputting a LSCV score for a particular bandwidth.
new de5af4b Fixed the probability computation to do one-sided computation.
new 544e066 Now outputs the query estimate to the file.
new 2bae8c4 Improved a lot
new 75a049f New Monte Carlo scheme implemented.
new ff5165e Initial checkin of the variable-bandwidth KDE stubs. To be completed very soon.
new f76c92b
new 54a23f4 Variable bandwidth KDE implemented. Need to look over to see whether it is working correctly or not.
new 233630f Bug fix in variable-bandwidth KDE, where the preprocessing function had a overflow problem.
new 2e161d5 Added the naive computation of variable bandwidth KDE.
new 858b26d Fixed the double-initialization in variable KDE (kernels_ object).
new 746890c A little tweak in the variable KDE Monte Carlo pruning scheme. Now need to re-factor out the common code between the fixed bandwidth and the variable-bandwidth code.
new e9c3905 Compliation error fix.
new 656395a fixed fx silliness
new b930ca6 density estimation usign erf kernel
new 99658c4 A little tweak in the way Monte Carlo sampling is done - now tries to the maximize the lower kernel value to encourage more pruning.
new 821244f Compiled
new 66cdafd Now the bound refinement algorithm takes the (1 - \alpha)-th statistics instead of the absolute minimum.
new c935484 Made a permanent private temporary vector for sorting, instead of allocating everytime.
new e8a7a31 added conversion to prenex normal form
new f910b4b
new 0c8acae added some utilities
new ffa9f15
new dc5ef9e added smallcheck
new 532a30c
new 5b3fc2d created kkf for niche
new 04c5c12 first sane version of smallcheck!
new ca86a0f updated l1reg_klr
new 8e6a0d6 removed redundant function def
new 266e380 moved Show stuff to one place
new e2541be updated l1reg_klr
new 7b107ed Added the leave-one-out feature.
new 9ddb3a7 Alphabetized the parameter list.
new b5ab0c1
new 521b089 Fixed the initialization problem for the case when the reference did not equal the query.
new 789fc5d refactoring some printing routines
new 263386b renamed pretty printing functions to be more accurate
new fdc40a9
new a9e4aaf stable build with a more sensible dir layout
new 8f6ce0d
new 2cfa3b2
new f2976fb Some fixes to the pruning rule.
new 6a99f40 Before adding in the bound refinement optimization.
new 38d1a02 Bug fix: did not reset the bound statistics for used error in the base case.
new 4b5a2e5 We do have a functional nmf executable running experiments for the paper
new 2d34b03 removed [the beginnings of] difference lists...decided not to use them
new 16f978b fixed the build :o)
new 1d79fa5 Current version with all optimizations added in.
new 580f7e3
new 4fe254f Bug fix: a real solution is to have different stats for the query/reference tree, but this should fix now.
new a0caa3b
new 2eb98b8
new 2fa0138 More optimization.
new c19805b added a functioning SmallCheck.forAll
new 99befd1
new 67cf9d1
new 6f74cce Alternative Monte Carlo scheme added back in.
new 514b783 Now dumps the relative error of each estimate to the file.
new f27c0ac Added the brand new directory for the final public release of local polynomial regression code.
new fb32c34
new 7c6354a
new 7007321
new 1a31f63
new c1743f4
new f76b881 new import
new 55fa95e new import
new e5debdf fixing botched tylesBase import
new 4304de3 fixing botched tylesBase import
new fbb586f fixing botched tylesBase import
new 14e1413
new 00ccb20
new baf4b81 Removed some files.
new b29e2d5
new c814cd1
new a293ab4 Taking out core common functions in variable bandwidth/fixed bandwidth code.
new ebb4900 switched away from -pack and towards my new idea for hierarchical moduling
new f0fedf1 Some more re-factorizing common parts.
new 4ab7192
new 4bb372e Decrease in 42 lines of code.
new 101693d Eliminated over 100 lines of code.
new 530f33c Reduced 140 lines of code by refactoring.
new aaff9e9 Latest change commited.
new e3ce619
new 7cf1bbf removed kkf
new 893fd75
new 083d033
new 785ab64
new 2b9b910
new fc90f26 Vanilla finite-difference LSCV bandwidth cross-validator added. This one is definitely faster than the old algorithm.
new 731375d Bug fix in dualtree_kde_cv.h
new 932e57b
new a4b4f58 Added the missing file.
new 58c46ff Bug fix in computing the plugin bandwidth.
new 556437e
new 29b175d Bug fix in LSCV score computation.
new b23d1ab Compilation error fixed.
new 628f186 Code refactorization.
new 43f9054 Added in Monte Carlo approximation.
new c510c59 Removed the matrix-factorized FMM modules since they are in beta stages.
new 1eae75f Removed references to Monte Carlo.
new 70a9f2c Added the convolution operation for doubly nested kernel sums.
new 8529746 Series-expansion completed for kernel CV code.
new ba344fe Bug fixes in prunable function. Need to go through again to make sure variable names are mixed in accidentally.
new 1c55db0 General performance tune up.
new 6b60ee8
new 8329812
new 9e9a040 Code cleanup.
new 7b04f6c Added the modules for doing spherical harmonic expansion for inverse power distance functions, but they need to be completed!
new 894e75a Some more addition to spherical harmonic expansion.
new 35a1e10 switched SmallCheck to a new representation
new 32a9418 merged conflicts
new 2905c42 Multipole moments are computed correctly as of now.
new 6a5b0d6 fixed the problem with the destructor so that it doesn't cause a memory leak
new 65a41a2 Added the local expansion for inverse power distance kernels.
new c4e3cb6 started on Big-M compiler
new 19f81f6 Evaluating the far-field expansion of inverse distance kernels sort of works.
new 61cc4a0 Bug totally fixed on far-field evaluation. Now moving onto local field formation.
new 58a160b I have debugged up to farfield/local expansion formation and evaluation. Now need to implement the translation operators.
new 08dcf47 Just one compile time error and we are ready to test
new 5dd38fb Compile passed
new 090806b For backup purposes, I have moved the experimental series expansion using matrix factorized formulation here.
new 715cb84 Implemented the far-field to local translation.
new ec7fcfa Coded up to F2F, and F2L operators. Now need to finish L2L operator.
new 61efdff Seems to run the first steps, but we need to change it so that the splits on h happen soon after w, this might give a better solution
new 71f8d07 Some bug fixes, but I need to go through these carefully.
new 5b6f8a1 Caught more bugs, I think I need to go through and check whether each constants are precomputed correctly.
new e21b1cf I think the far-to-local translation finally works!
new 872984e Added PLDI 2009 paper.
new df0f507 I think local-to-local translation works now, but I need to double-check.
new 57badd2 Need to reconfirm that it is working correctly.
new 3ffd709 With 99.9% confidence, I think the inverse distance kernel expansions are working correctly. Now need to implement oct-tree.
new 0a7706b we are getting closer to the global optimum
new 491eb82 Minor updates to PLDI draft.
new f236f72 New version, trying to avoid oversplitting
new fbfc396 Added several new modules, and INSTALL, README, and Makefile.
new 5365f36 Minor update to Makefile.
new 2c64265 Added prerequisite information to INSTALL file.
new 411ee30 update for fx_ functions
new da4c997 Still haven't found what I am looking for, need to work more on the last method that doesn't work
new 2ea4499 Corrected some problems with the tree depth
new de229d2 Added the generalized oct-tree for higher-dimensional case.
new e6180fd Minor bug fix in octree.
new b9aa349 Fixed the node ordering to resemble something like Z-ordering. Now performs Z-ordering per level, and stores the node list level-wise.
new ef9ec45 Rearranged and added several files.
new 6868064 Bit interleaving/deinterleaving stuffs added for fast neighboring node finding for octree.
new 7a4bc06
new 3ffa999
new d81f1ca
new 139bd58
new 42c7269
new 3b53955
new da48b28
new e3eedeb
new 5f08dd4
new 2add2c2
new 5f71dd8
new 42b2297
new 67c46e2
new bdad316
new 35edb8d
new 1790a24
new ea74d64
new 78b0064
new 5ef0b3b Implemented build system.
new fb20ad0
new dacae0d Initial checkin of the FMM implementation.
new f09889f Now builds the octree, but need to confirm that it is being built correctly.
new 8b79244
new c4ff0be Templatized the octree to use arbitrary stat types.
new 5b47b6e Change due to templatization of octree.
new d49bf63 renamed 'mp' to 'mathProg'
new 9fdc2b9 fixed build errors
new 2480245
new e5e9f96 moved 'pprint' to 'pPrint' for cosmetic reasons
new 48137e1 moved utilities from mathProg to tylesBase; will refactor further
new 7b053c0
new 897a1cc moved utilities from mathProg to tylesBase
new 173d224
new 327fdd5
new 44d6107
new 57de943 cleaned up everything to use TylesBase
new 932f808 removed util.ml
new a19650e
new 6c14133
new 84dde15
new 6e534c2
new 07fe362 Changed the octree code to take multiple point sets.
new c801050 Code change due to octree change.
new ddcb3a9 Need some more effort to compile
new 27332fd Need some more effort to compile
new 5e086a2 Fixed conflict with my working copy.
new 3e08faa
new 3612e7e Compiled
new 627cf33 Upward pass phase completed.
new 213d57c We have some progress but it is not working yet
new be00752 We made it obligatory now for the optimized_function to have a GiveInitFunction, it makes things easier
new d096cf0 Prevents dividing into infinitesimal boxes by putting DBL_EPSILON limit in the code.
new a07122c Added the print function for octree
new b09093b Octree has been changed: I think there was a bug in adding each newly created node to the node list. It was added to the level above than it should be.
new e535471 Fixed another bug that did not index the points owned by each node properly.
new 4a962f9 There are still bugs but some were found
new eed6646 fixed config.py header
new 294945e we almost got it close to working
new 0d83239 It is more stable now, but hasn't worked yet
new 9a92d6f It is more stable now, but hasn't worked yet
new 5babf6a Separated out the utility functions for octree.
new e661433 More crucial bug fix in octree.
new 1902b7d Added the function for computing another interaction list for octree.
new 32200b7 Kind of finished, but need to go through the code and debug.
new 86d921c Checked in the statistics class for FMM module.
new 0d3a0be Some more bug fix.
new f7ec3bd More memory bug fixing for octree. Be careful not to confuse PushBackCopy and PushBackRaw.
new 21caa81 spelling
new 4aacd9e single tree support
new 5d31d83 single tree modification
new bfaf188 bad percent sign
new 627ec38 Memory bug fully debugged.
new b960d0a Change due to memory bug fix.
new e21265e comment typos corrected
new 16928c4 We keep findingbugs here and there, scaling doesn't work yet
new be7983a Some extra flags to lbfgs so that warnings are not whown
new 488c126 Added the bounding box printing
new 5960091 Kind of works, but there is numerical stability issue that I have to work out.
new 4372e1f Temporarily turned off all series expansion stuff in DownwardPass_ function to see whether all nodes are being accounted for each query point, and it does account for all. Now need to turn them back on and debug.
new 96fb09a Bug fix for list 4 computation for octree.
new 7b702de ENABLE_DISK_MATRIX option, default off; fixes to fx includes, uselapack index_t usage
new 11ef1ca Crucial bug fix in octree. Bounding box was not being computed correctly based on the z-order code, but is now fixed.
new 4504b01 Bug fix in List 1 and List 3 computation. There was a duplicate node issue.
new fa567a0 I think it works, now switching back to series expansion stuff.
new 9abd121 Turned on the series expansion stuffs, now working reasonably well!
new 86eb230 Code restructuring of the inverse distance kernel series expansino stuff.
new aef6d17 Added the series expansion convolution pruning for kde cv stuff.
new 9dd8370 Added the test file for hypercube tree.
new 15a21b2
new 16f48f0 FX compatible update
new c4214b7 Added Lines module.
new db13bc4 Added About module.
new 4b3941d Added the parameter to specify the order of expansion.
new 58b8445 Added the inverse distance power kernel.
new 319fb46 Added About module.
new b5e9923 It's the first time gop seems to work very satisfactorily down to 0.4% error rates
new eca58e3
new 7440334
new 15d6d0a
new 3fb7bc2 Minor cosmetic changes, but need serious modification of how the approximation is done.
new 4dac9ba
new f396eb2
new 71adf37 fx documentation added
new 4c0d653 fx documentation added
new bf6da22 fx documentation added
new e7cdd1c fx documentation added
new bcac310 parameter type fixes
new 26903be
new 8045fd7 added documentation
new 5636d40
new 0a51509 fx type fixes
new 030606a Removed the local polynomial directory, going to start fresh with combined regression/conditional density estimation code.
new f26a2a2 fx type fixes for mog_l2e
new e0c3ffd fx type fixes for opt
new d316456 opt path changed to mlpack/ and build file changed accordingly
new 8187396
new 9da4ef6
new 197f485
new 9970cff fixed a pattern-match warning in smallCheck.ml
new f651e34
new ff5f361
new 230baa9
new 27d12db
new 3339d76 added Option.map2
new 24a929f
new 7f9cdd3
new c55d572
new b73f012 Initial checkin of local polynomial regression/conditional density estimator code, but it will not compile. I will have to finish it.
new 048ec2a Moved a inverse power distance kernel to mlpack/series_expansion.
new d30ccc7 Relocated the inverse power distance kernel.
new 6693cbc
new 62aaeb3
new de4ca42 fixed cflags for basic_types
new 6f2d9cf advanced to new fx
new 1ad3573 changed ENABLE_DISK_MATRIX to DISABLE_DISK_MATRIX
new 29c4412 General cleanup before the release.
new a5d67b3 Minor parameter tweaking.
new ca1ebcf More checkin of the derivative stuff for inverse power distance kernels.
new 697f179
new 020426b mog_em and mog_l2e directories merged to form mog and opt directory renamed optimization and parm_nbc renamed naive_bayes
new dd961d5 useless files removed
new 161b47a optimizer path corrected in mog/mog_l2e_main.cc
new bd230d4 Major cleanup before adding the inverse distance power expansions in Cartesian.
new 039c2c0 More cleanup.
new 68b256b merger of mog completed and the naive_bayes README changed
new e0773e2
new 7004432
new aeed11f svm documents added (partially)
new 7d4620b
new 4d07f00
new 51bdf4a
new abf914b
new af4a5f8
new d6cf7a6
new dabd1ed resolve deprecated functions
new 3c79cb4 Changed the lapack installation so that people can use their own or just download it from netlib.org
new 1050b8d Fixed the bug so that it doesn't ask the same question when compiled outside of la
new 9a28821
new fef2e9b infomax_ica updates for fastlib2
new bdcd5b2 more infomax_ica updates for fastlib2 release
new 2a3499c
new 95f47e5
new 63f087b Everthing is working. but has to be cleaned
new d024d2b
new 2f15242 Fixed a problem with the lock file
new b29e87d
new 1b65e66
new 86cd02a
new b1f812d
new eca1ed9 More draft files added.
new a2add8a
new 689fe5a More files added.
new 4532f48
new 4c29d72 More templates filled out, but they don't compile yet. I'm in the process of finishing it.
new fec830b Main driver added.
new 835415f Close to compilation, we just need a function to initialize the matrix
new 9c7975c
new efd7f7e
new a66a897
new d28f662
new 807d846
new 9e06a8f
new 893a0c5
new 86dacd2 Added the new files, and now it compiles, now need to actually finish the implementation.
new 99827cb Preprocess/postprocess templates added. still need to finish...
new 5845988
new bb9665d
new b395088
new 583e8c1
new 61144be
new a7531f5 fl-build-all added, modified buildsys.py to generate a custom rule that contains the subrules recursively.
new 9f306c7
new fe3206d
new 7c35cf8 Fixed a problem with the new_dimension
new f2b5822
new 9b57256
new 89a5564
new 52c4476
new e326c40
new 8bc8130
new a8e373c
new fc8bf64
new 2184d97 Seems to sort of work
new fac08b2
new 8bb6019 Now compiles, but need to verify that it is working...
new 7212ff1 Naive module added in, but still debugging.
new b2e86d9 Namespace for la/blas.h added back in, sparse/trilinos/test.cc compilation error fix.
new 32cfd3f Minor update to the relative error parameter adjustment such that it guarantees global error.
new 3e757cb Bug found, I need to debug now.
new 389447b Bug found in nwrcde_query_summary
new b0fdb6a Bug fix in nwrcde_query_summary.h. When incorporating the delta's, we should not add pruned and used error components.
new 1d58121 approximate rank nn added
new fdcefff approx_nn.h delete function corrected
new 51ea728 Added relative error computation.
new f381dca Now supports Epanechnikov kernel, but I need to optimize the pruning rule more.
new 07b378d Fully working. Need to make some more changes before I run full scale experiments
new 360e8ba Tester file for special la
new 73fd976 Predictor corrector main file
new e7cf428 approx_nn.h modified from home
new 023e10c Memory bug fix.
new 205d54b Took out a commented code.
new fad1f47 Upper bound is maintained for denominator sum.
new 3b00099 Removed the upper bound maintainers.
new 56929cc Code reduction.
new 0de0795 Compiled the svm now I have to test it
new 1510eab
new 58195b8
new 35dbccd approx_nn.h completed, main.cc modified for testing
new ab3af7b Edited the build file and added monomial kernel expansion.
new b7628b0
new 0274e77 compilation error fix.
new 04f4695
new d4e25cf Some bug fix in the monomial kernel expansion, but still in the progress.
new f056f30 Still not running properly
new 58458a4 Repaired code
new 432b408 all files completed - testing and debugging ensues
new ee155d8 main file contains error message for lapack
new 2574fa4 There is something strange the inequalities cannot be satisfied
new 01096a1 Added some datasets for validation
new c9ca545
new ad495d0
new c959cd8 Fixed the inverse power distance recurrence such that it correctly computes for r^{\lambda} for \lambda positive as well.
new efd679b tracing errors in the lagrangian
new d0ea72b init running and test datasets added
new a35c9c6 Epanechnikov transform now uses the inverse power distsance kernel expansion. Now need to plug in the error bound stuff for F2L and L2L stuff.
new 667f07f Fully written code, but still doesnt give desired results
new b36e100 "seems to be working I need further testing"
new 97a1cc4 Plain code. That is the code has hardcoded values for the vectors
new 9c77696 Added the direct local accumulation for Epanechnikov kernel.
new 181fc89 Some code reduction, now looking at the correctness of the local expansion evaluation of Epanechnikov.
new b0154a6 Bug fix in Epanechnikov series expansion. ComputeDirectionalDerivative needs to compute (-1)^n D_n. I should note this somewhere.
new e6170cc F2L prune enabled for Epanechnikov, it only does exact F2L, approximate F2L will be added later.
new 8032a5b ComputeProbability_ fixed and main and approx_nn.h Init functions working
new dff8813 Still not working, but better than previous version
new 76677dc Bug finally fixed for Far field to local translation for Epanechnikov. I still need to come up with a good test suite.
new 3bad655 Minor change in how inverse pow dist kernel is evaluated for negative lambda.
new 9c1022f Compilation error fix.
new 9a280e8 Now using TKernelAux stuffs to support series expansion!
new 9fad463 Minor template typename changes.
new f108c53 Problem solved for the moment, the whole problem was with the lagrange multiplier. I had to increase it
new 4f77526 Long overhaul to support initializing series expansion objects inside stat objects.
new b070e16 Warning fix.
new e958d11 Move the farfield moments into the reference stat.
new f3a920b nn algorithm working and exact and naive match
new 6b03dbf Header file clobbering fix. Renamed math.h to math_lib.h, math_impl.h to math_lib_impl.h, and string.h to col_string.h
new a8654af fast uplod
new a629439
new 6061d18 Things seem to work, but we have to put something on LBFGS ao that it shows whether the goal was reached or not
new 80f2146 approx nn running, need to check its correctness
new 0fff290
new b38acf2
new 0dc6a2a Some restructuring - moved local expansion from postponed to query stat.
new f255e73
new 1e414ac The code should be doing series expansion, but I need to verify it.
new 703f341 Series expansion added for regression code.
new debf8aa Bug fix for Far-to-local translation. I really needed to compute up to 2 * max_order number of stuffs in aux classes.
new 5283464 Series expansion seems to work.
new 50acb4c Array index off by 1 error fixed.
new 6e81efe Critical bug fix.
new 8b1f0ad --recursive and --help option added for fl-build-all.
new d1c4f6d Header file conflict change.
new e8ce1a6 need to fix the way I compute node size and also why it is not faster for higher error probability
new 635eefb
new 1f7055e
new f88722b
new f8afffb
new ffca8ba
new 03623d2 minor modification so that it handles only manifolds
new 791003f Dependency fix.
new dd739f9 Various missing dependency fix in build.py files.
new 4821642 Distro build option added.
new 345f39b Fixed it so that it exports built *.a lapack files, but we still need to look at eliminating the need for .lock files.
new 492ea84 fx doc fix.
new 5a81530 randomization added but still not figured out certain problems
new a3ab9dd some things that matter. I had the problem when the labels are in a row vector and not in column
new 59828bd Added two more datasets
new b005d49 Added a file that has the run-time parameters we use
new 0365a08 disabled writing on the disk
new d14b9ff
new 5c257d4 Patched the code for reading in multi-target values per each training point, but currently only supports single target value regression.
new 061a269
new 36b4731
new ed96c7d Netlib distro of LAPACK/BLAS hardcord g77 as the fortran compiler, overriding the user's preference which might be gfortran. If there is no g77 compiler installed, this would result in failure of compilation. I fixed the build.py so that it replaces the relevant hardcoded compiler choice in BLAS/LAPACK build files using Nishant's suggestion.
new 73b2037
new 7a48bb3
new 28c5663
new 12528d7
new 0210033 Fix to the gradient kernel in Cartesian coordinate.
new 6acfa5d Multitree template added.
new d1baa75
new 052e089
new 7b59d1a Made it to run on cygwin yeeeee
new de72150 I added Soyeon as a user
new d76b537 Added the LINE_MAX macro so that it works with CYGWIN
new 5560a51 Nick introduces sophia in the world of CS wisdom
new 684f579 Added the build file that I had forgotter
new e211505 Minor addition to how the gradient kernel can be computed.
new e819800
new e38f1d6 Autodetection of curl/wget
new 0aa0210 auto detecting wget/curl
new 07c8d01
new 9b82875 Code before changing cholesky factorization to dynamic stuff
new ae6f8c7 Code before changing cholesky factorization to dynamic stuff
new 760e6b9 Code before changing cholesky factorization to dynamic stuff
new 39d7e53 Various restructuring for performance reason.
new 1eb6381 Optimized the base code a bit, now starting finite-differene pruning...
new 457ae8c Some more fixes.
new b070a81 Naive multibody ported, now have to do finite-difference.
new 9bc9c05 Lower bound accumulated during base computation.
new 49648ef Minor change so that MultiTreeProblem::order is referenced whenever possible.
new 4852272 Some more fix, but I need to make sure that the number of (n - 1) tuples being accounted are coded in!
new 1feff2c Pruning function almost done, but need to check and accumulate the number of (n - 1) tuples.
new 2c26ad0
new 6f7973f Segfaulting problem fixed.
new da3ff1b Now adds up the number of tuples pruned in the base case, but need to put that in the general cases as well.
new 163710a
new b872d98 Added a more advanced result
new d9887d6
new e634416 Working codes
new 67bcb23 Working codes
new 9ed9777 Working codes
new 0ee9563 Working code
new 0d83d08 Working code
new 7494bc0
new 564e98e
new 490e3be build file
new d2995c3
new 1ff247a
new d9d8e90
new b0183d3
new 4ca11a3 update
new c4e2604
new 0619f41
new ffdfdcf Some more optimization to compute (n - 1) tuples when computing n-tuples.
new 3592a5b
new c6707f3
new 3a2c2b2
new 75be5cb update2
new b41cefd Added an executable that computes knn, need to add documentation though
new a82e175 Build file fix hopefully for Macs.
new c79d1f5 Added a utility program that computes all k firthest neighbors
new 554baea Some more changes to do relative error pruning.
new 1bcf1c7 Relative error pruning added, but need to confirm.
new 76066d4 I think relative error is working!
new 82f261f Naive computation added.
new 0658b8a It compiled
new 02ec250 graphical models : basic data structure
new 3f079b8
new 0d5602e dual tree traversal added and certain other changed made, like trying exact before sampling, but haven't tested it yet
new dea5ee4
new 9b58a89
new ecfd27b Now computes relative error l1 norm.
new ec77c40 The single tree seems to work with the tests
new 22bac4f Some minor changes
new d34377d
new 4a1b055 tqlong: graphical model : sum-product algorithm
new 89158c5 dual tree traversal added and randompermute replaced by RandInt and various other modifications made
new c0bf5c1
new 001b7e0 main file added to drive the dual tree version
new 61f9433 final tested version with dual tree behaving weirdly
new cba1fc0 review&add comments
new f2ab789
new aa8a5f9 Code reduction and cleanup.
new e8c3f6d Nearest neighbor, futhest neighbor optimization tried, but doesn't make too much difference.
new bb354c4 Pruning error fix.
new 55bc6ad
new 9e2bd3a Took out all nearest neighbor optimization, because it doesn't help.
new f2cbcf7 Took out all nn opt.
new 1c0fba0 corrected for dual tree and tested, timings testing not done yet
new 334e9ad 10-29 in progress
new b8cf1e2 update
new 129c776 Implemented the multiclass separation maps
new 4926cc8 tqlong : graphical model - bipartie graph template
new e374e0e
new 4818d77
new 26e698a
new 4d607ca Our first attempt to hit the problem
new a9ed5b7 tqlong: Graphical Model: FactorGraph to be template
new 5f9eed5 tqlong: Graphical Model: move definitions to gm.cc
new c1c2147
new 94fb25c
new 0892d65 We extended the separation maps so that they now can accept text files with the neearest and furthest neighbors
new 77c1743
new 7a2d9d1
new 0ef58f2
new ba27048
new e299dbd
new dc2675a
new a97cd7d
new 4af50d2
new c197e8e
new dfe5637
new 6353ac0
new 5c8c61b
new ff65b29
new b33fd90
new 8946073
new f0a928e
new 4b4564b
new 7dc103b
new ffac7f1
new 85f066d
new 549678e
new 8d41bd5
new 606832f
new 1c86f2b
new f1935d2
new 138c214
new 661537e
new a23d6c9
new a39d588
new b4ed091
new 88042a3
new 43798b4
new 4f40e1c
new 33b5aef
new 26ca01c
new 58a2c28
new ad18e2b
new 8b345a8
new 170eb9a
new ac8899d
new b621b32
new f3f1498 Now does not approximate the case when one of the nodes is an ancestor of another node in the tuple list.
new 7837e65
new fb84ec9
new 4ae7bf7
new bd8f631
new bae7072 Monte Carlo sampling needs to be optimized so that it iterates over all points.
new e46f65a
new 8c14005
new 5cb390e objective function calculation
new 155ac46
new dc2ac39
new a0fafb3
new 1940f07
new ec55548
new 74ca8d1
new ef2e435
new e4afac0 Now the canonical case splits and recurses on every node index, instead of splitting one at a time.
new 985d5af Compilaton error fix.
new 9779ef9 Changed math::Pow<1, 2> calls with sqrt calls.
new a901215 Now adds up Monte Carlo prune statistics separately.
new fb4846f
new a09a9be
new 84fe6f9
new d30529b objective2 is added
new acc7211 Now uses 90 % percentile confidence band.
new e164891 Now the basecase is also rolled up in the recursion loop.
new 058f9ce Recmoved the upper triangular square matrix implementation
new 0b715c4 Build file fix.
new cdf8964 build file fix.
new 96d5f9b updated
new 571efde
new 73e0d12 now does prioritized dfs.
new e8fc858
new 3ee5386 update
new 1337275 update
new d6f21d6 Modification for multitree algorithms with training labels.
new 4f7b61c Modification according to multitree template modification.
new 9cbba2a
new 1361aae
new b868ec8
new 6cbdbd9 update
new a0f164c
new e033bb1 Fully working code
new 0845a8c Fully working
new bb14db3 until 1st&2nd derivatives w.r.t beta
new 7942fad updated
new a017615 until w.r.t. beta, p, and q
new b5b6760 until w.r.t. beta, p, and q
new 7380593 until w.r.t. beta, p, q, pbeta, qbeta, pq
new f449fad
new 5f34bde
new 73d60ac
new cd0eeb2
new 5a2f01c
new d46927a Change needed to make multibody work.
new 24b95d2 Multibody code change due to the template class change.
new 0de957a sampling
new 97ffb07
new 610b12d
new 995ae22
new b813ace
new 2b7c460
new ce88788 update
new 72f230b
new d8e896b Change to support two-body query reference problems.
new 63a3d1a Three-body change due to template change.
new 0f2fca9
new 76f098c
new dd1f48b update
new 38e4b5b Change due to the template change.
new 93a381a Template change to take datanode pointer.
new 278873c
new eaecd87
new fed5c4d
new 6ee8ff0 update
new d5a9e67 Shuffling back the results now according to permutation.
new 11a5bc0 Beforre nick leaving
new 5f52637 Change due to template change.
new 97590fa ready to debug for the calculation of objective fn
new 861cda8
new 75896bd
new 49b791f
new aba1731 it compiles
new 9ed05e9 optimizers.h and .cc moved to mog directory from optimizers directory
new 1e1b1aa error
new d303e1c Multitree multibody code update, now the Nadaraya Watson regression code is generated from the template.
new 4ec4ab8
new 4d3d888 Fixed
new 3c8e600 Code cleanup: took out a dead code.
new 9107af7
new 0473ebb
new 4e38c1b Now tallies up probabilistic/hard errors separately.
new 6b6ad29 done with debugging until objective fn calculation
new 686ff00
new 73d9a75
new 37a43c5
new 49ec8cc
new 8f677f9 error correction
new c484aa0 compile
new 7d2c981
new 7443bcc
new eabac71 Huge performance tweak based on round-off error detection.
new 65138e5 Changed so that the probability is not square rooted.
new 4af13e7 Fix to the Monte Carlo sampling routine so that it is less agressive.
new d4b9782
new 815c78b
new fa031e9
new d835be4
new 0022437
new 028659a
new d7eea2b Trying to integrate opt++
new c6cfb97 objective fn and gradient vector Done
new 23b51b0 Prints out how many tuples are pruned.
new dce0acf Completed objective fn, gradient, and hessian calculation
new e7268cb
new 0623c55 Now the base of multibody kernel combines positive and negative contributions, but appropriately assigns to the appropriate component.
new 48d8fde Some more optimization.
new 607ed11 More stable answers, but a bit slower.
new fca6f51
new 61c7f58 Memory leak fix.
new b6a325b Compilation error fix.
new 72fc27f Finished first stage unconstrained optimization
new 946d786 Added the template generated KDE without Monte Carlo acceleration, removed multibody code since it is now a part of the fast multipole method package.
new e99767d
new 9f2e97b
new 968ec7d
new 9597e02 Still compiling
new 6eb377f Still compiling
new 99aa090 Compiles but doesn't link, need to instantiate the static member objective
new f53edc5 Now it compiles
new 0fb0c40
new aa6143d
new f136aa8 approx nn single and dual tree fixed up and experimented with.
new 83919c9 Bug fix: The results are correctly shuffled now, using ShuffleAccordingToPermutationColumnwise_
new ed24a9b Some crucial fixes to the base case, now need to look at the finite difference case.
new f2d8516 added contrib/niche/hshmm
new 34b4310 updated hshmm
new cc33410 Some more changes.
new 549a653 Some more tweaks.
new b136312 Switched to more aggressive pruning.
new 0d9cb96 Added the static version of the kernel evaluation of the inverse distance kernels.
new 7107c5a seems to compile, it doesn't converge to a solution possibly due to an error in the gradient computation
new ee9848b Test for unconstrained optimization passed
new f653688
new b91a70d
new 401435e sampling compiles
new 3b418ba
new e1d975a
new f60ba2c
new 003ee37
new e6a4921
new 9ca61b2
new 2178b2a
new 596294f
new a9070ba
new 137bfd6
new 7d188ab
new 262ef50
new 33713d8
new 5d1c6c5
new 602cc13
new 2c715e8
new 6a320e7
new d6e280b
new ed8c8ea
new da0e6e7 sampling works
new c54a024
new 2fbdcda
new c5691e7
new add814f
new 4fd5b73
new b6a8bcf
new 119eb51
new ddfb885
new 4ceaada
new 1ed32df
new 582e51a
new 9a45ded
new 084102c
new 881a16e
new 1d7d6e5
new e94ccaf
new 34e14bf
new 859341b
new 1c47bb8
new 48ece06
new 35e9ccf
new 23a6450
new 3db93dc
new 907e33d
new 8874f41
new d902075
new bb7f6d3
new 7e9c55a
new f2cb901
new a3dbeb0
new 29daf6a
new a36af65
new 4474c59
new a746b79
new 1ccb9e3
new 8c10e54 Big changes with multibody code change, but the multibody code now needs to be an iterative-refinement version.
new 54861cb Constrained optimization compiled, it needs to be further tested, also I have to examine whether Hessian comes initialized or not
new 2e08f55
new 9dc947b Commit before iterative-refinement based optimization.
new 9320f3c Bug fix in the monte carlo sampling that did not check whether the three indices were out of order.
new bbfc04f
new f96d698
new 103d3f9 Scaling option added.
new 6e6d1ae
new 499aa23
new 3f6acf6
new 837fc3d
new 5fd0651
new 460792e Last commit before relative error incorporation.
new 32272fb
new bb473d3 dogleg
new a12d1e6
new 305f058
new 2c005ca
new fc67c33
new 55dd92a
new 20c1322 dogleg works
new 95b6648
new 78e2c5e
new 1a69b33
new 925fc1c Steihaug works
new 0120395
new 1281654
new b9136cf
new 55a2df0
new cac3950 Quic SVD error incremental update
new b23b388
new 3441dd9
new 1966b08 it works
new 8fd8e6b QUIC-SVD tested on small matrices
new 7215fef Fix to LAPACK build - now forces to use GCC4
new 46b7ad4 LAPACK build fix - forcing the usage of GCC4 and GFortran. Fixes the LAPACK compilation to use -O3 flag instead of -g flag.
new 94a08af DEBUG_DESTRUCT_OK added; DEBUG_ONLY enhanced
new 75eec74 Compilation fix for GCC4.
new 576b20a
new 69e30a1
new a3f8f51 QUIC-SVD bin rule quicsvd_main with command line parameter
new c9a0068
new e964920
new 6ed80e3 QUIC-SVD doxygen documentation added
new 6b1f692 QUIC-SVD add timer
new f8afdbd QUIC-SVD add timer to fx documentation
new 6e47b28 QUIC-SVD small changes
new 727e3fb
new a8b5b92
new 96a0109
new bf9906a
new 97c7a0d
new 61004af
new 59b992a
new 53e46b2 added data files
new 69ba4cc fixed thread.h DEBUG_ONLYs and kde's VERBOSE_MSGs
new 7284f62 QUIC-SVD add lapack svd run time
new 45fc26d QUIC-SVD add lapack svd run time
new 9627ef8 QUIC-SVD add relative norm difference
new 6e177ab QUIC-SVD small change in comments
new 7bceb28
new c3194d4
new 17777fb rank error and distance error computation included
new 7df6564
new b54b49f
new f3814f7
new ba75f06
new 9a883a2
new 35fe543
new 2a4c40c
new bc56ded Added the documentation for templatizing matrix and vector to be instances of GenMatrix and GenVector.
new 1380a5d It is working
new c04fd57
new e5110a0
new 410dc8f
new 71c23c0 Still lapck doesn't compile for cygwin
new e4df1d1 Fixing lapack for cygwin
new 6990e91
new 179d0eb
new 62ce9b4
new 56bd52f Now blas/lapack works with cygwin
new a2354ab
new 463898e rank error and error probability computation added in main_dual.cc and comments added to approx_nn_dual.h
new 1e032ce
new 7884629
new 4bb2db9 fixed QRInit test for new LAPACK
new 101e623
new c156764
new 6ecd2d1
new 8c99468
new 202d378
new 73016a0 checks added to see if sampling is done properly
new c2d4245 one check fixed
new bec373c Fixed some minor bugs in mvu
new d6b2816 Added CART code from Alex's class Jwaters 11/28/08
new bad9262
new cff985f Turned off subspace computation.
new 039896b bounds fixed and main_dual changed a bit
new baab66f
new 5d9d7e4
new 22303c2 hf bound function
new 817ce0a
new 5c1feac default values of doexact and doapprox changed to false
new dad7947 fixed optimization lib name
new 633150c outputting results added to main_dual.cc, but only problem is that if you do multiple methods together, all results come in together in the same file
new d58db87 demos added
new 5717900
new e59c049
new 7d93ab1
new 9f94985 demo_export.m renamed.
new fee606d Missing files added.
new 99b8fe0
new 5d420ec Current progress - variable values are being passed properly, but need to put default values in CreateFcn functions.
new eb22c2a Library problem solved.
new 233b6f0 KDE bandwidth optimizer call added.
new 7c146d5 gplot works, but need to have PCA and produce two-dimensional dataset and test on it
new 62648e1 quicsvd_main with exact error estimate to be compared with the algorithm's estimate
new 83b9bd2 Scatter plot for KDE added.
new 321bc0c Bill's EMST algorithm added to the demo.
new f616061 kernel matrix generator
new 09a9291 main_dual printing results option added
new aa4d532 kmg
new dcec7ce kmg
new 4b3863f kmg
new 1639df2 kmg
new c5f369a Changec INTMAX to MAX_INT
new 9fb9920 quicsvd_main add S*VT to output options
new ef83b61 Remove values.h inclusion.
new 8823b5b quicsvd_main add S*VT to output options
new acab1f5 quicsvd_main add S*VT to output options
new 024e7eb quicsvd_main add S*VT to output options
new 7951e24 revert to best working THOR
new d9dffb6 reverted to old, better working THOR
new 66f04ca revised nbc for demo
new 895eabd Probabilistic pruning added.
new 8abd836
new ee6f36e Rejoice! --fx/no_docs_nagging now available
new aeb44d4 Dataset no longer compiles with warnings in gcc4, THOR no longer uses deprecated functions
new ca9d073
new 6a3ff31 M cart/cart_driver.cc
new 57c58ca Removed the makefile since it's auto-generated by fl-build.
new 4901298 Interfaced in PCA, EMST visualization, etc. Now need to incorporate NBC, decision trees, kernel PCA...
new 6bef67c fixed some accuracy reporting bugs in q \neq r case
new 252d406 Kernel PCA started.
new c3b33e0 Kernel PCA working, but need to add another button to input the bandwidth value for the kernel matrix.
new 283190a
new 39e4b93 More work on kernel PCA completed, now onto range search.
new aeb8a8e Approx rank nn interfaced.
new 7b65cb1 Changed to the general purpose double type, but the driver file should be templatized as well, through fx_param_str fx_root, type, short int
new c1c37f9 Orthogonal range search interfaced in, now need to do plotting...
new 195a8a0
new cecdaf6 Ortho range search visualization added.
new 03f49f0 Added the plot of rectangle windows.
new f49c270 Probabilistic error computation refined using square root summation.
new 6991535 Lots of things fixed, now need to work on NBC, etc.
new 202d546 Lots of things fixed, but still need to interface NBC and decision tree.
new 26b9d12
new ad216fc
new edacf6e
new 1ef86af add polynomial kernel matrix generation
new ac3b1d5 Various changes, bug fixes.
new cc6bba4
new 870840d
new 75eb807 Added more things such as the timing bar.
new 6769930 Added the new file.
new 59cdc18 Some more changes, now need to look at KDE...
new 161827f multitree template edit.
new de106d2 Various features added, now verifying KDE.
new 791f3c1 KPCA fix.
new 726fcad Started adding NBC.
new 70e4463
new 722e827
new 90f03bf
new be9ebdf Decision tree aded.
new 7649a24 Decision tree output added.
new 5c01a14
new c97d1f7 Some changes made.
new 9e130ad misplaced parantehesis fixed.
new e83957f GUI is now resizable.
new 2c5f76d Path fixed.
new 286c8b6 library path file added.
new 1e6e6d3 textfield resized.
new fc049b0 Range button widened.
new 4f63506 data file name passed properly from the listbox directly.
new 5843bf9
new 7371bd9
new e70b95f
new 6b02649
new 51b8dfc Lots of broken things fixed.
new 77e2a57 color changed.
new d3c3007 crossvalidation.h bug fixed
new ae0e72c
new 40e864a
new 22ca275 Commiting what I have so far now, now need to work on NBC... and timings.
new 5038825
new f040183 finding clusters with emst
new 371140d
new cc77392
new 55a265a
new 6fc5517
new 4ed9185
new 808cb6e
new ef0d9e5
new a0bd034
new 4c39f57
new b253ffb Added running/done labels to the figure.
new 355a0d7 fixed emst clust
new 05f050c preliminary NBC commands
new 12c4871
new 80036bb
new 9377361 Lots of bugs caught, now need to interface NBC.
new 94cfbed
new 8a79742
new 795a8ca Color code added for EMST.
new b3f3733 Now plots 5 clusters only.
new 2bbe857 Textbox output added for each paper reference.
new 4e83016 More change to paper ref.
new 1814d82 Michael's paper added to KDE.
new da239b6
new 98ded8d
new 30430dd
new 4e6faf9 Timing added.
new 9fb655a
new 3d809ab MLPACK final demo version.
new 1d30f04 fixed gcc4 not found issue
new 219399e and fixed fl-build-all
new aa74c96
new 10a0f9b
new df4f02f
new 05f585a
new bc8465e
new 426f02f
new a02fd24
new 47a0b11
new 77e4eda
new 5ae71ea Sample share need to be worked on.
new d356ba1
new 34ec5af
new 96b41f0 Added MD code to fastlib2 repository
new 35ab165
new 553e5b5
new 32ce2f2
new da5afc3
new 09283c9 correct hessian
new 704ec3a
new 59dbb4b before scaling
new 8225eae correct one error first_stage_y[n]-1
new 2509773
new da6f02d
new d3772da
new f772df1
new b558111
new 9b64cc0
new 05ee6a8 trust test
new e4f4033
new b3050e3
new 2e88ece
new 7d2e45f
new dc3b180
new 15513ed code written as per smola's book
new b97f86d Dont remember if this is useful file. Nevertheless commiting it
new f975e23 all written as per smola's code. Will need to change
new 2daea2d Performs incomplete cholesky by dynamically adding columns
new 3426061
new 2a7d921
new 65662a8
new 4a45f07
new b8ea212
new a9762b2
new 8ce4fe8
new 16dc07b
new 840da98
new e87fcf1 Compile error fix.
new 0b31376 Bug fix on the Monte Carlo pruning where it could have lowered/decreased the tallyed up lower kernel sum bound. Now uses the finite-difference bounds, but more optimization is needed.
new af5495a
new 5559cfa
new 51d639f Changed the leaf size limit to boost KDE, but need to think about how to also provide speedup for the multibody code...
new ecc40c9 Template change to compute the exact delta once and share it with the probaiblistic pruning module.
new 071968a Code change to incorporate the lower bound change in probabilistic pruning function.
new 39b22fb Compilation error fix due to template change.
new dca8c03
new 1937500
new 786e156
new de910cb
new 7a0b3df
new 6ccac81
new ee2c142
new 5b5a7ab
new f09984f
new 2cdf204
new 13f68b5
new 3c3b4a8 Michael Holmes' nested summative form algorithm initial implementation checkin. Stubs to be filled out.
new 73591b7
new 1c23a7e
new 5002925
new 4c40219
new 50a3f88
new bf81c09
new 3579d69 correction before objective
new c06932c correction before objective
new 3f46628
new 04512a3 Some more fleshing out of the necessary prototype functions.
new 9759005 objective correction
new 8645567
new d9b668e
new 8b3811f
new 0fcb43f Function operator added.
new 55188d2
new 70b3f4e gradient correction
new 9fa89f6
new bc4690e before handling scaling
new 98a94b9 scaling
new da345b8
new 972deaa MMF
new 96ac998 Index restriction checking need to be verified again probably, but the basic structure seems finished.
new ab228b6
new 48920df
new 0e0e1a9 check term1 objective
new 2973210 objective check completed
new 859d678
new 3a22ecd Kernel function templatized, supposedly implemented all necessary stuffs to support a doubly-nested naive sum.
new 5e67718 KDE CV initial stub added in.
new 0ec12fa fixed checking for gcc4
new 7c16d0c This is the new file, with changes to interior point code
new acf4847 Fixed base/test.h to fastlib/base/test.h in textfile_test.cc
new ef15ceb
new 22f6d71
new 3559b65
new dab5c3b
new 1a4babc gradient for beta checked
new 3795259 gradient for beta checked
new 48ae9c7
new 0caba13
new dd9e2d0 Init function added.
new 8c00cab Now I can compute double-sums using the framework.
new c39fdc8 Monte Carlo compute is now correct, but need a way to dynamically adapt the number of samples.
new ddfab45 KDE CV Monte Carlo testing... Now need to add in a stratified sampling with trees.
new 6ef176d MMF triple
new 5a6e9b7
new 53c57b8 gradient corrected
new 6b16ff4
new 1160400
new 433fc2b
new db8cb0f
new 6b7965a
new 630b238 gradient checked
new c0f20c7
new 4d58326 MMF triple states
new d33ad78 Started stratified recursive sampling. Still more to fill out.
new 14f06c3
new 4e13a57 gradient/hessian checked
new 9827c6e Added the class representing the strata.
new d34fe11 Stratified sampling implementation in progress.
new 44ed792 MMF sum to unity
new 6f7c539 MMF sum to unity
new d35996b correction completed
new a6da3a8 Function prototype change, stratified sampling in progress.
new 1fc87c9
new e8362dd
new 6761941 objective2 correction completed
new 744bc5b checked and before adding hessian update
new 98188bf
new da8eac0
new 08dbe6b middle of adding hessian update
new cc05b7e Checking in of the old THOR KDE code.
new a1b58a2
new 61831b5
new dc53313
new a541246
new e1f6978
new 79d3dd7
new 7bc3d7f
new 0b02730
new 87f7c74 Working. Will now go on to change the starting point selection
new c8d6d91 Working. Will now go on to change the starting point selection
new 30838ed
new d1031b7
new d82a490 empty density tree directory added
new 5afc2e3
new 8981c0e
new c3ae699
new b27337c
new 124a619
new bdfbece Working fine(atleast looks so). Will change stopping criteria
new 95977e6 Working fine(atleast looks so). Will change stopping criteria
new 51208b3
new 8df20b8
new 6f8fd4c
new e517622
new fc5f170
new c8233ec
new 26a404c
new eb79541
new c47264c test convergence
new c2c08d8
new 58c2469 the dtree.h file added for the first time
new 081af8d
new e18c300
new 38882c1
new 6d3edd1 dtree.h updated
new cee636f gradient check
new 8f1614f main.cc and build.py added and dtree.h updated
new 5b3a0f4
new b31a2d9 approx_hessian
new ba939c7
new 3887889 main.cc and dtree.h updated
new de1f02a ComputeValue function added in dtree.h
new 8818695
new fa25583
new 3a5b224 Critical bug in the base case has been corrected. summary statistics in the base case should have been accumulated after the pruned information is updated, and this is corrected now.
new d226352
new 7fb8bb1 now the base case is replaced by a single-tree traversal, then followed by the inner loop (THOR style). This gives much needed speedup in many cases.
new 1069fce crossvalidation and tree drawing added
new eb10a36 Compilation error fix.
new aa7d0bf
new 20ed118
new 8f8afd1
new 3ae539b
new 1e9c071
new 53f43db
new f7fff15
new d2ad4a2
new 9a7a071
new 9d91a73
new 59d7ef2 MaxDistanceSq(const double *point) function added. This file really needs a cleanup.
new 5d646d0 everything works as expected just that it is overfitting
new c1d045b Made the tree types public.
new 0e2ef16
new 8d3aec9
new 719e282
new 4bf1d0f
new 37481e1
new 25eadd9
new 260c5c7 Compilation error fix and basic stratification using priority queue works now.
new 8b5fe6c Monochromatic trick added.
new 8a429f2 Fully working code for 1-D setup.
new 5cf1354 Fully working code for 1-D setup.
new 0566464
new dbfe4d6
new 00913b8
new a2c9630
new f6e9b0e Some fix to incorporate the precomputed number of tuples during computation.
new b0daf2d
new 709bef8 Turned off Monte Carlo probabilistic approximation, now trying to do everything with exact methods.
new bfdec89
new f1eec83 changes added to enforce minimum leaf size, other comments added. But idea is that once this works, continue testing with it, while I change the code to deal with nominal data later
new 84d774d Perfectly work. Commiting before I make changes for multidimensional case
new c36e4ad Perfectly work. Commiting before I make changes for multidimensional case
new 25f3ee6 Perfectly work. Commiting before I make changes for multidimensional case
new 38bb66f Perfectly work. Commiting before I make changes for multidimensional case
new fbe95ab Perfectly work. Commiting before I make changes for multidimensional case
new ba9ca68
new 0d09bc6
new f351b3e
new 22f3561 MIN_LEAF_SIZE removed and not testing on huge datasets which is taking forever
new b9c1cd9
new 47c7ba5
new cbe70d6
new ac4ced5
new cbb220c
new faae4c0
new 9a476ae
new fdd065a hessian update
new fb4f288 hessian update
new d5ba5e7
new 437b227
new df4b6bc
new c6bf8c0
new 9b11410 Initial checkin of the potential evaluation for multibody case.
new 83729c3 hessian update test
new 4c42e2d Shortened kde_problem.h by breaking up into multiple files.
new b2a7e1d
new 6dfd56d
new 8e44a6f Potential code compiles, but there are stubs to filled out.
new 52b89d1
new b75a9e2
new 71e7f00
new e7ca621
new 5ba1550 The code is compilable, and stubs are being filled out.
new acb81fe
new 2737fc5
new d8a9302
new 11ac282 First prototype for multibody potential evaluator checked in. Now need to apply series expansion.
new 1e5f0c8 Taking out bugs one by one.
new eaed08a Bugs stamped out I think. Need to implement series expansion.
new 1b9f888
new 228a926
new 97249f6
new ba86658
new 7896057
new e49b69b Templatized the computation part.
new d6575a0 fixed build script for macs
new a9d467b
new b42bbfb added code for ObservableKernel
new e482119
new 2cdd87a fixed fx/no_output_types name disagreement
new 7ae5733 add solvers for general eigenvalue problems (for both symmetric and nonsymmetric matrices)
new 163e801
new 278c0d8
new 924b15c
new 151b2ea
new 5d17db9
new bf88456 hmm
new db1786d hmm
new 988367e hmm
new c0ad249
new 4d402d6 Chebyshev fit utility added.
new 2982edf LAPACK is built without optimization for Ubuntuu problems.
new e99998c
new 5185e4c hmm
new facb2b4 Error upper threshold could be less than zero (right hand side of the pruning rule), so I thresholded it.
new 1ab4367 Compilation error fix due to nested sum class change.
new a8f6b60 Fixed so that it is not templatized in terms of the tree type.
new 16697cb Probabilistic case does not prune when the requirement is 100 % guarantee.
new 09bf2e7 Rough idea implemented.
new 4f0f22e CFmm tree template added.
new 505ded9
new 52b181c CFMM tree in progress.
new 38f43cf Some more fixes. Now need to plug in the tree within the tree part for CFMM
new 2154f7b
new 153e1fe allknn_balltree and allknn_kdtree added, support single/dual trees
new 4b9eb26
new 7d2d108
new fbd64f8
new f12dc6c Some more brainstoring on CFMM tree... Recursion part needs to be fleshed out...
new 47dea76 CFmm Tree compiles but I need to go through again and see if it's working correctly. After that then I have to implement the main CFMM algorithm, which is probably an easy modification of the original FMM.
new 70b22fd
new 696b517 Segfault fixed, but still need to verify the correctness..
new b1ba107d Now need to correct the WS index merging part.
new 0add521
new 5d082dd WS index computation added.
new 396dd9b Chebyshev fit error computed properly.
new 81b66a8 Added the stub for continuous FMM, but needs to filled out (rather replaced with a working version).
new afec28e
new 9981613
new 3480a7f
new 938eb87
new e2ae2ca
new f8041bc
new a141908 added niche/lds, preliminary
new fbebb1a
new 8dcdaad
new cfc0353
new d7123b3
new ce819f2 Some more changes. Now need to work on the bottom-up computation.
new c74412c Added the link from the WS node to the CFMM tree node.
new 7e1efcb
new e5972ee
new d50d3b6
new 86111e3 Added the init flag that tells whether the expansions have been created or not.
new 7f0a44e FormMultpoleExpansions method completed... Still filling out stubs...
new 65f0511 Just have to complete the algorithm...
new 98f2c50
new 1727025
new d867fd7
new 0860d2e
new 800df18
new a1fb7ad Reorganizing the optimization directory so that I can push MVU and isoNMF
new 1e1c299
new 91b8851 Restructuring optimization
new 693061d changed the names to comply
new 575987e This is where mvu and isonmf will come
new 14ab40c
new 26be9be
new ccb0af8
new 9423a34
new a6e4d28
new 168f9b5
new 3d22888
new 2fce500
new 749672e
new 7add48f Keep fixing mvu so it is releasable
new e598054 new user
new 8743977 a small bug in the build file
new 1a73d43
new 2a48167
new 8fd0a04 It compiles now but I need to add more documentation
new 1bc75e4
new a6acd42
new 17964d2
new 0bce573
new c474c51
new b4b73e7
new 0f05119
new 144c756
new a8cae89
new ef5b075
new a5ca67a
new ced4b21
new b93b121
new acf1c2f
new 7b167e9
new ef80cdd
new 250c884
new 4f00d14 Templatizing the hypercube tree utility so that it accepts CFMM tree...
new 486297b Lots of bug fixes on CFMM, now need to optimize.
new cc32928 Base case kernel for the CFMM added.
new 02ebea5 Some minor changes in CFMM for computing WS index for each node.
new 89d453e Max tree depth added for CFMM tree
new 2427edd Code change due to CFMM tree interface change.
new 3d52669 added documentation
new 582ed64 added regression and ridge_regression but I haven't worked that much yet
new 64ea619 Max tree depth CFMM fix.
new 9629b43 Hypercube tree depth limit option added.
new aa9b189 FMM edited for adding tree depth limit.
new fb2e059
new 4a36bed
new 7ffbb87 CFMM finished.
new 4a63a74 Added the necessary files, now I need to compile and test it
new 54dc865 added an extra utility on the matrix so tha you can create diagonal matrices with a single element
new 3c57477 Changed CFMM order to 2.
new 608426a it compiles
new a25d73c seems to be working
new 53d10fa Took out sibling pointer from CFMM tree.:
new 72469c7 Bug fix: CFMM tree now uses nonadaptive octree.
new 621aa34 Major bug fixes.
new 3c9605f Bug fixes.
new c57d22b Final commit of CFMM.
new fa9a48a Ridge regression is working, I added a main file too, so that it can run as a stand alone application
new a20ba32
new 22e4614
new b78f055
new fd8e34b
new 481adcc
new 9e59e7b
new 85100b1 Bug fix in the base case: There was a problem when the distance approached zero, and this is fixed now.
new 7172428
new 79bd95b TranslateFromFarField in inverse_farfield fixed. Instead of CopyValues, it should have been AddTo.
new d1a321d
new 96b37c4
new 8c301af
new 31e6b0f
new a309deb
new 6c65bc6 Some lower level optimization.
new 187031e
new e1f9a77
new f818423
new bad24be
new e392689
new adf2648 added cross validation and eveyrthing is based now on SVD
new f421d31
new 874820b added code for multiple lds sequence generation and calls to zoubins stuff
new 602da03
new 92d2430 Code compiles, SVDRegress fixed, now proofreading Crossvalidate.
new 9503147 QUIC SVD moved to MLPACK.
new faf44d1
new 5b84551 mmf
new 9698f87
new 8445d88
new 274d6ae
new 038075f
new 3b45063
new 922fe8a Regress and SVDRegress fixed, now the intercept is added to the linear model that is generated at the end.
new 7305058 Crossvalidate function debugged.
new b0fc3d0 Some more bugs shaken out in ComputeSquareError function.
new 303ae9f Minor cosmetic change to the driver.
new 9b1a740 QuicSVD code interfaced.
new b148e44 graph
new e962a17 added q point vs r node prune
new 6542891 graph
new 32680a6 graph
new 88fe1ba restructured MMK code, templatized HMM, and added Multinomial distribution
new 33d9175
new 5cbd3d4
new 9831634
new 35dc2b7
new 2f43323 finished load_profile and modified test_hmm_multinomial to compute kernel matrix from file-specified hmm profiles
new 771750f
new 704a0e0
new 2abfb24
new 08ef14d Monte Carlo pruning plugged in. Now need to debug.
new efb46df Potential infinite loop fix in Monte Carlo sampling.
new e73ba78 Another bug fix in index choosing in Monte Carlo.
new 5f7ff50 Some comments added.
new 2e07104
new d860024 The basic form of feature pruning based on VIF added.
new d458c11
new 60c8a3c
new 1dc216d
new 675394f Main framework coded up. Now need to put it in the driver file and debug.
new 04ea03c
new 97a23ab
new 552145e
new 4f171d1
new 4526500
new 9d75dd8 rearranged directories
new fa1182a The basic options added to the driver, but need to debug more.
new 732ddaa I think cross-validated regression is working. Now need to verifiy VIF feature selection method.
new a81037b Starting of Fourier series expansion.
new 2b268de Refined Fourier expansion test.
new 2b1ae01
new d1f0ea5 changed output and added charges to base case
new d3cb766 Documentation added, still need to verify feature selection.
new 7cb76d1 Verifying feature-selected regression now.
new 9e54b0e I have proof-read the variance inflation factor feature selection part.
new 5dc14d8 The test case for variance inflation factor feature selection added.
new c13bbea Some helpful outputs added to the test driver.
new e04f683 Linear algebra directory started.
new 3a038da Some bug fix.
new f827016 fixed symmetry in base case
new 7ddee6c
new b78af0f
new 9de1b9a added stuff for hmm data
new 1c5f55d
new 96ece25
new 9f3fb2a
new 682c411
new 5263617 added archana's code
new 50d4080
new 6f68a86 CFMM driver file fix.
new 945112d Changed int's to short int's for the multiindex mapping to save space. Worked on a bit on Fourier expansion. Now need to work on the error bound.
new c199d08 Fixing Fast Gauss Transform compilation error due to series expansion library update.
new f8bc12b Added the implementation of complex matrix.
new 635d5da More progress on the Fourier series expansion (computation of coefficients and evaluation). Now need to plug in the error bound.
new c82c27f
new dcca3d1 Initial checkin of the compressed vector experiments.
new abc67da added kernel kmeans
new 636942c Compression and decompression works.
new 3372eff Changed short int to int to prevent overflow.
new 53dc27b Bug fix, but compression/decompression overhead seems to be greater.
new c2c0db7 added hmm_testing
new 00fbb7e
new c9baa44 Testing started for Fourier expansion.
new b89bb6c Fourier kernel added.
new cb3dc06 Fourier expansion being debugged.
new 4498664
new e26dd26
new 548c1c4 Some bug fix in the series evaluation method. I shouldn't have ignored the complex part until all the sum components were added up.
new 7941718
new 1b66f9c Dependence on dataset_scaler taken out.
new dba2167 Compilation error fix, namespace issue resolved.:
new e88ee0d Compilatin error fix due to code overhaul.
new 17bec02 Compilation error fix.
new fcee103 Test file for CFMM tree added.
new 22830de Need to implement method for incrementing the vector.
new bf55cd3
new 7270b61
new 711e69e Add stochastic gradient descent optimizer for linear and nonlinear SVM classification
new 6419f75 added query point ref node prune
new 28d5e92
new 43e8455 fixed potentially bad printf
new 21924ef fixed a much outdated Copy -> InitCopy
new 65f32f6 fread/fwrite retval checking
new 8f1e9e5 removed added links and fixed #define LT -> LTSC for OPT++
new b5ef722
new 13aacc7 fsdfsdf
new d94902d
new 5625eb8
new ead08c0 fixed some stuff in the documentation side, so that it becomes easier for UBUNTU users to install it
new e2c1a70
new 0f3860b
new 34ccc71
new e0800d6 automatic installation of opt++
new eff589c Disabled multi-threaded builds. Now fl-build and fl-build-all runs with j = 1. This fixes the problems with Opt++
new 0a34b79
new 751e555
new 76c8b9e
new 2373d62 Added in the A^T A SVD method.
new 4817237 Now need to take care of the date features.
new 673253d Added significant amount of documentation. Next step is to write more tests and debug
new 9aee5eb
new b6b9135 fixed Doxygen a little bit
new 38298bf
new 03b85f5 added niche branch of mmf
new 9453535 added niche branch of svm
new f2a7235
new 2b68f0b
new a487cec
new ec2a18f fixed uninitialized vector, worked on link and multi-tree
new f44553c
new 6ad5725
new c0ff9e4
new 4db278d
new d1a8759 removed fl-build's use of j except when specified; corrected some #include's to use explicit paths; other minor fixes to mvu and lbfgs
new f464d34 PrintDebug for complex matrix edited.
new 8097297 worked onlink sorting
new d00281f
new 11fb7f2
new c183a65
new ca77348
new 5fb5e8e
new 67aa284
new 5f24de7
new d59772e
new ee34110
new 3f43cd0
new 0b5995e
new 5a0f65d
new e68f036
new face384 can save and load data for good testing
new ca851d8
new 100592c
new 2dd7a67
new 6384c30
new 16075f9 copied approximation functions and updated bounds in multi tree code
new 18b7b34 small changes to reflect rbfkernel->mmf
new 1f43b62 finished copying functions over and added integral routines for distances
new f309a30
new 64c1c10 changed format of results
new 719be92 Bug fix in preprocesser. I'm modifying this to save the indices.
new f62f202 The preprocesser utility is done. Now testing regression.
new e1524fa
new e573c74 NOTIFY added in some places.
new e0bcc44
new 32b21e9
new 4ec1529 added some fx documentation
new b0e475d
new 54f3b93
new e484fee
new 234eb60
new 957f2d7
new 6382588 fixed exchange computation in naive and prescreening
new b7ddc16 Added the random combination code from Knuth's book.
new 93ec649 Some bug fixes in RandomCombination function.
new be55ad9 Going to try the point-based Monte Carlo.
new 3a52975
new 24bdc3c
new 79177b8 The covariance matrix is now precomputed for VIF selection.
new 5951e3f massive speedup for mmk
new bab3f7c Moved the optimization under fastlib
new a3cc4a9 Compilation error fix.
new a1e1e06 Made some fields public
new 473ed89
new 80d5de2 Now reports how many points violated the relative error, and the associated maximum absolute error.
new 138f43d Now reports positive/negative relative error violations.
new 7ca72f3 added testing for array of C regularization parameters
new 1a9b673 made parameters member of module
new 93cc5bd dtree.h and main.cc changed for diettrich
new 9668e15 fixed some overcouting in link, added sorting and merging of integral lists
new 072c97b
new af7c6aa
new 7423cb8
new e740508 Fixed MVU after moving optimization
new d037269
new d921355
new 0140a34
new 74c028f
new 2946cb8
new 462f898
new 9f16a75
new 314643a eval added
new d8b01ff
new 57f811b
new c2a50e0 added kfold cv
new 6539759 changed documentation and minor param stuff related to cp and cn
new c0e75ff fixed some minor things on the build file and added an extra namespace for optpp
new 1ad08b7
new 2e1b60b
new 31c0a92
new 1ee8fd3
new 1ff6470
new 3b51be7 NoConstraints tests added for all Methods
new 3b1bd11
new 9747c63
new a1b6696
new 37a60d8 Box constraints, Linear Equality and Linear Inequality added to Objective function class along with a skeleton for future work
new f940f0a Testing BoxConstraints, Linear Equality/Inequality using LBFGS
new 3fbe96a
new fc28861
new 598fb79
new faac94f added hmm_generative_classifier
new f3928b5 fixed link integrals
new fb5fe9a
new 874f800 some changes made to the test file and it is added to the build file
new aaba545
new 9211f73
new a7378e2 Moved the covariance computation stuff inside RidgeRegression class. Now need to move the featureselected regression inside as well.
new e153658
new b05ec44
new aac187d
new ed2bebf
new 7d0d933
new 8cfdc6a
new 397968d
new 2f56f28
new f33bd44
new 6410cbf
new 2913150
new 800ce9d
new fef2d99
new 64501e6
new d39deac
new ac9707b
new 8e7498c
new d48ad9b Move the crossvalidated regression inside the RidgeRegression class.
new 6a92816 Took out a deprecated function from RidgeRegressionUtil class.
new ce28bc9 More code restructuring. Crossvalidated regression should be back online.
new c271789 More code reorganization.
new bcccdef
new b9e1dec
new 4c5796c
new 4c543f4
new 9c18892
new 8235fee
new c4189c7
new 3664bdb
new 1d1c24b
new 80dc42b
new 5df41a4
new 8a25b58
new 2e0b2a6
new 6083f56
new 54338ba
new 19ae306
new 5163035
new 1bcb336
new 476a63a
new 5a20b7b
new 0dec5e8
new 6bb5c53 This is going to be a working version of the comercial fastlib
new 4b61993 testing copy
new e18b9d3 I did something wrong
new fd07b0d This is fastlib3 for prefection
new 7261c32
new 1734142
new 933a67c optim
new 22e5c8a
new 73656eb
new 9608418
new 8d12bd9
new b265c73
new 8c4a46e finished first stage I need to write a test
new 5634d05 some minor additions
new 9895ade
new 9574402
new 22d23f6
new 24266ad lbfgs
new 5b76edd
new 12d6b0d
new ed53fdc modified GenerativeHMMClassifier to save learned hmms
new 2844733
new 52e1d28
new 58881f1 This should fix the annoying initialization error. should_free_ field is set to false when the constructor is initially called. This could be potentially done with the OT-framework using OT_DEFAULT_CONSTRUCTOR macro, but this essentially accomplishes the same thing.
new 5ca870e
new 9d58532 changed tolerance for smo to 1e-6
new 2ff6946
new 65d0f51
new 41fcb8d
new 5997e50
new 05123c1
new de27205
new 8d9ba63
new 77cfdcc put normalization inside integral code, added permutations
new 24f6416
new ec35454
new 14ad237
new efe1a95
new 2e1f992
new 46e5b46
new 6b3555c
new ad413fc
new ed7d367
new 48037ca nearly there a big effort to templetize evrything in linear algebra
new 87a6c02
new 4fed81a
new acc37a6
new e4b8238
new 506d4bc added docs
new 21455a8 added weighted bounding box averaging
new 4498a8f
new 362ab75
new 75c4edf
new 8a6c941
new b1bf5bf
new 8b0c37c
new 8049b2f
new 156e2db
new 1c1dbf7
new 3c742a5 still developing
new 292e1c7 compiles
new 3a95371
new 16f56e1
new 032b154
new c309437
new 2f7f5d7
new 876774d
new f139817
new 1161408
new 37e4726
new f9d6201
new 6e925a2
new c52383f
new 4108ac1
new 8670797
new a7bfc35 Templates in la are workoing now along with tests
new 98622ba I had forgotten to add this file
new f967425
new 7985a28
new 8884c3d added a big collection of utility functions
new e966557
new e89e571 Initial template of CMakeLists.txt added for some of the core directories.
new 14e874a config CMakeLists added.
new 4a93983 added F_m
new 5a9cc57
new 8176b2c
new b90d48b haven't tested utilities yet but coding is done. Thinking about extending the overwrite/init functionality everywhere in la.
new 45d0d38
new 856a682 fixed cfmm base case
new 5c8071f adding one electron integrals
new 2385d05
new 2b6ee63
new 927494b
new af207d0
new c924563
new 7342fd7
new 8b6c214
new cc26218
new e79d84b
new 4f347b4
new e47189f
new 728d933
new a5ed72e
new d8b0be2
new 92a2203 Some changes in opt++ for soyeon trust region
new 21cac83 getting closer
new 112380b now it compiles
new 98beee0
new 1a4a2e7
new d257821
new 022370d
new e2227e0 added niche/spike_train_dependence
new 51f236d
new 73f7068
new 8f15bd8
new 1831dc5
new 62f5603 added some one electron integrals and comparison code
new 5f88e0c
new f44769f
new f6b3e77
new 0071fb5 finished code for creating points
new bb8d77a fixed and standardized comparison against naive
new 7f641a2
new d277c76 fixed storage path for fxrun
new 902eaaf
new 4ece095
new 95e1223
new ed7f12b
new d2d28ba
new 4494931
new 7d4bde6
new d873cf6
new b9a0e0d
new 535abb5
new 9848d08
new f2b5657
new 4e2171d
new 5cb66d4
new 178c742
new 3c86e86
new 719a4fb
new c34cded
new cada161
new 06b6fd7
new 2189a86 More templetization of the la domain
new 8a83718
new 30367aa
new 9bb129f
new 05096e0
new 4207c13
new 54d90fc
new d654a97
new b703fd9 Temporary commit so that we can move to a new repository
new 9284516 Finally matches the Vijay's results.
new caabfb4
new 5e50bd7 bug fixing for multiclass SVM based on opt_smo. New implementation for stochastic gradient descent solver for SVM: opt_sgd. Experimental codes for hierarchical propagation solver for SVM : opt_hcy. UCI_iris data sets added.
new 68b4bf4
new 4a548b7
new ecc3fc7
new 843d105
new 5569fc4
new 51f9e9b
new faca207
new a3d6e2d messed with schwartz factor
new b27fdce fixed num pruned shell pairs
new 770cdf7 "fixed a trivial bug"
new cf5b9f2 sorry about that
new 2d2b5f0
new 69cc935 Added a sample datafile
new ba1e833 updated implementation for opt_hcy. In kdtree construction, right child no longer contains the splitting point.
new 6f80774 Took off this assertion that created problems
new 6b9ae1d fixed a bug with fx_init
new 084f8a1 bug fix for opt_hcy
new d876092
new 29b07a0
new d9a1c12
new 65b4905 code consolidation for opt_hcy
new 1b9b6cf fixed pointer bug
new ddcee1c
new be9ca9c
new 84a471f
new 55a2df6 fixed timing and docs in cfmm
new c109654
new 4cad445
new 7fd1f20
new f725beb gonzalez tree removed for now and just plain old covertree tested here
new bfa821b memory leak fix.
new ba9a869
new 2b83fa3
new 3cfc929
new 8cad464 Error behavior for Monte Carlo is more reasonable now.
new 2419ae4 Fix in the Monte Carlo sampling to return positive and negative components separately.
new 8f42325 Some parameter tweaking.
new 4255da7
new aca2073 Monte Carlo approximation has been changed to per-query estimate.
new 87c8dad Added the PostAccumulate function.
new c829f7b
new 2f06856
new ccbe7ec
new ad45d25
new 08178be
new 43b81f8
new ae121a1
new 7b54a2a
new a40fb88
new 19a5062
new b7b68dc
new 955a30c
new 32ec61c
new 1601d63 Modified multi_physics_system.h to
new da28272
new 10880df
new d59a9de
new 1e18c6f fixed weighted average of bounding boxes
new 0911ce6 fixed bounds and error control in multi tree
new 69d4193 fixed link sorting
new 8490375
new f0ecda6 fixed naive storage to work with fx-run
new d7c351b fixed naive storage to work with fx-run
new 8e0d6f0
new a82d282
new 81126b0
new d4d75e7 storing integral components
new 4ec026a
new dfb40ec
new 7a27f51
new 2c7d79e
new 64ec52b fixed oeints, started new verison of scf solver to replace old hf
new 0a40928 Added the option to use different dimension for normalizing.
new 8f0cb21
new 53ef16b
new 7967b57
new 3c12cf2
new 35b2e6d
new b04b1e8
new f88c311
new 63fc116
new 2b19fc1
new 2ef20fc
new 1ca6bba
new 578596d
new d3598b5
new dfda8d6
new ae413e7
new 6544511
new adf7754
new 01d0ad3
new f0bd382
new c573b43
new 5f9cfef
new 6922374 New algorithm: greedy approximation for large scale SVMs
new 633bb9d
new 4563351
new 6a2e2e5
new 2d6fbb8
new 7d61c4c
new e497c48
new 6a3f62e niche - started new, nice hmm code
new e1108fe
new 0b93368
new e6a429f
new b7ca883 zhmm compiles
new b57b4c3
new 3f104c8 commiting after long time. Will add classification experiments
new 2b8ab0a commiting after long time. Will add classification experiments
new 8aca707
new 1054e79
new 3dea7a9
new dbbc436
new 9721cbe first commit of thor_md for parallel molecular dynamics
new ab98dc1
new 1272c52
new bf29a8f
new c414631
new ff3dcb4 Stochastic Conditional Gradient Method (scg) added Sparse Greedy Approximation (sga), i.e. Frank-Wolfe method updated
new 2126954
new 515eada prelim testing for mixture of 1 complete
new 5f06ae7 added diag_gaussian.h
new 1e9c0b0 added la_utils.h
new 0610b6b
new d744f40 finished baum welch with testing, onwards towards viterbi
new a0390a4
new 2255d3c
new 39a6b21 finished first final cut of kmeans_nonempty code that uses MCF (minimum cost flow) solver from ZIB
new 6d1eeb7
new 0523477
new 2cca429 more final version of kmeans_nonempty
new f130231 adding schwartz bounds to multi-tree code
new e5c738f
new f76c68e
new afaccca
new d4bebeb
new 78bd1c7
new d3166a4 changed last argument of both CopyColumnFromMat functions and CopyVectorToColumn to const
new bb11cf0
new 402c4d1 standardized fock algorithms for scf code. also added schwartz prescreening to multi tree
new 7141077
new 330fbb9 fixed scf integrals and compilation issues
new 822d15a
new 5ec185a
new 31ede7c
new 788a75b
new 8eae721
new 62123f9
new 621fe62 fixed memory leak in mixture.h
new d353a7c
new 9285f6a
new 59b92f0 I think the HMM implementation is complete
new e6998a3 I think the constrained kmeans implementation is complete
new 5b241ab
new 01b75c3
new c7e1834
new c30e5eb
new 5a975a9 renamed zhmm.* to hmm.* and removed the junk
new 573cb17
new a5e9713
new 06475da
new 80a546a
new 0b795fa
new 447fe2b
new 472246f
new 19157c6
new ea2e483
new c4b1f3c
new d030f9d
new 23bec25
new c2f3351
new ec9eaac
new aba8f94 changed mu_ind to lambda_ind
new fba63b4
new 1a47eb4 FW algorithms updated
new b9f19c6
new fc48d6e prelim version of latent_mmk for discrete observations is complete
new bd34156
new 2bf62e3 added generative MMK and isotropic_gaussian
new 9583c66
new b92b482 fixed link density check
new c6b7f1a
new 377f3d7
new 6955648
new bc4942d
new b5c7199
new 6547171 display testing accuracy option for SMO's shrinking technique
new cefe775 added test engine for mmk and svm
new c078b36 added object traversal capability to HMM and Multinomial classes
new 91d1fed
new 523c8c0 iteration information removed
new e34c98b
new 194db55
new 6059612
new 9980889 bias update for nonlinear sgd
new e1505bd
new b1e9f8f
new 7042d0b
new b3320be display gap on termination
new 3b1a81d everything but CFMM works with SCF code
new 560680f
new 8e331df display gap
new 148115d
new 947383f mimic online senario using random permutation
new 03cad5a
new 890bb06
new 5533671 updated scf output
new c504d98 kfold cv for lmmk
new b472829
new c532c69 cleaned up printing for scf code
new 31b1a80
new cc0640f
new 8e6a7c5 added hmm_kernel_utils.h
new d9e4018
new ce6831f
new f65dc77 added test_inbio_kpca.cc
new 6fc9847 nearly done with test_inbio_kpca
new d805af0 finished test_inbio_kpca.cc
new 90f306b
new 66e246c
new fecab99
new 57552ed
new 87a9529 added niche/kernel_pca
new 371a81b
new 9a043f2
new 62021b0
new 1f43314
new baa9764
new 39da534 fixed bug in core matrix computation
new 19d322a
new faf223c implementation of Pegasos in opt_sgd.h
new 829bc4c
new 40640b8 infinite max iterations for sgd
new 25ae6db
new 4cead5a
new b30e4ae
new 8cf5702
new fb81e4a
new 053b938
new bfa2ea6
new 2e4095b
new 284fa09
new ab7c49a
new cd6b3c6
new 2019d30
new 08afbfa
new 1dec666
new e50f53e
new f400e52
new 92cc972
new f3688a9
new 9c6d231
new 47ba426
new 6c44072
new 2bd60a3
new dd9a239
new e1a25e2
new 5f5c458
new 73454c7
new c6396c1
new a3f975a
new 85a289a
new e4ba759
new cc483b2
new 5d9aeef
new b2a90c7
new 124b450
new f566a80
new 217d993
new d462090
new e4f5fa3
new f29aa57
new a0b1a80
new f9f2b74
new ba352ce
new 2071e95
new 31aad2b
new 9d51e4e
new 9820166
new 5ddca7c added core hamiltonian to comparison code
new 6317c12 svm_optimal
new 7c4e232
new 339c681 fixed nuclear charges reading
new f639d77
new bbc967c
new dc9ae3f
new 411c37b
new 4942040
new 4a997e9 added ability to read density matrices from QChem
new d1a1427
new 2fc19b9 included "assert.h" in fastlib/base/common.h
new 100447a allowed cflags to be called by linker as well (added under Ryan's supervision)
new 7508290
new 2f09a21 removed periodic distance funcs from bounds.h, and moved to periodic_tree.h in my own contrib directory.
new ffb85d8 added qchem density reading
new 5546001 fixed strcmp for qchem input
new fb81b86 1. rename: opt_sga.h -> opt_fw.h 2. in opt_sgd.h, INFINITY -> index_t(INFINITY) 3. FW examples added in README 4. sga->fw in svm.h
new 05a8feb
new 0dbb004 minor modify on shrinking of SMO
new 5f878d0
new 7094350 minor update on shrinking and n_iter stopping criterion
new 7caeff4 modify unshrinking
new 13ad551
new fd60e64
new 116da9d
new 2c53433
new 157bdab
new 85cca44
new 75afb35
new bd3ef12 max_n_iter<- 10^8
new 56dd2e2
new ce70111 max_n_iter<-1e8
new 382de77 n_iter->ct_iter in calculating portion of away steps
new 9b241f8 added synchornization calls to thor_md.h
new caba56d
new 8a8255b basic libint interface works
new dddd687
new c836024
new 1f6553b
new be25903
new 24cd913
new 083925d more improvements to integral code, fixed major problem with CanPrune_()
new fe3150d
new 43bbf31 fixed remaining_epsilon in PropagateBoundsUp_()
new de675f0
new 0a519eb
new 60ff36d
new 733bcb9 tried fixing remaining references in FillApproximationCoulomb_
new dc0cfa1 tried more error fixes, worked on normalizing integrals, fixed reinitialization of matrices in comparison code
new 82ebc4a
new 451279c
new 9298dde
new af8b548
new d038a9a svm smo
new ff6becc svm smo
new 353639e svm smo
new 67dcac7 fixed permutation error for density matrices, added normalization to integral wrappers
new a07cd8d updated exchange error
new 6e5d81a
new bced7ea
new fef2150
new 97fbb5e few book-keeping fixes
new 67f72a0 changed to prescreening comparison for error
new c7740aa do w_scale in training session
new 3016f8c added .../niche/bayes_net_kde
new 0b79411
new 73ffa94
new b664806
new 5a0408f
new b9cd20e
new a71ea00
new 07168c8
new 1307b20 added L2-SVM using SMO added a variant of FW: opt-par: search direction is parallel to an edge
new 0cd3173 remove usage of w_scale
new b9eb935 separate pegasos from opt-sgd
new 65c79b6
new ef82d73 add no w_scaling option for pegasos
new 95815d6 pegasos with bias
new 2ce5b43
new f61c37e
new c77a1d1 add n_epochs option for SGD and Pegasos
new b8abcec Coordinate descent for linear SVM; L2-norm regularization option
new c4ba7bf in online algorithms, permute data set within each epoch
new caad94d modified epoch scheme
new 48acb5c
new bc73999
new 4abcdae CD working now
new a957451 DCD sqrt bug fixed
new 4c0f1e2
new 34eccce
new e90c458
new 72acfa3 add bias for pegasos
new cc1f801 opt-pegasos.h: amortize w-scaling to prediction session
new d928d04 1.move pegasos's w-scaling to training 2. add projection option in pegasos
new 048c68c display projection for pegasos
new 18d9a9a
new 5ca76b2
new b941d1a
new 9296070 display gap on termination
new c2978dc
new ee519c0
new 0ea2c77
new 992eab6 add an option to calculate primal objective values
new 47b7ce9 add opt_sgdwb.h
new d64bf5d fix bug in sgdwb's prediction
new 7df3dd8 pso
new 4335c4f tried to reduce memory usage of multi tree
new d40b572 added ability to compute combined CFMM/LinK energies
new f106391 fixed memory usage in CFMM/LinK comparison
new a1ec87e
new 8ecec2e opt_pegasos.h: fix bug in calculating obj values when no scaling
new 4d0c878 removed matrix saving
new 5933286
new 31d7100
new 881b3aa opt_sgdwb: fix bug in calculating obj values
new a959297
new 3126c5d
new 95c6112
new a74b888
new 55229e6
new 285eb1e
new ad25c1e
new ab4682e
new 4117808 fixed multi output
new cc2812d added storage of overlap and core matrices in comparison code
new 8b9a2bd added storage of overlap and core matrices in comparison code
new dba1b02 added documentation for nuclear centers
new b614cb7 added documentation for nuclear centers
new 15e2259 fixed exit failure for multi tree runs
new c7ff793
new c49cc9d
new 2fe93b2
new 0dbb008
new 8720bcd
new 0412b4e changed eri code over to higher momenta
new 32baab0
new 2664063
new 3c55411
new 8a7b5f2
new cfface3
new 52c9602
new a2e9f40 Created IntegralTensor class to handle unpermuting integrals
new f11cfb7
new 789096b
new c4ffacd
new d61960b
new 73678ce fixed auxiliary integral calculation and added ssss integral support
new 4eb68e7
new 98976a4 fix bug in do_shrinking
new 1562c02
new 0fc48a5
new 0b27f22
new d504c53
new db9e8de
new 6018c33 added higher momentum overlap integral and some test code
new 399edb4
new 461faf5
new ea9bdd5 added kinetic and nuclear integrals
new 7655fa1 working on higher momentum SCF code
new 2fe7d1e
new 6b4c245
new 9eaa732 fixed kinetic integrals
new add7976
new a183c74 add implementations for LASVM and Robust Ivanov
new a12eee5 ID_FREE etc
new d4f4198 energies correct for single atoms
new fbd8d92
new 8b38336 working on F_m
new ebf6c55 added other F_m computations
new c05b6c9
new a463e97
new 625a7dc
new ec7e670
new 55ea70c finished prescreening, started on link
new 9833cac link working
new 4aa2f79 updated CFMM
new 4c20235 updated CFMM to handle higher momenta
new ea5ca79
new 1f29a5b
new 1060fb6 wrote BasisShell tree, working on testing it
new 1431176
new 54391d1
new 69fa9b0
new f4c0584
new 6d9ac90 shell tree tests working
new 1e2303d
new 767f43a added matrix tree
new 9eac93d wrote matrix tree tests
new 7ff3f1d
new d7e1dc7
new cc5f5f5
new da147b9
new 87f02b0
new ef18272 fixed bug with Init functions of AllKnn which do not take module_in parameter - now module_ is set to NULL
new f1f29e6
new ece8476
new 01063a0 base case and tree construction working
new 62d38a7
new d5d0d1b implemented absolute error pruning and bounds infrastructure
new f13928c
new 7affbc5
new e3599cc
new a4f3360 sgm2
new 979a03d
new 32bd698
new 1e06a72
new 0bb0569 added and tested bounds, fixed node counts
new 091221c more updates to work with higher momentum code
new 8ad071a changed build file to work on either machine
new 04e20e9 trying to fix memory errors
new 48b14d9
new e94c281
new 31265a4
new ca527a8
new b452d07
new 63b0f27
new d132dbf trying to fix memory errors
new 1eb5f87 fixed memory leak error
new 7ffa578 fixed splitting of off-diagonal matrix tree nodes
new 1bead99 cleaned up for testing
new 5907277 fixed memory leaks
new 9d5f9ce
new dfa7926
new 65ef1f5
new 643b3c4
new 3e0c6c5
new 981a1c6
new 60e04b9
new 3fd08c6
new a865d83
new ade47ef
new bf9e2c9
new 47427a6
new e8d0680 09_04_09
new 598f5db split coulomb and exchange recursion, added prescreening prune
new e0b4b86 fixed memory leak
new e1eee39 fixed memory leak #2
new 850657c
new 6efca8f
new b16adea grad_norm 0.001
new 909953f Now support L1-SVM-C (hinge loss) and L2-SVM-C (squared hinge loss)
new 4a2969d
new b2b3ac0 09/08/09
new 30d8d97 1. add SPARSERE solver; 2. regularization_ -> hinge_
new a33b521
new 5212d6a
new 19d5c9d
new 0dfc756
new 9559371
new 9a8a644
new e8bd88d
new 1811531
new 636ec94
new 378ad83 EMST on cover tree
new 0ee10cc
new a9c89e6
new 6d6360f
new decbd39
new b622799
new 893a0d0
new 81f94d0
new bb26d9f
new 1110840 added loghmm.h - it awaits compilation and testing, added fmri programs
new d8a8079 normalize=0 by default
new b141348 %f->%g for coefs
new 4c4160c %g->%16g
new 8dc3f97 implemented cover tree emst
new 107d12f
new aed2c7b some updates to loghmm.h - nearly debugged
new 63e541e
new d33cc42
new 88878b7
new 82feab2
new 746ceec
new bbb6f30
new 764cc3a
new 1ddfa37
new 7551433
new ac11b40
new b806c9a
new 17572aa Initial upload of the open-source CMakeified fastlib
new 88bd474 Oops. Wrong version.
new 7be8f9f Correct version of OS, CMake-ified fastlib this time, I promise.
new 61f6270 Add branches subdir
new 02a5e0a Add tags subdir
new cd9aa1d kfs
new e49d83f
new c83b88b
new a3f5b96 hybrid expansion pattern
new 9592f73 Identified bug when reading Mac files (eol = '\r')
new 9bed4b6 Added Mac eol bug to docs to warn people direly.
new b932bbf
new 0a22637
new 23d4a08
new 76b474e Added Inlcusion pruning in Cartesian case
new 214d2cc
new 18bc17a
new 7025101 Removed manual flag-setting that was messing up CMake automagic build_types.
new 7e565d2
new dab0f05 Inclusion pruning for 2pt, corrected
new ffd1189 experiments for SDM
new d3a1be3 remove msfw, since it's integrated in opt_sfw.h
new 5dde8e9 display portion of away steps
new 293fe0b if-> else if
new 04866c9 remove redundant init for grad_bar
new 0f9d8e8
new 1c0ad36
new 76f83db
new bd59c10
new 12005e9
new 399f9ea
new 54b2922
new 624c150
new 8b836cd bug fixing
new 826d498
new fcc6ebc
new 020bf07
new 037b5b5
new ca7d574
new 3ed0f3d
new 0ae2c49
new 76d694a
new e2c67e1
new 871411a
new 37be34b
new 34d328d adding comparison code
new 7d53463
new ddf967b
new 5e726df
new cb820ea
new 2f07b75
new 3b5a269
new de0e75c
new 975f4b9
new 957c83f
new c041e18
new 26977b6
new 4fbfef1
new 461e1a4
new 11dd8cb
new b5a2588
new 2040f72
new 447d560
new 19f7bfa
new 30559c5
new 331e535
new d8d8a92
new 05db56e
new 70b03cf
new 461991d
new 640c1c6
new 7f1c4a3
new c619b48 speed up kernel calculations for NORMA
new 5189604
new 9ec11e3
new d422711 speedup kernel calc for ct<n_data_ cases
new 5ed4607 speedup kernel calc for ct>n_data_ case
new c7c1061
new c4c0f0a
new 469733e Corrected inclusion pruning
new dad47e5
new 39ccfb4
new 6811af2
new 60bfa8b
new cea289f
new ed931ad
new 03d86bf
new 3a03b06 ddcm det alpha
new 9b436aa
new 0f1a486
new cb95a13
new 5de724e
new 4de4e1a
new 8740dd0
new b784339 local kernel machines
new 9b6b21d
new d4a93be
new 5899bfe
new 55491dd Optimization half-working
new 8f16882 added note to narrow native fastlib optimizers' deps
new 5b1a12e Weighted 2-point correlation
new 7a1d01a fixed typo in opt++, removed test code unwittingly checked in.
new dbd1c7f
new d3a4aeb
new 6254734
new e0d580e
new 74fd239
new 7b6e1f5
new 089bb18
new 73d59a9
new 89a51c3
new bbeb78a
new fa48f92
new 626e898 partial
new a462614
new 61a948f
new 16c21ac
new e1a3541
new 96cc4f0
new 8aa58e4
new aedbb76
new 12f5ee4
new d5fbf74
new 15722a7
new 5d27a2a
new 0b0a62a
new 1c29b8b
new abca1cb
new e1d4b04
new cbbd64c
new 7806baf
new a651c71
new 101be21
new 9d23ef8
new a51349d
new 26fc2b0
new a744993
new be44b42
new c9a188d
new 17f0e57
new 2caa4ba
new ea546fb
new 1cb141e
new f33fd01
new 4fbfb43
new af768cf
new 6bffca6
new 061c560
new 44104f9
new 297b937
new 62a98d5
new dd0fc50
new c83427b
new 09c3e7e
new 78a8ae9
new 90df6b0
new 95eeef0
new 05d28d2
new f08e72b
new b6af4b7
new 802da07
new fa85253
new adfceb4
new 196bb16 updates to ppk
new f2ffbc3 updates to ppk
new a4c5d7a hopefully corrected bug in ppk of diagonal covariance gaussians
new 2ceab6a
new 3fed811
new 53f0207
new 8e03cd5
new 00e4664
new b4b1519
new ed91d29
new caac882
new 1f58ee6
new fe67692
new d794c1c
new c8fd95b
new 4cac025
new aa0f7d8
new 8baae7c
new b523f3f
new 167ec22
new 224e93c
new 915799b
new 13fb8ef
new b4701e3
new 578a6e4
new 2f059a4
new 5c40064
new c2897ac
new 2f7c28d
new 1636038
new 3de473f
new 1735eb2
new f8a3b96 added sorting of edges
new 0cc7c01
new 14c40cd
new bfd78c6 Moved optpp to opt++
new 870fc10 In a bold move, removed the README instructions for fl-build.
new 6295c52
new 649626a
new 172c1ae
new 700f4f1 Fixed optimization dependencies broken by moving files.
new b821974 Fixed some broken dependencies caused by moving around optimization code. In the process, added ridge regression and quicsvd to CMake build system.
new 7524e80 Added an example to demonstrate compiling & linking with OPT++.
new baede87 Updated README to include info about OPT++.
new 73e7a43 Removed noise from toplevel cmake file.
new e9020c2
new 06c1f28
new 1382230 Linking failed if opt++ was installed someplace nonstandard--fixed.
new c575811 Added directions on where to download opt++.
new b9ebc9f
new 64a57f3
new ee6d40f
new 0e3e11c
new f1ce206
new c70c52a
new eef9207
new bef179d
new 1db8e4a
new 86e8a5d relevant files
new edb9eb2 Working set of files
new 2b16b3a untested code
new 1373d5e
new 0d3059c
new 9563e48
new af0b45b
new 217f767
new 321f089
new e86eddc
new 6948313
new 64beb31
new 8120f28
new b034a52
new 3b71627
new 94b0b05
new 69b03eb
new 04ad0be
new c0425b5
new eb6def7
new b7ca2ba
new 8bd3c32
new c9e19ef
new 8c06531
new 13b0c90
new 5e9fb73
new 4890be5
new ce92ec6
new bcf7396
new 2ff5e86
new 929b7f9 remove annoying file
new cfecad4 remove annoying file
new ce83cd2 started changing copyright info
new ba94010
new 5d0da65 Fixing copyrights.
new 53b99eb Fixing copyrights -- done.
new fdfe1cc Generated fastlib includes shouldn't be in svn.
new ce70dba added trilinos libs to cmake link libs
new 5540449 starting to update to trilinos 10.0; disabled a #define that mangled code, certain things are templatized that weren't before, that might cause problems.
new 8de87e1 fixed many of the easy typos, most having to do with templates
new 75961e1
new cf71e1a
new 553f987
new 3a6d619
new 5a0df64
new 72c7954
new cb70c38
new caa3f67
new 0079be4
new 4839ca1
new 97f0607
new c858dc6 Added sparse matrix code to fastlib, added Trilinos instructions to README. Removed trilinos 8 code from the source dir.
new cf53fab
new e0ce98a debugging
new f31bc76 Tiny change to fix link errors when building fastlib as a shared lib.
new 74cfa25
new d3c2d3d
new 6daa6a9 debugged
new 91d0fbf
new 79c288f
new 83178cd
new c44bab7
new 958f5ad cleanup, added documentation
new ca0d063 added sorting and documentation
new 74f2b84
new e2fb9d7
new d6b7833
new 4759706
new 6f5d921
new aaa7d89
new 92c873d
new 3b53120 wrote GeoMST
new 00e8c1c
new 0f7310c cleaned up output for experiments
new 418ecef
new e87c316
new 068781c
new 033c0ca
new e3dbe8e
new adc5906
new 005fa69
new c4c8671
new 12f24f2
new 0bdf564
new 5983a5f
new dd4315b
new 45fc9b9 works for 1d
new 4e0ecc5 stil buggy
new 370a812 Seems to be working with a 2-d setup also. Need to test even further
new 8bcaa13
new 8d185f0 Seems to be mostly working
new 3f49a33 Tested and certified 1
new f160e6d Tested and certified 1
new 60c664e Tested and certified 1
new 24f8878 Tested and certified 1
new 9a3935a Original version. Will make it simple
new 5b85971 Tested and certified 1
new 6b4222f original version
new 6046611
new c0e92be
new 5c795ea Looks working 2.0
new b5aef78 Looks fine 2.0
new cdddfed Looks fine 2.0
new a53c5d3 Looks fine 2.0
new dc9c749 Looks fine 2.0
new fbae28f Looks fine 2.0
new 78371ae Looks fine 2.0
new d0248de Looks fine 2.0
new a899a1b Looks fine 2.0
new 7bc98cb Looks fine 2.0
new a820bd4
new ca24b2a
new 21b0a1a added the single fragment algorithm from Friedman & Bentley's 1977 paper
new 980990f Working version 3.0
new 6a115f4 working version 3.0
new 2518e6c working version 3.0
new 3864172 working version 3.0
new 231d838 working version 3.0
new 5036556
new bed8f16
new fee3d27
new 62fbfc0
new b313bfd
new 21a7717
new af6ec96
new fc20faf
new 067abc9
new e4d2e9a
new 5426a38
new e4b96e8 Not fully correct 4.0
new cdcab89 Not fully correct 4.0
new 1cd6c5b
new deabcde
new 262bdb2 commiting before crash
new d77dabb commiting before crash
new c9316bc
new 11903a0
new 4283dc3
new b6de438
new 60f47b1 Seems to be working 5.0
new 32bf7a0 Seems to be working 5.0
new e7c8896 Mostly working 5.1
new 3d807e3
new a8d0111 Mostly working 5.2
new 2e9e550 Mostly working 5.2
new 17dcdfd
new a4471c6
new b06f029
new ddb87c3
new 9d8b135
new bee3f75
new 09ab197 Checking in linear regression.
new cb70c74
new ec9c191
new 927e30a
new 85fcfcf wrote NEKMA multi-fragment algorithm
new f2ce9c0
new 9f790f9
new 7687af9
new f7f2852
new babcaa8
new 3cbbe92
new 927218d
new 503f818
new 55eda4f
new 4533022 VIF initial checkin.
new b95d3ee Deleting the makefile.
new 2473254 2dPCA
new a219ae8 fixed bug in nearest neighbor finder, corrected multi-fragment algorithm
new 3ed3489
new 701823f
new 4ec6bf8 fixed multi fragment bug
new 99e5e77 ddcm2_01_23
new 5f62e02
new 79aa13c
new 4e2f0cb
new 84495d3
new 4cb9405
new 93e6a4e
new 6619965 fixed bug in cover tree version, needed to ensure valid bound in CopyCoverSets_
new 8ca6fb6
new 16dcc51
new 22a1d63
new 64c0644
new ae3b029
new 9196a38
new a816f5c
new 97cb0e4
new acab6b8
new 03bd161
new a54c596
new 269f37f
new c15f8fb
new 904a08b
new c811626
new faa412d
new 83f51a6
new 28e6fe2
new 00f9d9c
new dc423c6
new d4ce07b
new 004733b
new 9b1f998
new e85b941
new 1951675 Opt++ should not be enabled by default
new a292a97
new 7aa80d5
new 787d550
new 8db5444
new 485aa7a
new 327cf71
new b418ff6
new c120cbf
new c662033
new 3eaedc7
new 8c712ba
new 616e7d6
new 540185c
new bb94020
new 5266045
new a093cfa added new prunes to cover tree: setting upper bound for ref in base case and implied bound in ref descend
new fa8b9ce
new 459056e
new 7518445
new ac1369f fixed error in implied prune, must have d(q, r) large
new c1b855b
new 3d05e70
new d64e22e
new 1bef211
new 2f868ec
new 024f75d The use of cmake deprecates and prompts the removal of the entire old build system
new 35ae579
new 9105408 added .../contrib/niche/regularizedISM with mvu example of csdp
new 00a42f1 added write cvxmod program -niche
new 3d24c74
new 64cc795
new 74684d5
new dc5e91d
new 8e0d14e
new 6ec1dad fully working
new aa87b9c
new 4315c82
new 613aa09
new 855e804 As per Sooraj's request, tylesBase is no longer necessary and has been removed.
new 34275a0 Move 'fastlib' to 'fastlib-old' repository
new af4512a Add fastlib directory structure
new b6ca176 Move fastlib2 to fastlib/trunk
new 10d499c fastlib2 directory is no longer necessary and is thus removed
new f6864dd Move fastlib-old (originally 'fastlib') to fastlib/branches/fastlib-old where it will sit until the end of time and nobody will touch it because it's old
new 9488a24 Move fastlib3 to a branch of fastlib
new f326674 Move cmake branch into fastlib branches
new fd8d827 Remove empty proposals directory
new 281b9d0
new a7daf89
new 9047035
new 430d710
new a751e96
new fc6a327
new 143e917
new 22d7b11
new 8cb4ca5
new 5ef153c
new 8d93c71
new eb64004
new ec99cf4
new 277bf82
new cb9a0af Don't need this structure inside of this branch
new c55a19a Move things in trunk/ to here (incorrect branch structure)
new 62d11ee Unnecessary nonstandard directory, if necessary, should be generated by build system
new 404b584 Should be generated by build system at compile time and not in source repo
new 932992f Unnecessary directories that should be generated at compile time (missed these on the last revision)
new b9d8871 Move fastlib directory to src (this will eventually be done in trunk/ once this is merged)
new 420980d
new f295f96 Do not autogenerate this file, no need to reinvent the wheel
new 62d5dae No need for this anymore
new c7c6524 config subdirectory is no longer needed as basic_types.h is no longer generated
new 55537da Clean up trilinos search (use PATH_SUFFIXES), and we also need to look for MPI headers. Dependency on trilinos should be eliminated...
new 004df67 Update include locations
new b4e16d3 Update all #includes. From:
new 9d4524e Missed this file: changed #include "fastlib/..." to #include "..."
new c66c772 Remove unnecessary debug output, forgot to do that before checkin
new 4fd20ba ctags cruft shouldn't be in repo, was probably put there by accident
new afbd141
new 1e6bff6
new e3837b6
new c712fd1
new 632272a
new 3957428
new 2c6796c
new 82b493f
new ed0953c
new eef056d
new 3321e25
new 75fba88 Do not use different directories for cmake stuff; this ensures every directory has its own Makefile.
new 757dd25
new 6ac39c7
new 8375658
new 70120b2
new 96cfe08
new 1a01617
new 43a5ade
new 648b6e0
new ab1237b
new 180073b
new fd9d509
new 5883a62
new be20f8f
new bbb49d9
new bd93e18
new 8060b5c
new b8cfcc3
new 3124fac
new 97fa9b8
new 4fe05da
new 52e0e91
new 29ebc61
new eb4f410
new a9959a2
new 42eb128
new e1ef0d3
new 49c6024
new d4780a8
new bcf94be
new 1217823
new ea8f405
new 08d30c9
new b3f1f02
new 0cbcb06
new 0d7daa3
new 070821c
new ed9a04c
new ba97d01
new e6795ae
new 23d8593
new b728041
new 04fdfe9
new d7439ec
new da0acd8
new 7e97790
new 2d35b76
new d67cc49
new 9de1e4d
new 99efd33 Oops, this should not be here
new cd939a7 Add distclean target (does not work fully yet, needs to be made recursive)
new 3bbdf12
new 9a9d4e0
new b0e8b49
new 07a2030
new c6fc02f
new a659b70
new 3432feb
new d3005c8 2dPCA project on major basis
new 4e8b444
new 7429a63
new 62cbb7f update to kernel kmeans
new 485afe3 various updates to new_hmm
new 7a7672a updates to spike train dependence
new 07f37f6 updates to regularized ISM
new cb04945 added initial dynamic time warping code - needs debugging
new f20f3d7 holy shit dont use arraylist with capacity version of Init
new b111ab2
new 9760b97
new 54ecbaa fixed InitRaw member function of ArrayList to allocate memory for capacity, not size
new 23764de
new 05be769
new 5234a26
new 75f55c5
new 5bb5315
new f0c3ade
new 15c9cdc
new 51d3d62
new d302f8c
new ff6f092
new 74c734b
new b6ce88c
new 88178a3
new f217ac5
new 06abc92
new fbc11c8
new 6583baa
new 779eb2a
new e8a2488
new b35a0af
new d614c2d
new 037159f
new f99fe74
new 3943f10
new cd03db8
new 4775882
new 3c9a9d4 changed dtw metric to normalize cost by path_length
new 117f927
new 8edc1f1
new 8d78719
new 315fdf6
new 8d882f9
new cda6ba9
new 7c2b4ee
new 384c50c
new 788fbb4 dtw - final checkthrough
new a7bfa05 added dtw visualization tool
new 57ec385 fixed fucking retarded bug in dtw code that was due to hard coding of time series lengths
new 84adbf2
new 37bbaea n-point correlations, wrote basic kernel function
new 807c521
new fcbb1de
new fa99d24
new bb74227
new 8a2c7d0
new 8cc6ea9
new d21b0c4
new 836e918
new 079d326
new 2691f29
new 08af692 wrote base case and naive code to use it, few more problems with passing partial tuples around, tests to come
new 07bdd8d and now, to actually add the files
new 3da818f
new 0209010
new 61629c6
new 3349de9
new 50c4bf2
new ecf67b0
new 0dbc5b9
new 117299c fixed a few small errors, made test cases, naive works for 2 and 3 point tests
new bfafd6e
new 3ff64bf
new f03930d
new 1495dc2
new d1b3512
new 735c6db
new 9e35c20
new f16b10c Corrected distclean target for Linux systems. Removes cmake cruft for in-source builds.
new 9b66db4
new 6a949c0 Make clean before distclean (DEPENDS clean did not work right, so this hack will work; after all we already made the assumption we are on a Linux-based system for these commands)
new ecd5859
new cf16433
new f94803c
new 056d0dc
new aed5949
new dba8c53
new d745f6e
new 7da7245
new 80ff127
new b37abd5
new d154976
new db089e1
new 1492d66
new 33c2694
new 2a1aecb
new 0fed7b0
new d90f8e8
new 2313f0f
new 5307477
new 95cf89e
new bc25b22
new e22f2c0
new d59ca37
new 60abc3f
new 25d10ab
new c0b84d6
new fc51136
new 30492c1
new bbb62c6
new 47ae3a4
new 3f61e77
new 08997e0
new 823721b Update #includes to be relative (we should not assume fastlib/ is always in the include path, this keeps it simple).
new cf52e84 Make #includes relative to fastlib
new 9d01fc9 Move CMake utility files to root directory of build (cmake should be run from there).
new a64b40d One more #include relativity fix
new 4a72dd1 Revamp cmake:
new 7b48800
new 2e4cd79
new 89f90fd
new da979e0
new 03c11a7 wrote depth first recursive code, fixed bug in base case
new 374ca15
new af0d158
new 5fdc6ac
new b9bf2ef
new a9c5067
new 76bb2bf
new a6ce2cd
new 334f060
new cad1e31 Revamp cmake structure again. Builds all targets each into their own directory as well as linking into libfastlib.a, making building it all as well as working on individual components simpler. CMakeLists.txt files also commented and clarified to be less confusing.
new 4043770 Oops, misspelling. Dangerous because it would compile fine but would not link fx into libfastlib.a.
new d11bc02
new e090dcb
new d21e710
new ce82190
new 23357b3
new 9027bb6
new b7c5eec
new 8df8534 Passive Aggressive
new da59136
new 482d02d
new 5b7c896
new b258e54
new 758bc8b
new 7666c2e
new af88f34
new 65514f9
new dae378e
new b14e64a
new c45595c
new b0868cf
new efd8cbe
new 191d35d
new e2ae44b
new db62b5c
new c0d6b1b
new c0ef673
new c4b3440
new e4a65c2
new 76ee44e
new 35eee56
new 5ac8685 code separation into more cc and h files
new e784b06 code separation into more cc and h files
new f33cb45
new d29115f
new 3618692
new 79f6b1b add cross validation
new 4bff7c7
new fabdaaf
new bab3632
new 7bd1169
new bd087b9
new 8956430
new 67a82c2
new a8a5ee2
new c7e645e
new 3dc1a6c
new 63c7c47
new a7cc659
new 13acbdb
new a1e7674
new e411738
new 2229385
new f752711
new 0f22ff8
new 5476712
new 1056196
new 199292b
new d14b4a1
new ad0a366
new 3a81b5b
new 6ff1a8e
new 01f93b2
new bf854ec
new 3e921bd
new 929a085
new dcb49ff finished first cut of multivariate dtw
new e0fff04 added straw man - nearest centroid classifier, yields 47 percent accuracy
new c4b937b better organized multivariate dtw and added multivariate dtw to dtw.h
new b76c8ee moved dtw.h implementation into dtw_impl.h
new 693272a
new b0b54d6
new 1b05266
new 7b44b8b
new c7a38c9 Initial release of "regularized risk minimization" project
new 5c0a388
new a1d8b2a
new 940f81a
new 4e670f8
new d93641d
new 6edd4ee
new 5647dc3
new 689f873
new 179d480
new 5d652a5
new 145854c
new 0ba0a21
new 85294a1
new a0c376c
new b396228 Do not make intermediate libraries; just collect filenames of files to be compiled into libfastlib.a.
new bf56c32
new ee98c6d Don't build intermediate libraries, compile everything into libmlpack.a
new 26de988
new 09912ad
new 3546b5f
new 205b978
new 8bb75c6
new 93eccb5
new 3853d6c
new f92a87b
new b2b37fb
new 60083d2
new e27fa09
new 2c4b9f8
new 6ed512f
new 324aa63
new adb571a
new 5cf2e78
new ed9297f Update include directories
new 7e488c3
new d516461
new 3cc3b5f
new bb8b449
new b4a2009 wrote and tested counting function
new 8e5694a wrote basic hybrid expansion pattern, wrote function to test node lists
new 23fe359 Move header files to correct directory in build (include/mlpack/)
new 0819d96 Install header files correctly into include/fastlib and include/mlpack.
new 47a41b1 finished hybrid expansion, added bad symmetry output to node checks
new 465ef3b fixed bug in hybrid expansion - can't exit checking a node tuple when a pair excludes because the tuple may still have bad symmetry
new abb2f53 actually fixed it now, replaced decrementing a global lower bound with just summing up the bounds as I traverse the new list.
new 46024a8
new 21affb0
new 9303b6c
new ebff658
new 439f678
new bf36642
new 0d61ef0
new 6b4c4ef added multivariate dtw that does one global align using Euclidean distance between vectors in R^n
new 9cc3a05 small changes to how files are read in
new b3d7281
new c68ff0a
new de2fb9a Set svn:ignore to 'build' in root dir
new 7e06699 Copy over contrib directory so that I can start adapting build.py to cmake
new 5ec6ce2 Require 2.8
new ed820d7
new 8afc9c2
new 06a96bd
new ea7a2da
new ded9354 What? Somehow missed copying over emst in MLPACK. Commented out cmake MLPACK program install guidelines, they need to be redone.
new dae4646 Add emst to cmake build.
new f59c762 Remove some unneeded comments. Test for doxygen-update on churchlady
new 00b1265 Include thor in build (it was not there) and move mmanager over, to be tackled later. CMake will now find and link against pthreads (required for thor).
new 0196952 cmake build information for thor
new 903df89 end(), not last(), and fix some fx syntax which has changed
new 85cd625 Huh?
new 34ca847 Fix differences in function signatures (.cc implementations were using const char *)
new 046e717 Set up cmake infrastructure for contrib, and by default compile those which already compile without me having to fight with it too much
new ca309ce Oops, still have to set up physpack with cmake (should be very simple)
new fe06dc2 Set up cmake for physpack (do not build by default)
new 41c8157 Make sure executables are installed correctly (may still need polishing)
new fd095e9 Apply same change from branch to trunk ("Huh?")
new f554a56 Huge merge of fastlib-cmake into trunk, done all wrong (svn merge failed... surprise?). All the CMakeLists.txt files have been copied over and all of the other relevant CMake files too. I've done my best to keep it as simple as possible but unfortunately that was not entirely feasible here.
new 2bd6856 Revert 'src' to 'fastlib' so I don't break everything fl-build does.
new e7180c2
new 9f1be4c
new d74c46d Fix nnsvm so it builds correctly (fx_ calls were out of date) and add to CMake build
new d5e7bde Add mmapmm to fastlib build. A few code changes were necessary stemming from some earlier base/basic_types.h changes.
new 20ac49f Move code that finds trilinos out from sparse CMakeLists
new 4daef98 Add kernel_pca (which required sparse) to default build, modify a few things (ticket #13 is related) so it compiles fine
new ab824e4 Need to figure out why those two lines have been causing issues
new 57b7896
new 9d3bbc0
new 4af1ef4
new 2751c04
new 5ead8b1 Don't use local trilinos headers, use system ones (it's CMake's job to figure out where these are)
new 2f47bc7 mmapmm support by default in fastlib means a lot of these methods now compile right
new 2b671c8
new 87d5ddc
new 170cb0c
new d26d4c1
new a43c601
new 3bf44c5
new f43c238
new d56bd5d
new 2205622 Incorrect #include line, should use relative paths for fastlib stuff
new 503651e #22: replace lots of preprocessor macros with what they actually are where possible.
new 8a9f77b Missed these macros
new 8dfec9d Allow selection of SCALE_MASSIVE, SCALE_LARGE, or SCALE_NORMAL in CMake configuration (default to SCALE_NORMAL if not otherwise specified, and check to make sure multiple options are not selected)
new 13434f1
new c560a54 Use boost::serialization and boost::program_options and link against both (to be integrated into trunk)
new 0e9913e uint -> unsigned int (same thing but 'uint' does not exist on all platforms apparently)
new 630d88a working on multi-bandwidth version
new f21093b
new 25448dc
new 8604c26 Do not build mlpack_contrib or any of its pieces by default
new 949d811 posix_fadvise is not defined on all systems
new 9349cc5 Create fastlib-armadillo branch, where we will attempt to try to replace GenMatrix with armadillo's implementation.
new 93a2e1d Fix for #26; forgot the type specifier after LI (since the LI macro now requires a type after it, so it works for all types) #15 (standardized output system using cout) will solve all these silly printf problems.
new 7cbf28d
new 0a87fd5 Fix #27: incorrect use of LI macro (same as #26 but this fixes it in the fastlib-cmake branch)
new 454c757
new 33eb54b
new aec91e3
new 57c4012
new 965e87b Added Boost program options for command line
new a2c5042 Added Boost program options for command line for allkfn
new ba52867 Added Boost program options for command line for allknn
new 4c87975 Added Boost program options for command line for allknn
new fe8d6a0 Added Boost program options for command line for naive_bayes
new 46a2ce9 Added Boost serialization for ArrayList
new 31096fa Added Boost serialization for series_expansion
new 5b2be37 Fix syntactical errors in CMake files
new b7e7052 Allow TextFile to return its own filename
new 81c4c7d Add compatibility layer to convert between Matrix and arma::mat (this is NOT fast! but it's only here for compatibility)
new fa17828 Add header inclusion guards (how did I forget these?), clean up formatting of base.h
new 2d6c2a8
new 37c248a
new 23eb459 Separate dataset classes into separate files, and then adapt them to use arma::mat internally (as well as on their external interfaces). Update CMake to include our new files in compilation.
new 370f363 Use arma_compat layer to allow Thor to interface with changed Dataset API
new b7d7b03 Update all MLPACK methods to use arma_compat layer so that they can use the new Dataset interface. Eventually all this arma_compat stuff should be removed, but for now it is fine.
new f185d9b
new f3b24dd Add useful compat function which emulates Matrix::MakeColumnVector() functionality (albeit slowly)
new 0dea3c1
new c372e36
new 21967af wrote permutation free version
new e86d43b updated cmake list
new 7ae10b6 Ensure each built library links against BLAS (#28). Apparently this was fine on Linux systems but failed on Macs; hopefully this will solve the issue.
new 870fee0
new 4932907
new 16b6973 Don't use deprecated values.h; prefer limits.h and float.h instead.
new 98ca8c0 Rewrite tree to use armadillo.
new 7afd03a Update mlpack methods for tree API changes
new ac5c6a7
new 313ba6b Split up bound classes into separate files for each class, and then separate files for interface and implementation.
new 7fa1737 Stop using GenVector in data (quick and simple replacement)
new 3bdf634 Add GenVector to arma::vec compatibility functions to arma_compat::
new e7f0605 Change TAU to a preprocessor constant to fix odd linker error on Mac (or at least attempt to)
new ac54173
new e448a0b Permutation free version works for just upper bounds as long as I recompute all the distances after each split. Need to work on UpdateIndices_() to figure out why keeping them doesn't work. Add lower bounds after that.
new e5218d5 fixed bug in UpdateIndices_, was using wrong index
new bbbffc0 noob test CMAKE
new 4ee7531 noob test CMAKE
new 3abe95f
new 3147f74
new d213608
new 61a7043
new 77185c8 Change name of variable so -D TRILINOS_LIB_DIR=... can be used
new 9142af1 Rewrite LMetric<> to not use GenVector by default, then modify a couple other files so that all works. Partial template specialization was required for MidDistance() in DBallBound when working with TMetric = LMetric<2> and TPoint = GenVector. DBallBound was also changed to use TPoint = arma::vec by default.
new c87b2ef Fix calls to LMetric<>::Distance() to use arma::vec with arma_compat layer
new fb5d4e1 Serialization to fastlib/src
new 6896f02 Undoing serialization for matrix as of now
new 392b533 Rewrite DHrectBound to use arma::vec internally and in its interfaces. The kdtree methods needed some modification and one needed to be moved into an implementation file (since it was not templated).
new b6e426a Modify thor methods to work with change of DHrectBound
new 0b30bab Modify MLPACK methods to work with DHrectBound API change
new 29042cb
new 108a506 Create fastlib-vector branch for swapping ArrayList -> std::vector.
new 8e055a5 Converted rangeset.h to use std::vector. Needs testing, still.
new aa89283
new ae70f66
new c6ace5b
new 799ca87 Update TKdTree methods to use armadillo vector and matrix instead of GenVector and GenMatrix. I also removed unnecessary uses of ArrayList, replacing with arma::vec where possible.
new 944fedb Fix calls to TKdTree assembly methods; replace ArrayLists with arma::vec for what are essentially fixed-size arrays (ArrayLists were unnecessary for the application)
new ae7c0f1 I'm pretty sure the user is aware of what they typed. Don't echo it when they type --help.
new ee59960 Restarting KDE.
new b51f48e Unfortunately, CMake won't work at all if it's being told to configure directories that no longer exist, so I commented out the directories removed in r5575 so it won't freak out anymore. Maybe there is a configuration option where it will ignore directories that don't exist?
new 989968a
new 0580fb5
new bd3aa15
new f22ea0e
new f640752 Attempt to compile boost unit test.
new 561ae39
new b0e2d1c
new 8debca9
new 97e5eec
new c17a1ce
new d42ed02
new ff4692e Switched MinHeap to use std::vector. It is now basically a wrapper for std::push_heap, std::pop_heap. The speed tests I did indicated similar performance to the previous version, though more testing could be done on a machine with more RAM.
new ccd36d7 Sped up slightly. "Safer" code.
new 1edafcf
new 55237a2 Link against mlpack and Trilinos
new 0be9463
new 1cdf3af
new 29f385a
new 3145a0a
new d715ce5
new 17bbb7b
new 0013410
new aabf873
new a1e7a16
new 63b9519
new 01a36b1
new 826236e
new 38bb8dc
new 367d8b9
new a2231b6
new a7fea27
new c4e3a19
new 2a87a0f
new 1afacc4
new e242f93
new 36d37a7
new 16fae3f
new 4f095fd
new 09192a0
new 8810e2f
new 3192e29
new 1b0b118 When a user enters no parameters or -h, fake it so FX thinks the user is asking for help. The mere fact that I needed to do THIS to make it work... I have no words.
new 12d0a5f Did not mean to commit this minor change; it turned out to be unnecessary
new 5b5af13
new 1ca456b
new 2f21199
new 12523d0
new 0fc77af
new 9100cbd
new 9d632ac
new 5120512
new ea564d3
new 49e11de
new 9c7407b Make parameter description give --submod/param instead of --param to eliminate confusion
new 94ab9e9
new 7fc7719
new d6a422a
new ee8d453
new 9d10dad
new 9e55a77
new d82d2fe
new 5e45c01
new a437385
new dc9ad35 Modify fx output format a little bit so it's a bit easier to understand. Code is ugly but it works... I can't wait to rip this entire system out and replace it with something sensible
new 763f786
new aed59f9 added lower bounds to perm-free, stopped recomputing invalid indices
new 49a5b23 More accurate documentation that meshes better with help screens
new 537c979 Oops, fix -h and -help
new b1ff13d Update documentation so that it actually works, and make sure we tell the user that they can actually give a dataset as a parameter
new e434965 Add cheap utility CSV saving method for allnn
new 9713eaf Is this a joke? I mean, seriously! allnn ships with no actual way to save the data that it's calculated; I've rewritten so that it might actually be useful to someone, ever
new 4f475b8 updated code so that user can specify number of ICs to find via num_of_IC. Also, fixed bug in very final step where we forgot to transpose unmixing matrix W before multiplying it to data
new 4022981 Set required parameters and defaults for non-required parameters
new f7f6db6
new 69bda82 Properly document allkfn, which was not done at all. Maybe now, people can use it!
new 2e0b6ca Properly document the allknn method. Previously there was a parameter that allowed selection between single- and dual-tree mode, but I have removed it, defaulting it always to dual-tree mode; I found it was a potentially confusing parameter.
new 766d854 Update some mistypings in allkfn documentation
new 6d4b1b7
new a0a801a Document emst; remove non-working --use-thor parameter. Names of some parameters changed for consistency across all MLPACK methods.
new 4a9a55c
new 1726a90
new 63a22f2
new 0fb5a03
new c1b32aa
new 249f540
new cab0357
new 81bd53e Add documentation on file formats for HMM utilities
new f539d09 Rename HMM executables to things that will not potentially conflict with other utilities on a user's system
new f329dc2 Document hmm_train executable entirely, and change some outputs from printf to fastlib standards where necessary
new 84f2bae Looks like my brain tripped on terminology
new 58faa6b Change some parameter names to indicate where model files are required
new 8a5204a Document the hmm_generate executable
new 3b3eef7
new 59b6b6c Documented hmm_loglik utility thoroughly
new 32c4166 Remove usage() declaration
new 68b6ecc
new 777b8b0 Documented hmm_viterbi utility
new f5b00d9
new 9af9eec Update documentation partially; it was noticed that this does not work successfully. I put in some debug information that helps track down the invalid MulExpert() call which causes it to crash. This will require later investigation. Also, this doesn't output any results at all in any way whatsoever. Seriously, is this a joke? How could anyone possibly use this software in any way if it doesn't give any output? Ok, rant over.
new 27550b9
new 13b94eb Update CMakeLists to properly install fastlib and mlpack.
new 152b2b0
new 2fd42c6
new faf1c22
new bb58a53
new 439ba9d A readme to get installed to /usr/share/doc
new 068f74c Install README_MLPACK is /usr/share/doc
new e65e14b
new 0af56be
new 8f46665
new e445ba1 affine NMF
new 95f5981 Switched from ArrayList->std::vector.
new 1a00c8e TestRangeSet() changed so that it actually will fail if the expected results are not generated. There may be a better macro for this, or we may want to switch to something not made in house (assuming TEST_ASSERT is).
new 92b0434
new 14e1036 Tag fastlib-0.4 release.
new a87005e Add GPLv2 as license and copy doc/README_MLPACK to README
new 4aa738d
new 7c642fc
new 416a393
new 6573e0f
new eda2484
new c6f4424
new 15fb168
new 1431bfb
new aa3aa4b anmf
new bede1f6 anmf
new 3eba517
new b8b20ad
new cacdf7c
new d927c5e
new 9516ccb
new bc737c4
new 9ef0e6c
new 6557418
new a23e1a2
new adf0838
new 856edbf
new b88420a
new 3364748
new 42b5b17
new fe45c52
new 8358aee
new 5d30b5a
new 1ce1487
new 6121a39
new d6b130a
new bae372a
new 0af1ed4 Fixed TestQueue so that it actually fails if things don't match.
new 9691dfb Forgot to change this back before previous commit.
new 1656613 Queue is now just a wrapper around std::deque. It will be completely removed later on as the things that call it are updated.
new 10e397a Updated comments. Removed constructor nonsense.
new c7dabde Rename branch to indicate its new purpose, switching from in house implementations of things in the standard library to the standard library implementations. Examples: ArrayList -> std::vector, Queue -> std::deque
new 875b53c
new c8d4487
new 3fbaaa4 Queue deprecated and removed. std::deque should be used now instead.
new 9cff100
new 9ed53b6
new f080754
new 4b6c2c3
new aaafb86
new ef0b873
new 79d77fc
new 8e60d79
new 99d0cbd Finish transition of tree to arma::vec and related classes, and remove some methods that were commented out and unnecessary
new 0248694 affineNMF image_type
new a82bac5
new b299218
new 66c0aa6
new 93b254d affineNMF image_register
new aa3bebf affineNMF CMakeLists
new b1ed52d tqlong CMakeLists
new a92a61c affineNMF register_all
new 1bda6c6 Remove ArrayList and String. This commit breaks many other classes.
new 208f199 affineNMF ANMF_test main
new a7039a0
new 99be022
new 78ea59f
new c0f479a
new 32b761f Back to FASTLIB.
new 2d0ab8c
new b21448a
new 63f147f Adding the metric object.
new 579de7b
new c774175 Adding L-BFGS optimizer with the test.
new d2756f6
new 34de381 Compile error fix.
new 208feb4
new 5d12924 wrote multi-matcher with inefficient base case
new d4224ab Reimplemented String's tokenizer for std::string. dataset.* now compile, but are completely untested. There are certainly bugs and improvements to be made.
new 59853f1 base case & output debugged, on to pruning
new 7cc3ed9 More things that compile yet remain untested.
new a20886e More untested yet compilable files.
new cc75654 successfully debugged for small 2 and 3 point tests
new ee3d805 improved pruning slightly
new 755df75 fixed a memory leak when copying arrays of GenMatrices
new 6cb7a40 fixed memory leak, should be fine now
new cb0f94e cmake target fastlib compiles, as do several of the tests before cmake gets to mlpack. fastlib/thor currently does _not_ compile and is commented out, the cachearray.h stuff is going to be painful.
new 58d10b2 fastlib/thor compiles now, except for allnn.cc. Things in here are still very broken, even if the compiler doesn't complain.
new d868f4b Remove last references to Vector class
new 3e9973a wrote code to time single matcher code over multiple matchers
new ee5f9a5 Correctly initialize DatasetFeature members during Init(); it should be noted that the features_ vector does not clear() itself upon calls to Init*() methods, but this will be irrelevant when we ditch the Init() style of methods and use constructors.
new 2e2b5d6 Ugly hack to get around failure of math::MakeIdentityPermutation() -- should be using fixed-size arrays there (todo).
new 2986908
new 6c50cd9 fixed small error in naive multi main
new 9b60acd More stuff compiles, all untested for correctness.
new ada6228 Preprocessor macros are bad when they make programs perform in ways users don't expect. Preprocessor macros are bad when they make programs perform in ways users don't expect. Preprocessor macros are bad when they make programs perform in ways users don't expect. Preprocessor macros are bad when they make programs perform in ways users don't expect. Preprocessor macros are bad when they make programs perform in ways users don't expect.
new 07c79d9
new f7bb3c0
new 6484b3a Add new parameter to tokenizeString that will save the last token if a stop character is encountered. Make it look a little nicer with a few comments and a using directive. Also, fix the last condition (should be || not &&) to capture the last token if necessary.
new 06c40e5 Initialize int correctly in SkipSpace_(). Also fix some logic in ReadFromArff(); re-adapt to use strcasecmp() == 0 instead of potentially confusing !strcasecmp() (the counter-intuitiveness may have actually caused one of the bugs fixed here)
new b4dbd8b Fix ReadMatrix() (it was trying to write to places that don't exist). I think the implementation in fastlib-armadillo is less bizarre and will end up being used here (arma::vec lends itself better to this task than std::vector). Need to merge those branches...
new 224983f Rewrite the ReadMatrix() code to be almost identical to that found in fastlib-armadillo. Should have merged them earlier...
new 9a49e64 Merge fastlib-armadillo/fastlib/base into fastlib-stl/fastlib/base
new 79ae6f6 Merge branches/fastlib-armadillo/fastlib/file into fastlib-stl/fastlib/file (breaks build until I merge data/, in just a moment)
new 37f5f49 Merge fastlib-armadillo/fastlib/data with fastlib-stl/fastlib/data. Runtime dataset_test fails, but it compiles ok.
new 04ffcfc Fix bugs introduced into DatasetInfo of my own doing. * ReadPoint() is broken, but still works. It checks for \0 characters, but std::string does not terminate with those. Leaving it there for now until it gets handled by #37 * When adding a class feature from ARFF... actually add it to the features_ vector in DatasetInfo. Oops.
new ee2f995 Merge fastlib-armadillo/fastlib/optimization into fastlib-stl/fastlib/optimization
new d466aca Merge fastlib-armadillo/fastlib/thor into fastlib-stl/fastlib/thor
new 11c091c const char * --> std::string
new f6674f8 More std::string usage
new 0c216c8 Failed merge not noticed until template function instantiation...
new 7e384ed Merge fastlib-armadillo/fastlib/tree with fastlib-stl/fastlib/tree. This should have been done earlier to prevent duplicated work (some functions had been switched to arma::vec and std::vector in different functions; I stuck with arma::vec because fixed-size vectors made more sense in those particular cases)
new 20ba756 Merge all??n methods from fastlib-armadillo/mlpack into fastlib-stl branch
new 46f7b7b Fix allkfn so allkfn_test compiles (however, it throws an error)
new cc81ca5 Merge last bits of fastlib-armadillo/mlpack into fastlib-stl/mlpack
new e0ea516 Merge fastlib-armadillo/contrib into fastlib-stl
new 0b72285 Merge CMake files from fastlib-armadillo into fastlib-stl
new e03ad93 Merge changes to CMakeLists.txt from fastlib-armadillo branch to fastlib-stl branch
new 9340904 Remove fastlib-armadillo branch; it has been successfully merged into the fastlib-stl branch
new 1b801e8 Fixed L-BFGS test.
new f00f3dc Fixed tokenizer bug. Added a hopefully finished unit test for the tokenizer.
new 8b5f312 How did this happen? Oops...
new d91faac Fix bug introduced a while ago; when quicksorting to build the tree, we have to keep our local matrix up to date (the temporary matrix we passed is modified)
new e5ac749 Remove ridiculous copypasta from AllNN::Init() and AllNN::InitNaive() (it could be trimmed further, even). Change Matrix queries_ and references_ to arma::mat type, but pointers were required to make it work right.
new f4c89b8 Compile with debugging information by default (so that DEBUG_ASSERT_MSG and similar macros will still work, as they are DEBUG_ONLY). Should make optimization the default for compilation when tagging for a release, but default debug is more convenient for development.
new e07ae52 Oops, we need to tell the compiler to set the DEBUG macro flag.
new 41f827f Custom DistanceSqEuclidean() function for arma::vec objects.
new 3e6e204 Removed error checking for converting numbers to strings when unecessary. Made error checking for string -> number conversions more intuitive.
new 1fe20db Remove last instances of Matrix and Vector from allnn.
new 04bb7a2 Removed useless Init method in rangset.h. Removed unused #include in tokenizer.h.
new 1aadb37 Removed unecessary #include.
new 9342b95 It was dumb to not have done it this way to begin with.
new 3996a6a
new 037005d Changes in contrib/ affected and broke kde/, so don't bother with that for now
new b3ff9d9 Function specialization is no longer necessary
new 6dde3d2 Remove last references and uses of Matrix from AllNN class.
new ad8d868 Remove Matrix, Vector, and ArrayList classes from allknn. Compiles, but test does not pass.
new 66300a0 Add debug option to stl branch
new 44b806a Turns out this is a better way to define the DEBUG flag (and by better I mean... it works)
new fe5e17f Propagate change from trunk CMakeLists.txt to branch... properly use DEBUG definition when told to
new 80513df THIS IS YOUR BRAIN ON DRUGS
new 64d5a14 We require different modifiable input matrices as input to AllkNN for now. That will have to be changed. (tree generation modifies the matrix)
new bc1baef Fix allkfn to not use Matrix or Vector anywhere. This one was very easy because it's so similar to allknn. Could it be... time for refactoring into a sensible hierarchy to maximize code reuse and minimize the codebase? Well... not yet...
new 53cae8d Fix main executable to stop using Matrix or Vector or ArrayList entirely.
new fd5a68e
new 3076fa6 Build union_find_test target
new 811eac3 Remove Vector and Matrix and ArrayList uses from emst method. There is no test for emst, so that will have to be done.
new cf3bfda
new 6082157
new c6b583e Convert linalg__private::Center() to armadillo. Created unit test file, because damn, these things get complex and I want to know that they're working right.
new 08f4697
new 5aa4818
new 6eaf1bb
new 84e45bd
new ad43291
new 371076c
new 0338a1d The textfile_test now passes.
new 1ee4d48
new 3ec56e4
new 170a1b0
new ac69f52
new 82a0109
new c05622f Passes its test now.
new 3ae08c3 A couple comment updates to reflect ArrayList -> std::vector change
new 8ff9e55
new 21c4de5
new a767434
new bd1333a
new 94df5d0
new c7f5437 optim::NelderMead
new 170f574
new fa6f950 Added some bounds checking
new e4efc7e Incorrect matrix access via [] instead of (x,y).
new 61d4fbf optim:GradientDescent
new 9eeea23 optim::L-BFGS
new 7d6766f optim:L-BFGS
new e04ee20 Fixed memory leak.
new a931371 Works for svm_c learner, linear or gaussian kernels for training and testing. svm_r learner is broken, even in trunk, it seems.
new 1413db1 The svm_r learner now "works" for linear and gaussian kernels for training and testing. After fixing the runtime error in trunk, the results were verified to be identical.
new 7935acc Make parameter passing to SMO::InitPara sane.
new 588449f
new a2723ff
new b4882a4
new 65bda76
new 77487a8
new 600ac54
new c532b1f
new 3b2aa16 Starting multigrid.
new 144ae61 More progress.
new a433a7e Adding the test driver for multigrid.
new 3e2ad97 More multigrid.
new 07d0ca6 Sparse greedy GP in progress.
new 1bf1a59 Sparse GPR has long way to go, but I will get there.
new 4528392 Removing old implementations.
new 0cc847c Auxiliary files for sparse GPR.
new b01d137 Probably done for today.
new 41e901d Starting clusterwise regression.
new 087689c More progress on plugging on Smola's sparse GPR.
new 7d4521c More progress on clusterwise regression.
new 250d99e
new a31c9f2 Some more clusterwise regression.
new 00bd084 More progress.
new 7fdb908 More progress on sparse GPR.
new ad7c21b Slowly plugging in Smola's sparse GPR.
new 9c5b2ed More progress on mixture of experts.
new 67db0b0 More progress.
new 153fdc7 Astyled.
new c0a0f7c Getting there.
new b1ab44c Getting infinitely closer.
new 938ef88 Need to just write the driver for clusterwise regression.
new c4f9405 CMakeLists.txt updated.
new 9e25d5d Slowly plugging in the driver for the clusterwise regression.
new a01d443 Close to finishing the driver.
new 72f822b Still fixing bug.
new 984ace1 Clusterwise regression should work, but needs testing.
new fd08a2e Getting closer to finishing Smola's
new c138a11 Getting closer.
new e90ed67 Almost ready to finalize Smola's sparse GPR.
new 391ec45 Graphical Model
new 862c4f6 Graphical Model
new b8d2cf5 Graphical Model + BOOST
new 4689f14 Graphical Model + BOOST
new 188d0a6 Graphical Model: variable belief + factor average
new f2f936f carefully verifying Smola's method.
new b858942 Still debugging.
new 6ca95e2 Plugging in mean/variance prediction for sparse gpr.
new d8b9f0a Minor edits.
new fee9bc0 Fixing.
new 3450aad
new 423dc84 Getting there.
new 5bb841a Smola's method should be complete.
new 42a9d5b Graphical Model: Message priority
new 17c3eb8 Graphical Model: Message priority
new dadf4bd Adding the driver for GPR.
new 7054037 Compile errors are gone.
new c701304 Finished the crucial part for multigrid.
new 40056db In theory, the coarsening procedure of multigrid should work for dense matrices.
new e868c25
new ea9cab8
new 623e059 Compile fix.
new 09eb6d7 Still debugging multigrid.
new 64281eb Still debugging.
new ce9260f Still debugging, need to look at the coarsening procedure.
new 2adf3ed
new e6156dc Test.
new 8aa7b26
new 36efdad
new abd7b66
new 9c33610 Switched over kernel_pca stuff to use arma & std. Does not compile, needs changes to be made to la and SparseMatrix.
new f71a91b Graphical Model : message pending
new 4b37da6 Graphical Model : message pending
new ce284cf message pending
new b1e34f8
new 7736d9f
new 757cd35 Revert CMakeLists.txt
new 04e421c
new 72cf45f add parameter --method to gm_test.cpp
new f20bc44 Adding --iter & --ctol to gm_test.cpp
new 5bbf597
new a2cbc57
new 3171d69
new 7ceed99
new ee3e9d0
new 3817699 No. We will not be outputting BLACK text. No.
new 4caa5ba
new 815f0d4 Pseudo fastlib checkin.
new eaf1b30
new 074c8e6 Rewrite WhitenUsingEig(). Fix simple (yet fatal) bug in Center(). Test case for WhitenUsingEig() also added, but perhaps at some point should be made more thorough.
new 56b8607
new 921de7c Affine NMF: graph matching using Hungarian method
new a27a651 Affine NMF: graph matching using Hungarian method
new 3b607e0
new f1dae5b Affine NMF: graph matching
new 5b6bd24 Extend functionality of Armadillo; cov() operates like Octave, but what we want is cov(trans()). However, that incurs a speed penalty with trans(), so I wrote ccov() (column-based covariance) which does what we want without that speed penalty. I'll submit the patch to Armadillo sometime, but for now we'll just include it with arma_extend.h.
new ab03ff3 Rewrite FastICA Orthogonalize() method and write a test for it.
new e7200c6 Template for maximum weight matching in bipartie graph
new 75399a0
new 992ec1d
new 5f63116
new 4b8acd1
new 26bbc2f
new 661c76a
new 0e8e8c8
new 27d9f5c assert() undefined, added #include <assert.h>
new 3b3502b FastICA now compiles, but I'm sure it doesn't work, and it hasn't been tested. The vast majority of methods from lin_alg.h have been pruned as they are no longer necessary.
new 3e857b8
new 8b991eb
new 75645ef Fix
new bf3e36d
new b7bf451
new 6e2c6be
new 5616e69
new 99a18f2 Checking in thesis research code.
new a7078cc Fix to the CMake.
new 555ec3b
new d05a488
new 954bb76
new f515b27 naive_bayes compiles now. Currently untested. Could also possibly use some cleaning up still.
new b934334
new 866b57c learning Qt codes
new 49d7f6c
new 2ee6c8e Prefix scan code added.
new 0a375c1 Starting distributed tables.
new a659099
new 93099a1 Adding the test for distributed table, will finish today.
new 762b3fb Fixing warnings.
new 9529d51 Removing old directories.
new f8ea0e9 Fix to CMakeLists.txt which I never use.
new 192a653 Getting there.
new 6484311 Getting closer to distributed table server.
new a72d631 Kind of works, now have to test.
new 5f5378f
new 7c01522
new 19d4953 There is a bug, I am fixing it.
new 66bc4c5 Fixing.
new 57b114b Getting closer.
new d3b212f
new 967c874 I think it works.
new f887b82 Will finish today.
new fea0d2e
new 377026d
new 8a536ed It works, now ready to build the distributed tree.
new 1d9e9fb Fix to CMake flags.
new 0fb85d2a Currently fixing the deadlock.
new cffa176 Fixed, now really ready to start the tree.
new 2dc394b Will need to fix the test so that it is more informative.
new bf96801 Changed the prototype for initializing a distributed table.
new ed2c5a4 Potential race condition fixed.
new 3f3a3fe
new e919b99 Bug fix.
new 6948564
new d24421c
new b2f803c
new fd0548f Took out efence.
new 04ba438 Dividing up files.
new 84057f3 Works correctly now, just need to get the output to be in csv format.
new f5ada1f
new 4b3a24a
new ba46e7f
new 4c7c053 Some obvious variable elimination.
new cbdf951 Fixing the distributed table with more threads.
new 10a111f Will continue tonight.
new 6b6d0a3 Uses data::Save to save as a CSV file
new 6067ca3 The new distributed table is on the way.
new 0178964 Almost fixed.
new 7509c88 New implementation to be debugged.
new 46f8d7e Still deadlocking, but very close.
new 4717710 Will continue tomorrow.
new 8745c73 learnQt add KeyEvent to mainwidget.cpp
new 109b038 Still fixing bugs.
new a910415 Getting closer.
new 37d4138 Fixing again.
new 1565c41 Inbox/outbox merged.
new 195bcfb Minor bug fix, now plugging back the point server.
new 7d186f0 All fixed.
new de79b42 Starting distributed tree building.
new a1b70eb Slowly plugging in distributed tree building.
new afb8219 Will restart tomorrow.
new 78ec7be Still fixing.
new 29cc71d It turns out my MPI implementation supports only single-thread, so I need a mutex around MPI_IProbe.
new 0de652a Put locks around each MPI calls.
new 721d81c Find and set up Opt++. I don't like that I did this but I had to.
new 71c6e65a Add CMake script to find Opt++.
new 3026627 Make optimization work. The test doesn't, but it compiles and runs otherwise (test appears to be severely out of date).
new 1b760d8 Fix MVU/MFNU so that it works.
new 6730e28 Allow compilation of mvu
new 445eb0b Extended the tree building to allow up to only a fixed number of leaf nodes.
new 97008c8
new 566e09d
new 8479809
new 0db5448 Serializing the tree so that it can be transferred.
new 0ae6b7d Tree building almost done.
new f61cb17 Getting closer.
new 5f31d78 Getting there.
new 4c1ecb8 Will fix at home.
new 86058ef More bugs fixed.
new 61b5e42 Fixed a dumb bug.
new 21a7ea7 I think the distributed tree building works.
new 271966d Restarting three-body so that I can finish submitting the paper.
new 2d0082e Plugging back in the three-body recursion.
new 68e5215 learning Qt translator ZH -> VI, some shortcut key added
new 7c90d96 More work on 3-body.
new 42a8d1b Back to distributed tree.
new 54a9e0b Fixed the serialization for trees.
new 4b7c003 Serialization for tree fixed.
new bcac2d5 Almost there.
new eea718a Graph Matching: edge detector
new 150433a Fixed the deadlock issue.
new bd15306 Slight deadlocking problem in investigation.
new 2dc19ee Switching to memory mapped file.
new 696146a Fixing compile error for kde.
new 9748878 Fixing interprocess communications.
new 6a795da Slowly changing the model.
new ead8a56 Will finish later.
new 44fefc3 Compile error fixed and fix such that the tree can be put under the memory mapped file.
new f590389 Full fix, now ready to plug back in the distributed table.
new 33bfca9
new 3a263d6 Extension to support memory mapped file.
new 223ef2a
new 1979d69 Slight problem, so need to fix it.
new 8f58016 One mistake found.
new e922f2b Crucial bug fixed.
new 887c3ac Bug fix.
new c69ca42 Another fix. Now ready to get back to distributed table.
new b7ff965 A little tweak.
new 8b866d3 Getting there.
new fe7b8d1 Now ready to plug back in the mailboxes.
new f731abc Three-body compiles, now finishing up so that I can finish writing the journal paper.
new 2afb83c Will continue tomorrow, very close.
new e6000ef More progress.
new b041063 Getting there.
new 9bde665 Plugged in the pruning for three-body, need to debug.
new 5290b79 Will continue tonight.
new ee11f46 Added a timer class.
new f26a37f Just have to plug in Monte Carlo into three-body, rerun experiments, and publish and graduate.
new 2742eb8 Adding the test for three-body.
new 4377491 Three body test compiles.
new 9be39b4 Script for backing up thesis code.
new ea09eb9
new 71d4c85 A little tweak on the script.
new 1ad0906 Will continue tonight.
new c25dc04 Adding the random combination generator to math_lib.h
new 574ed52 Fixing compile error.
new 52445dd
new 848718d
new f4d4396
new 38803c0
new 068263e Plugging in Monte Carlo into three-body.
new 1d9d3c1 Moving directories.
new 9c28da0
new 9d7abdd Slowly plugging in.
new 64615b3 Will continue soon.
new e326108 MC three-body.
new a098d15 Fix to the three-body, still working on Monte Carlo.
new 5bfa079
new 87a6bcc Compiling.
new 5c9a081 Compile error fix.
new fe020b4 Will continue tonight.
new 6bcb455 Will continue tomorrow.
new f9fdea8
new 1b4a625
new f6915f5 Slowly making some progress.
new 8da2138 Slowly finishing.
new 61ccc65 Compiles now.
new f07b414 Progressing.
new b33f127 A bit more progress, so close.
new 60c09c7 Kind of done with Monte Carlo three-body, will check tomorrow.
new 938c4b3
new 1668990
new cc4f227
new 753670a
new 3f16d48
new ab4a4fb
new 4768d2e
new 4aa623d
new e280f9b
new 65bb8b4
new 817a621
new a164582
new 415329e Crucial bug fix.
new 9fdb552 There is a bug in Monte Carlo three-body, so need to fix it tonight.
new 6b87fd2 Will continue tomorrow.
new 0321fd8
new 2360773 Fixing bugs.
new b7ddec5 Significantly improve (by a factor of 1.5 or more) DistanceSqEuclidean function.
new c45b445 More bugs fixed.
new 394f093 slowly looking at things.
new 378cb6d Probability redistribution should be working.
new f40be31
new 423bdf9 Quick bug fix.
new 8d48b6a Restructuring Monte Carlo.
new ef586ca Still tuning Monte Carlo, the most painful part.:
new 081bfc8 Monte Carlo part divided into positive/negative parts.
new fd4511c Tweaked the Monte Carlo a bit.
new b35a358 Another bug fix.
new 31d1baf Removed a warning.
new d146aed Some tweak.
new f045030
new 4943af0 Adding in the modified LMetric for distance thresholding.
new dd977ab
new a241f43 Speed improvements for MinDistanceSq().
new e7909a2 Improve speed of AllkNN methods by using new armadillo mat::unsafe_col() method (returns an arma::vec alias which uses shared memory from the matrix). The code now requires armadillo-0.9.90, since that function was new as of that version.
new f337e81 auction algorithm for assignment: drafting forward_auction() function
new 14af8cb Apply use of unsafe_col() to allnn and allkfn for speed improvements.
new f129bc2 Will debug tonight.
new 2526bb6 Fixing.
new 555dcd3
new 42d313f
new f47b18c Resolving some problem with numerical stability.
new 3bb80d4 Trying to fix the inf problem.
new ef22ffb Eliminating dead code.
new 47623ef Less aggressive pruning rule, will try to do the quantile idea for maintaining lower bounds.
new 5e1e788 auction max weight matching - done forward Auction
new a3786e7 auction max weight matching - done forward Auction
new 06d8f39 Will fix soon.
new 4d8e301 Crucial bug in CSV parser was fixed - before it did not consider a space as a delimiter. I would consider replacing the CSV parser soon with something more stable.
new b7dbb4f
new 2189abb
new f5ea5a4 Fixed the test for three body.
new d0fd9a7 auction max weight matching - done kd tree with median splits
new 891e3a4 Adding in the quantile based pruning.
new 125d4d3 Tweaking Monte Carlo.
new cd06ccf
new 437ba38
new b659939
new 2123ff9
new 119914e Bug fix.
new af94a9f Some tweaking.
new a33ebd2
new 74fe5e5 Seeing the light at the end of the tunnel.
new 1f8c51b More tweaks.
new 793a65c more
new cfb6787 Crucial bug fixed.
new cc13aaa Increased the number of points in nbody_simulator-test.
new 9b7a217 Will continue later today.
new d3fefb9 Monte Carlo pruning picks up right after the node which fails.
new aade209 Minor edit.
new 7e6894a
new f8cf33b Added the statistics report for prunes.
new 66a2406 Naive point dimension check.
new 626e148 Minor edit.
new d8ffe15 Still tweaking.
new 9c1adc4 Slowly adding the quantile prune.
new 85e972c
new 540dbf0
new fdba3f4 auction algorithm using kd tree completed
new d1fbc8c
new b0d8a4c
new 8d5ebf4 More tweak.
new 21d7e51 Have to get finite difference to work.
new 57d299b auction algorithm: start allnn dual tree
new 06e5b85 auction algorithm: start allnn dual tree
new 796c859 Kernel bounding for AT modified.
new e95f4ec Include arma_extend files in build and then install them to the include/ directory.
new 09ab01f One final Monte Carlo tweak remains.
new 30d57b5 More tweaks.
new 54a0b3a
new e7b5725 Will continue today.
new 2165505
new ad69925
new 8f4f961 Changed calls to math::Pow and math::PowAbs to std::pow and std::abs
new c98a143 Changed math.h to cmath, math::Pow to std::pow, and math::PowAbs to std::pow and std::abs
new 47ea93e Change 2 to 2.0 in divisions to enforce float division
new 1937adf
new abf9fe7 changed math::Pow to std::pow and math::PowAbs to std::pow and std::abs
new 288c8ae changed optimization_utils.h to std::pow
new 10177c6 changed lbfgs_impl.h to std::pow
new b7587cc removed math::Pow and its relatives
new 3c69609 This contains the implementation details for the deprecated math::Pow and family
new 8aca9b4 added <cmath> to the list of general includes in fastlib.h to provide for methods such as std::pow
new 6cce5b6 Finite difference fix for three-body, almost getting ready to run the experiments.
new 6d5f9d9 Revert math::Pow functions in case old code still uses them. They can be removed later on.
new efdd7e1 Will add kd-tree now.
new fb8197e Do not make test in default build (it fails).
new b60b8eb Fix syntax errors introduced in lbfgs methods in r6232 and r6233.
new 424f749 Apply changes from r5648 to fastlib-stl branch (allow selection of number of independent components).
new 28cf664
new 237fdd1
new 2e24e87
new 373463f Adding in the kd-tree.
new 52327d3
new 4dfd34d
new 6330b8d
new 0150941
new 79c7b94 Slowly adding in
new 38f0d99
new 7719a3f
new 5f58cea
new 304545c
new 6ab8127
new 6d1f5c1 Templatizing the table made this painful.
new 6d4aaeb
new 467b0ea
new 70c1835
new 11cc87e
new 11b691e
new 9b363fa
new 8393180 KDE compiles again.
new adfc306 Other tests compile now.
new e6c5571 Major surgery to get kd-tree integrated.
new 273ebdc Three-body code now uses kd-tree.
new 1d22a72 Kd-tree bug fixed.
new 0670088 Added the Monte Carlo trick which would benefit for large number of points case.
new 1de473b
new f1415fb Crucial bug fix for node tuple.
new 5d9ddcb Monochromatic trick added for three-body.
new 54cced9 Some fix.
new 6042931 Very obvious optimization.
new f53a498
new 0697c7c
new 9174edf
new 9b8d27e
new 141c8f6
new 84868d6
new e6a83e3
new 197472d
new cf9fa70
new 6a999c2
new 4d95124
new 0b0d5a8
new 8a5ec15
new 5fdae99
new bff201b
new 8640178
new 70faf2b
new 17c7c93 Getting to the HPC project.
new f2c71fb
new d52a005 Going full speed.
new 5e93ffe
new 8ee757d
new ceb0abf
new 7b1d8b0
new c2ec990 In progress.
new 29be8b4 auction using kdtree: command line parameters
new c47bca5
new 291a38b
new 97202f4
new d73dc7b
new 0b46bac
new c23bdd8
new 1e84240 Debugging.
new 63a32a3
new e9528ea auction: kdnode
new 4f52e7f Still fixing.
new 3c6b7a7 matching : kd node with statistics
new 4603982 Doesn't segfault.
new ca1c054 matching: single tree
new 84534ba Boost Interprocess sharing works, but needs deep structuring to make sure that there are no virtual classes. The tree needs to have offset pointers.
new bb4bce2
new d067589 matching: auction templates
new 7380444 Clears out the temporary file before each run.
new 57edf18 Don't ever put raw pointers inside memory mapped files
new 1cb05a8
new 89db633
new 9a2a2ec
new 49b1369
new add22c4
new 6de4f47
new fc5d18a
new 6b52876
new 32b770a
new 02b3556
new 0d10082 Starting HPC homework 6.
new 0540052
new ab58fa6
new 99da466
new 3bec9fc
new e318c28
new d01944a
new 85f0579
new 1cfefbf
new 2156a18
new bf892cc
new 1dd865f
new f3d01fd
new 90cb9b9 Done with HPC HW, now have to write the report.
new 656070a
new 94c18ca
new e174218
new 3cf7f09 Fixed the homework.
new 9df6dc5
new c11eaab
new 5dac959
new cd1f726
new 2640317
new e4f883c
new 2320b18
new 1a1286a
new 27fcfde
new 165d2d8
new b73f3a3 Back to parallel kde.
new 537ee0b Optimizing serial kde.
new 7a925c9 Support code to run the final experiments.
new 6de0052
new e36c293
new aaf45a7 Remove some amount of debugging output. Fix DeflationLogCoshUpdate_() (was missing a "- n" term) so that FastICA now performs nearly identically to the trunk implementation. Sometimes signs of output components will be different, but any other differences are trivial; it extracts independent components successfully.
new cc0cbbe
new cd1ef63
new f24b829
new 1b71510 Support code for three-body in progress.
new a5cd145 Fix "translation" errors in DeflationGaussUpdate_() and fix spelling in comment.
new 6045ed3 In progress.
new 68ffcf2 Support code complete, now just have to run the experiments.
new fb38105 Adding GP regression.
new 9dbbf92 Some edit.
new 9103703
new f50aba2
new 44b8e62
new 060c924
new 118e34f
new 388042d Back to my ultimate weapon, distributed kde.
new 97bf8a0 I'll get there.
new 36d65bd Fixing the communications tonight.
new 012b372 Fixed optimization/lbfgs/lbfgs_impl.h & optimization_utils.h so that they use std::pow instead of math::Pow. Also added a cmath include in fastlib.h
new 825270e Missed a math::Pow to std::pow in optimization/lbfgs/optimization_utils.h
new a329202 changed math::Pow for std::pow wherever it was called in the mlpack and contrib directories
new 85a4b44 Trying to get communicator (inter) working.
new 30dae75 Getting there.
new 1583639 I think I can start the HPC project.
new 9b40d92 I will fix it today.
new cc0c207
new 14d27bf All fixed, now moving onto more interesting things.
new 75d0629 Renamed the directory to distributed_kde.
new 2ca8666 Makefile change.
new 0130f2c Namespace fix for serial kde.
new 782a2de
new 7e28755
new ca61cfa Undid a horrible mistake
new a93c694 First pass at version requirements for Armadillo. One thing left to do; when looking at version.hpp (not arma_version.hpp) the syntax is different, so I need to rewrite the regular expressions.
new 952cca2 Update regexes to correctly parse version information for older versions of Armadillo.
new 747ca07 Starting HPC project.
new 8449fe5
new d9c2dd6 Restarting distributed tree.
new aa26bf5
new 96aad02
new ac72fa2 In progress.
new a823e19
new 624f8cb Unabstractifying so that I can use boost interprocess.
new 5a92cce Fixing tests so that they compile.
new cbb461e Fixed so that no virtualization is allowed inside the memory mapped file.
new 8c0e886 Compile fix, now back to distributed kde.
new adce18e Getting rid of warnings.
new eecdba7 Getting there.
new 1471f30 Segfault fix.
new 24a2e41
new 65a440e Will continue.
new 25b7cfc
new d6ff02d
new 5a49d81 Fixing Monte Carlo for three-body, have to rerun the experiments.
new 45a04cf
new cfedcf3 Getting there, believe it.
new 3076ad4
new 48b8a7b
new 9be0859
new 6bfed22
new 4e68402 Serialization for tree in progress.
new 843d10c Slight problem, will fix soon.
new 8993b82 Fixed the monochromatic case for three-body.
new 53e4906 CMakeLists fix.
new c76d4ba Another crucial bug fix.
new b36dd93 Problem encountered, so reverting back.
new abfebbb Another bug fix.
new d012010 Some bugs fixed, but getting there.
new cc8f1bd Clear error in template instantiation, so fixed in distributed_kde.cc
new b1a8be4 AbstractStatistic added serialization.
new 1b41b60 Fixing the segfault.
new 550af72 Bug fix.
new 2bcf4e4 Bug fixed, never mix destroy_ptr and allocate.
new 5c2e3a5
new 9ae18a7
new 433d950
new 12ee96e
new 698afa8
new e88476d
new c1fec32
new 5514b41 Going to implement distributed hungarian algorithm.
new 17b8924 Still in progress.
new a1cd3e6 Rename.
new 28a20fb Will continue tomorrow.
new 7eb5f40 Going.
new 9a8937a Fixing, almost there.
new 8e875af Distributed auction seems to work.
new b8ade4b Minor cleanup before finishing up the distributed tree.
new fe477ab Slight problem, so have to fix.
new b355c4f Fixing bugs.
new e33df1d Continued later.
new 78e184a Adding distributed local kmeans.
new 47b855c CMakeLists.txt edit.
new 855db41 Will continue later, now the multibody multipole.
new 7efb5da
new 72b2652 Going.
new 0282625 Will continue later.
new 162a40e Need to debug.
new 66f1449
new 4157cfd
new b470ab4 Some bug fix, now have to add in the distributed indexing of the points.
new 9509df1 Bug fix.
new 7b8b0c1
new a7ca371 Getting there.
new b2d69ba Compiles, but still on progress.
new cbe9a2b In progress, but getting there.
new 02a0a22 Getting there.
new 4411a92 Moving the points across the processes work, now need to send over the indices too so that they can be reshuffled.
new 3efca7a Templatized the indexing type in tree building.
new 6ebbe56 Deep changes in how the indices are maintained in the table.
new ea7fc1f Some changes.
new 8c761f6
new c95a1c8
new 964bdbf
new a164288
new 9e61e94
new c27aa09 reorganizing HF code
new fc26516 Adding L-BFGS.
new 1228a25
new 2bc7764
new d8b1e2f
new 1e469a0
new 282ae1a Fixes so that optimization test compiles.
new f4e6fe4
new 486c3e6 Continue tomorrow morning.
new f90cea6 Top tree should work now.
new b1740be Critical bug fix.
new 6341370 Another critical bug.
new 2c1040b Trying to fix.
new 0becae9 Getting closer to fixing the bug.
new 9bc67b1 Should be all fixed now, now ready to start the fun part.
new 3a5de54 Minor fix.
new 058581e Distributed kde to the finish line.
new bf5d5dc Intercommunicator example added.
new bf924ee Nocedal optimization method for machine learning, implementation via Boost.MPI
new bd060eb Starting again.
new 5969f85 Took out armadillo from distributed table.
new 31465ac Starting on the distributed kde driver.
new 55c6513 Trying to make the distributed_kde driver.
new 2e0eac6 Serialization for table should work in theory.
new dd0c347 Added the pointer correction.
new ef19ead
new e5bcd54 Adding the distributed dualtree algorithm template generator.
new 83c1c2b Distributed kde driver almost operational.
new 481ccb9 All fixed, now ready to work on the distributed dualtree.
new cf80519 Starting to fill up distributed dualtree template.
new a949b4f Getting there.
new 02b2c71 Some edits.
new d325d4a Another edit.
new ff25ddd Compile error fix.
new 5dc7d83 Compile error fix.
new 5e68b3e
new 701753b Added the serialization for dense matrix, finishing up the distributed dualtree computations.
new 42dfa6e A little dinner break, then continue bashing.
new c720a80 Almost there.
new c5cdce7
new fa6b35f Compile error fix.
new c7fd9bd It runs.
new 7f54c36 Continued later.
new e46c61d Some bugs in distributed kde, but it runs without crashing.
new 453e058 It runs. Now have to check correctness, and make the poster.
new c536d01 KDE test fix.
new f710382
new 452223d
new e696c0d Deadlock fixed, now adding in the test driver.
new b0445a3 Fixing the monochromatic case for KDE/distributed KDE.
new 4d3ce5e Compile error fix on dumbledore.
new 67ff1f2 Minor format change.
new 27dc529 Minor compile fix.
new a213350 Timer calls.
new 739794c Timers.
new b87e1f6 Default bandwidth value changed for experiments.
new 426322d Some tweaks for experiments.
new e2574e5 Another tweak in distributed table before parallel ssample sort implementation.
new bcdfd1f
new 0b38607 Added the prune statistics.
new 0b91bab Hopefully this fixes.
new 7bb0410 Closer.
new e726150 Last change before tweaking the allreduce part.
new e5df1d6
new 51dc3d6
new fd8f038
new 3711844
new ab45c18
new 5e05d2f
new d924021
new ce1f45f
new f19fb3d Minor fix.
new 5efdd7b
new 80ec8f9
new d72d057
new 262c7ae
new 940c6b8 Warning fix.
new c00b937
new 9c85891
new 484a23a
new 7cb28be
new a475a88 Cleaning up so that MPI KDE can run without memory mapped files.
new 523a1ed Compile error fix.
new 399fbc1
new 74a2877
new dfe5e47
new 3cf704b
new db7adf7
new f728345 Some fixes to KDE, now adding in the distributed table test.
new 055cf29 Fixing in the distributed kde test.
new 0ab9770
new b8e832b Trying to make the test pass, but this will be the checkpoint for the code submission.
new 0bb02f3
new b0e8aee
new 8e0891e
new 9a8da6d setting up build server packaging scm directories
new 9020467 Still trying to match.
new 14176c3 [svn-inject] Creating hudson/tags/ directory.
new 58b3dec Creating trunk directory
new 4f9d1ae [svn-inject] Applying Debian modifications (1.388-1) to trunk
new 28fb65a final hudson packaging cleanup
new cb9d066 [svn-buildpackage] Tagging hudson 1.388-1
new ecef898 corrected mistake in README
new 14aa6d1 Distributed kde test passes.
new bc3632a Critical bug in distributed tree building fixed.
new 10d41a5 Mixed Logit started.
new 120651c Warning fix.
new 3cef743 Getting there.
new 752165e Getting there.
new 39598c5 Checking in the DCM table.
new 6a460aa More work.
new 6bb8103 Trust region almost done.
new 3b72b9c Some code restructuring.
new d59af0f Compile error fix.
new 74099d4 Warnings fixed.
new 007211c Almost there.
new 01788dd Dinner.
new 890496e To be continued.
new 4987daa Back to N-body
new 702ca4c After dinner to be continued.
new 4d8d022 Added matrix generalization of mean variance pair.
new 51a5170
new 9ab23ca
new 44515e7 Subtable view seems to work.
new ec315d6 Some output fix for distributed kde test.
new f3f00db
new bc8bcc3 In progress.
new ecfbfac More brainstorming, back to distributed kde.
new 77e9f73 Set up optimization CMake configuration correctly
new 7f92073 Use source root directory as include directory instead of ${CMAKE_BINARY_DIR}/include. With the latter, the compilation will look inside of the built include files. Therefore, if a user makes a change to an included file, it isn't reflected in the build. This change fixes that.
new 841fd0b Replicate r6607 in trunk; prevent odd compilation situations where modified included files aren't actually updated.
new ed379c7 More work, back to distributed system.
new 313abb1
new 2cba65d
new e22ce23 arma::Mat<eT>::unsafe_col() was introduced in Armadillo 0.9.90 (require that). Only problem is, that hasn't yet been packaged by the Ubuntu maintainers.
new 4efec18 WIll come back today.
new 1e83ec6 Now distributed kde can run on number of processes not equal to a power of two.
new 33b42d2 Fixing.
new 2623fb0 More progress.
new 9c10157
new e410131 More parameters added.
new 7099a0c Going.
new 6324bfa Starting matrix triple product.
new 6cd89e5 Fixing the compilation error, and subtable capability added.
new 5de1480 Minor compile error.
new 5c9fbfb Random number generation in fix.
new 909b4b1 Going.
new ed3b74d Getting there.
new 577a000 Compiles, will continue tomorrow.
new 4ff4ebb More progress.
new bcf2a98 Plugging back in trust region code.
new 84ab313
new 2efd630 More cleanup.
new 68d76ad Will continue tomorrow.
new dbbf0ec Taking out deprecated functions, trying to eliminate DensePoint/DenseMatrix classes.
new f55a43e Armadillo-ifying the L-BFGS.
new 78fd088 Will get rid of densepoint and densematrix and linear_algebra.h
new 766f545 Going the wrapper approach in dense point to use armadillo operations.
new 3c50480 Bug fix.
new 998adff Armadillo-ifying
new 6b0aa46 Kind of compiles.
new b1c86be Compile fix.
new 16d063b
new e10a920 More progress.
new f6309e5 Code restructure.
new 09149f4 Sampling class separated.
new c5e0287 KDE compile fix.
new 643fc64 Another.
new d0e366b Will continue after lunch.
new 3df3712 To be continued.
new fee45c6
new 5acc09b After dinner.
new cb77a88 Will continue tomorrow.
new 1f75b2f Mysterious crash in distributed kde memory mapped file mode fixed.
new 6aaf119 Fixes before trying the new distributed gnp.
new 06920c0 Sub dense matrix added.
new 153aeb1 Astyle fix.
new 44ad591 Another check point.
new c4e7fbf Another checkpoint.
new 5881ea5 Another checkpoint.
new 87b9266
new 2faa938
new 3b13114
new 130249d Another checkpoint.
new cd310e6 Another checkpoint.
new 7a0ce13 Another checkpoint, getting closer.
new 77769ed Checkpoint.
new 83f39cb Another checkpoint, getting there.
new 90ddc3f KDE now supports progressive computation.
new 000343f Checkpoint.
new 2baac7b Done for today.
new b7726d3 Getting closer, now have to fix the segfault.
new 637fc74 Almost there.
new 84a6168 Almost there.
new 2e4ab58 Memory leak fix in distributed kde code.
new a0ea2b2 Need to ask.
new cca607d All bugs fixed, now just have to do performance tuning.
new b1d2746
new ea366c0 Crucial bug in the distributed kde test.
new 989b854 Found the mistake.
new b373b8e Some problems, will fix today.
new 35d35df Found the problem, will fix later.
new d8934d0 I think all fixed, now onto performance tuning.
new 1a15520 Adding in the distributed parallel triple tree.
new 59a5c39 Some minor correction.
new cfc11b7 Need to look at the tree building now.
new 814a413 Test fix.
new ec55ef5 Parallel sample sort in progress.
new 05c54e6 Will continue later.
new 9e01289 CMakeFile fix.
new 25bcf63 More progress.
new fe76131 Testing the parallel sample sort.
new e10555c To be continued.
new 4ceaff3 Distributed sample sort works, now have to rewrite distributed tree building.
new 87c6825 Going.
new d756d48 Another compiler error fix.
new 5ddb98c Compile error fix.
new ba14195
new f24c11e
new 8f4ae97 Refactoring the distributed tree builder.
new 605a7db Will continue tomorrow.
new 38e5416 Distributed tree in progress, added functions to generate points within a bound.
new 10d542e Adding the distributed tree test.
new cf94a26 Armadillo change for 1.0.0 incorporated.
new 0fd3ffe minor fix to CMake in the core.
new 1647017 Getting there.
new 153d1db Minor fix.
new b6e3eff Will continue soon.
new 15ffd4c
new 6464e79
new 5cf543e Some files reshuffled.
new 70ca820 Bug fixed, now finishing up distributed tree and new FMM.
new 7827f0f
new b5a0798
new 77338ba Complie fix for distributed tree builder, still in progress.
new fc60e79 Added the random point generation test for bounds.
new 9b8ac66 Final compile fix before dinner.
new 86a5f61
new dee23ad
new ec71739
new 7e1cf8f
new 88b55a8
new da4ea37 Getting there.
new 161c9ed
new 03b4a86
new 2a8c1ae
new a2cfd56 Devirtulaization of metrics.
new 23cffc3 Compile error fix.
new 5a767f1 Another fix.
new 53c5f1a Final fix.
new dd977ff Another fix.
new 0ce0b0c Done for tonight.
new 107bfa3 Have to fix the segfault in distributed tree.
new ca78d94
new eeca2eb Critical bug fixed, still looking at distributed tree.
new f38ecf2
new 4fbb06e Bug fixed, still continuing the parallel tree, but almost done.
new d03839c
new b861f5b
new 8f35a04
new 26f3cfd
new 672f90c More progress.
new afc3e07 Almost done with parallel tree.
new bd5e988 Will continue after lunch.
new 0284655 Experimenting with gcc garbage collector.
new 43cb0f1 Quick patch.
new 4924bfe Added the bound inclusion test, now finishing up the distributed tree.
new 2c8cf37 Done for tonight.
new 9db0ba7 Lots of bugs fixed. Almost done replacing the distributed tree.
new 1cd7b1e Lots of bugs fixed again, but very close to replacing the distributed tree building.
new bbba93c
new f3e1f06
new be01673 Cleaned up distributed tree builder.
new 9277e70 Adding more comments. Now ready to improve the distributed engine.
new a17c503 Further code reductino.
new 4c29211 Compile error fix.
new 6c706d8 Need to test the Morton ordering, and refine the tree building and the distributed framework.
new f2f3478
new aa77967 Trust region being debugged.
new a98b19b Need to plug in Hessians for test functions.
new dda80f8 Fixing the bugs.
new 86602f8 Trust region kind of works, but convergence is slow.
new e8a358d Added different methods for trust region search.
new 7af90b0 Took out prints.
new c568e20 Some trivial changes, before distributed overhaul.
new 7fd2447 One critical bug fixed in distributed GNP, where the reference tree was grabbed multiple times.
new 4542953 Added the prioritization for distributed computation.
new 3da2003 Bug fixed. Now need to deal with the MPI message sizes.
new 67b96aa Lots of improvement.
new a87a2b7 Rewrite of Cartesian series expansion using boost multi-array in progress.
new 3931f1c
new 0774135
new 4236662
new a09e5ca Series expansion library being integrated into the new library.
new 2b8d741 Removing deprecated files.
new 11666d6
new 06493b6 Slowly porting farfield expansion.
new 0cfe548 Combined series expansion auxiliary classes into one, code compression in progress.
new 1adb292 Some overhaul.
new 9f51c8f Another checkpoint.
new 737e01e
new 77b36dd
new 4c1a505 More progress on FMM cleanup.
new 2eef4d0
new ffbb06d Now need to work on local expansion.
new 034ef98 Copyright updated.
new e362732 Will continue after lunch.
new b647311 Added the sanity test for three-body.
new 9843333
new 9f6f817 More surgery.
new f1a09b4 Almost there.
new 46bc40c Complie error fix.
new 37f6546 More overhaul, getting closer to cleaning up series expansion.
new c527bc3
new 9781494 Almost done cleaning up Cartesian series expansion. Now have to work on the test driver.
new 65f17ae Compile fix.
new 82b9c27 More fixes.
new 122c901 The global mapping test for series expansion passes, now plugging in farfield and local expansions into the test.
new fd22e85 Slowly fixing the compile error.
new 06117da Getting the test to work.
new 17a068f Epanechnikov expansion test added.
new 71a668c Testing the farfield expansion.
new c7fd809 Done for tonight.
new 7b6365e Slight bug in p to the d, will fix today.
new f7ad801 Series expansion bugs in p^D fixed.
new 03f4f1e Minor fix.
new a085698 Nothing in this file is used anymore.
new 49397d4
new cea1364 Quick fix.
new 3072710
new 64c7b83 Changed distributed dualtree to use priority queue.
new d968b57 Compile error fix on Hogwarts.
new 75f6ff3 Another.
new 81a8882 Another.
new 51339ef Another fix.
new 30f98f7
new 97a6ed2 Short comments.
new 789ce56 More commenting.
new 07b3c6c Adding in the absolute error approx.
new 5eed83f Going.
new 0e9e93e Quick tweak.
new 635747a
new 64ef885 Fixing the pruning rule.
new d4a0d9b Starting kernel independent FMM.
new b96534c Will finish
new 9e3ec57 Converted to stl stuff, still some bugs
new b97812f
new 75bc87c Some bug fixes. Now that we are using a pq, we need to maintain the subtables from previous round, but need to think about throwing out old-unused tables.
new 408959f Warning fix.
new fac397e Need to write a non-sampling based binary tree builder.
new 690d1e4
new d2c018f Prioritization changed.
new 54d2ddd
new 3ce979d Refactor AllNN into header and source file since it's not a templated class (that may change). Copy the main executable over from trunk, where I modified it more heavily, then transition to armadillo components.
new ef82ad6 Fix bug in TextLineReader::ReadLine_().
new e59c15c Add an overload of data::Save() that was necessary for trunk allnn.
new b290805 Fix two bugs -- the first is a forgotten reference specifier. The second fix ensures the same tree is not built twice (if you pass the same matrix for queries and references); additionally it prevents the same point from being reported as its own nearest neighbor.
new 17b751a
new e727428 Bugs fixed, now have to check that subtables are not grabbed multiple times.
new 65a9971 I will be back.
new 51fd553 I will be really back.
new 249f191
new 37805ae More patches.
new 08cadb4 Warning fix.
new 3607e21 Compile error fix.
new 9e5140f Boosted the number of points in distributed kde test.
new 63c6232 Some more commenting before the naive parallel tree building.
new cbb232d Some more changes, now onto new parallel tree building.
new 6ddab15 Trying to add in the vanilla distributed tree builder.h
new 68d8b03 Done for tonight, will continue the distributed tree (vanilla).
new 44cb5cd
new a476de2 Getting there.
new e123484
new 60eb984 Compile error fix.
new 2a87978 Gettiing there.
new 711a5df Another compile error fix.
new 4f26c46
new d885d10 Back to parallel tree.
new f674873
new a621876
new 66d82e3
new 1156414
new f5156a5
new 91422d6
new b6c0c4e Going.
new 7398518 Adding in the vanilla distributed tree builder.
new f11690d
new 972de90
new bfa4a19 Going.
new f8f9675 Getting there.
new 44b3f40 cross-match read data file
new 2ab1fd0 Going.
new 21a271f cross-match calculate run time
new a1b7e24 Some minor changes, before optimizing the distributed GNP.
new 1a65af1
new 6f88100
new df92898
new c947e2f
new 9b6e8a7
new 1630da1
new 652cf80
new 0b48c2e
new dcfd268
new 5937855 Some mini patches.
new 7c2e9b4
new 3392c19
new 607cbcd Some code optimizations/cleanup done on the distributed framework, now need to replace the cache with a circular buffer.
new 00ea13d
new 996315a Rewrite bits of HMM so that they compile. This is not tested at all (and not expected to work right), but the changes made here mainly serve to make the buildserver happy with this branch.
new 2db893a And I was so close to getting it all right!
new 96d7f1c
new 643804f Re-debugged, now have to change to the circular buffer.
new ab600d3
new bb23461
new 627a587 Back to mixed logit.
new 9ee24d8 Back to circular buffer for the moment.
new b1f1a54 Circular buffer added, subspace tree being revived.
new 507ba4d
new 1a448b3
new 412f6a2 Adding in the distributed allknn driver.
new db9c7fc I will continue tomorrow.
new 3573035
new a8bfd4b Bug fixed. When the all-to-allv was being called, subtrees belonging to another subtree wouldn't serialized, so a post-correction step was necessary.
new e7fe16c Test fix.
new 8c2e31f Take two on the circular buffer patch, hopefully this passes the test.
new e9f9cde Test trial updated.
new 1064c88
new cba3152 Redundant copy optimization in MPI_Alltoallv.
new 4d5e10e Fix to the FindSubTable function. Iterator is not erased, but now the front object is put to the position that is replaced.
new d53555e
new 8c0e901 Minor fix.
new 59488bf more work.
new cdb8d7c More progress.
new bc4c333 Some changes.
new dba1a4a More cleanups.
new e8e53a8 Fixing compile error.
new 95845e4 Bug fixed.
new bdc0713 More documentations added.
new dd4e3d0 Done for tonight.
new a8466e2 Really done.
new f206588 Minor changes.
new 81ee383 Removed math::Pow from bounds_aux.h
new 95cba1d Added support for cmath in fastlib.h Changed all math::Pow<1,2> calls in mvu_objectives to std::sqrt
new de71c18 converted general_type_bounds.h to using std::pow
new a39d9ba More documentation added.
new 85319ce Changed contrib files using Math::Pow to std::pow and std::sqrt
new 4fe6fe7 changed fastlib files using Math::Pow to std::pow and std::sqrt
new 7bb657a Test checkin from ryan to see if anonymous checkins are really allowed now
new 58670e6 Formatting pickiness changes from gcolon7's r6924
new 0544867 Test checkin
new a1fa62e
new 8317e1c More documentation.
new 549b46c I will continue tomorrow.
new 05c0977 Adding distributions.
new 481af67 Back to distributed tripletree, my secret weapon.
new 99379fe Minor bug fix.
new d7c2f0a More work.
new 73044f9 Back to parallel.
new 8fd562e Adding a new script.
new b268a9e Further proof-reading.
new 25c3c31 Minor edits.
new 6540aff More comments.
new b1ff01e I will continue after dinner.
new 6bd0293 Hua Ouyang
new 4e98f49 Update series_expansion methods to use armadillo and std:: components.
new 5d64805 Update promixity_project code (which some MLPACK methods have a dependency on) to use armadillo and std:: components
new 4b1404e Update naive_kde to use armadillo and std:: components
new 8063d26 Bug fix in the ball bound random point generation.
new e50a8df Optimized so that new_from_old mappings are not sent for subtables.
new 39b9ece Kd-tree added in the test mix, plus now attempts to split everytime until the number of points is below the threshold.
new 1289246 Change KDE utility classes to use armadillo and std:: components
new 7720a3b Update all dualtree KDE methods to use armadillo and std:: components (not tested -- only compiled).
new c1e64c7 Convert FFTKde methods to armadillo and std:: components (not tested)
new 31f5571 Convert FGT-KDE methods to armadillo and std:: components (not tested)
new ad3c9b9 Check in converted dualtree KDE method file that I missed (not tested)
new f40c8ca Convert original IFGT methods to armadillo and std:: components (not tested)
new 8d56cdf Last of KDE methods converted to std:: and armadillo components (not tested)
new 3a47821 Cleaned up and optimized naive_bayes a bit.
new 895ddae Some fixes that I missed in series_expansion (now KDE should compile fine, but again is untested)
new e764af6 This file isn't actually even used. Remove it.
new b682a44 Update NNSVM methods to use std:: and armadillo components (not tested, but it compiles)
new 15795bd Change fourier_expansion to std:: and armadillo components (not tested, but it compiles)
new 4e82dfd Disable compilation of methods that require sparse because sparse support is essentially nonexistent.
new fb27b2b
new 93aa740 Changed so that the cache size is somewhat constrained per process.
new 7868bd6 Don't crash out when mlpack_contrib.a does not exist
new 028c0ca Ack, I forgot that I had added this line
new 01eb566 Added the option to enable or disable bounds checking in armadillo for fastlib-stl.
new b133f63 I think the leaf size now should be uniform across all MPI processes for distributed algorithms, so I fixed it.
new ce28ba6 added boost 1.45.0 to Boost_ADDITIONAL_VERSIONS
new 8d67411 Getting into the subtable test.
new f935d9f fixed casting error in fastica, changed isnan and isinf to std:isnan, std::isinf in kde
new 959d847 Turned off tracking for GeneralBinarySpaceTree to avoid subtle bugs in boost serialization/mpi.
new 68cc90f Removed the print statements.
new aa49605 Ready to go to Dumbledore.
new 3efb876 Need to restructure the algorithm.
new 7222edc Quick change.
new 970ba81 Small tweak.
new e16994a More tweakk.
new 6607ead Remove Init() functions for AllNN. Everything is now part of the constructor, and initialization lists are used. Some of the member declarations had to be re-ordered for the initialization lists to work correctly.
new c742183 Oops, I broke the build again. The constructor changes have to be propagated to the main method.
new 3c207c0
new 0561a6b
new 083b874
new b3f073b
new 51c86fe Minor changes.
new 10a2a6d Numerical issue solved.
new c3fa46a More errors fixed.
new bd1e308 Another.
new 58847eb Parallel tree building.
new d53b724 Distributed tree building in progress.
new e411115 Serialization for LMetric.
new d78abfc More patches.
new af923f0 Fixing the distributed engine now.
new b431fa7 More bugs fixed in parallel tree.
new d93a773 More bug fixes.
new c6c9362 Compile error fix.
new bcaf5ff Some changes in the distributed tree build.
new 2fe38c4 Some performance problem. I am looking into it.
new cae85fe Compile error fix.
new ff3c3ad Going back to the former, now have to choose one reference tree to compute at a time rather than expanding the entire priority queue.
new 96ff3d3 More tweaks.
new 5b14985 Now, the priority queue is only expanded only one at a time.
new 6a8b44e Bug fix.
new 4310b2c No more caching.
new a5a3cbb Need to investigate the slowdown.
new f3e94a6 Memory leaks fixed.
new f93aed8 Minor fix.
new e8df83a Minor patch.
new 8b217a9 fixing.
new c62c7d9
new 24ffb5e Bug fixed in uninitialized stack allocation. The problem was that I forgot to pass in the absolute error value criterion.
new 3c06331 Minor change in kde test.
new e11320d Back to vanilla.
new 00bb7c7 Remove deprecated constructors from AllNN.
new 723dea8 Tree serialization is more efficient now.
new a84f4c7 Took out a print statement.
new 442e451 Remove ComputeNaive() and put that functionality into ComputeNeighbors(). Since the tree building phase determines how the user will perform the calculation, having the two methods be separately named is superfluous.
new 338b007 Remove unused function; I forgot I had left this here.
new eef480d Did I really forget to delete these declarations too? Apparently today is not the day for my memory to work well.
new 2bed37a started new implementaion of n-point, wrote Permutations and tested it
new af72d8f Fix in the pruning condition which was introduced when the hybrid error condition was plugged in.
new 49f6a92 Minor compile fix.
new 9cfa5d7
new 46f30f2 Move into mlpack::allknn namespace; and separate implementation from declaration (add allknn.cc).
new c0d58e8 Some bug fixes. The query stats were getting resetted during the distributed computation.
new de6db2a Update mvu code. At this point it does not work but it does compile.
new 260ae78 Unbreak everything: update references to AllkNN: AllkNN -> mlpack::allknn::AllkNN
new 7c9fc7f Subtable test fix.
new dbff51b
new 814ee4a
new 3bf40fc wrote and tested single matcher
new d76e0a3
new 3c5c262
new 4b2425b
new 94de8cd
new 90cc94a
new 7e620da
new ddc7df4
new 747828d
new 2e081df
new d14ad71
new 54b604a
new 7bded6f
new 09d3390
new 915cd9e
new 5adef38 wrote old auton-style multi-tree n-point, did very basic tests, needs more testing.
new a4339f5 Crucial bug fix - table lookup was too slow in the previous version.
new f7ffe08 Minor edit.
new c9a28b5 Changing the tree.
new 2587358 Changed the leaf size.
new 5838820
new 1da7909 Refactor AllkNN API; move Init() functions into constructors; update tests to use new method definitions.
new a6ef2bc Update KDE to use newer AllkNN constructors.
new a4417d9
new d6a8d72 Update CMakeLists for L-BFGS optimization method.
new 4b0bcd6 Remove old build.py files. As per #14. Did I break your code by doing this? Use CMake; see http://trac.research.cc.gatech.edu/fastlab/ticket/14 and http://trac.research.cc.gatech.edu/fastlab/wiki/UsingCMake
new 4d3026c Revert accidentally committed debug output changes.
new 11aae40 Remove the fl-build tool (#14). Did I break your build by doing this? See http://trac.research.cc.gatech.edu/fastlab/ticket/14 and http://trac.research.cc.gatech.edu/fastlab/wiki/UsingCMake for more information.
new 3c54c48 Replicate r7054 in fastlib-stl branch: remove build.py files (#14).
new e2e2445 Replicate r7056 in fastlib-stl branch: remove fl-build and fl-build-all (#14).
new e9965e9 Templatized the kernel type, and now plugging in the series expansion.
new efa9a4a Removing abstract kernels, now everything is template.
new 8c81ec8 Fixed a bug in kde-test.
new 44f37f6 wrote naive npt
new f300d25 Pushes in the right expansion type.
new 11066a8 Templatized the series expansion object for kde.
new e5f0828 Slowly plugging in series expansion.
new 822a5f1 More restructuring.
new d1f2ba3 Quick fix to a test.
new 6cceb3d Memory requirement for series expansion fix.
new 71488bc
new 667b1e0
new ddec03a
new 20f6fb0
new 6fac389
new 5982a03
new 1876f2c
new 8f4d52a
new ac39f31
new 483c41d
new 98ef7db
new 5f127f1
new 60f0a70
new a6f24fe
new 8834649
new b0354f8
new 66b23cc
new e8cb460
new 2da31e6
new b0242a4
new 1deea24
new 8f59b9a
new e48bcb8
new bb70fc8
new e23520b
new ea8395e
new eb30273
new a072bcb
new 0738409
new 5474561
new b513219
new 96f6884
new e875e7e
new 2f65551
new 6d13629
new 8ac4546
new 98919b7
new 40ccf8e
new dc6ffeb
new 63f4182
new a550e76
new c5a5188
new 7a46894
new 1275e70
new 4ab8b9b
new 75fed04
new 553a665
new 9d8e477
new 6bce0c5 Slowly adding in series expansion, almost there.
new 4e69193
new 3ac10fa A little break.
new 98bd0d2 Almost there.
new 51c0f84 Series expansion is now plugged in, now have to debug.
new d507955
new e5dd24c feature selection using submodular function inducing norm: started
new c869844 Remove FORTRAN from CMake configuration. Turns out we don't actually need it, and I never thought to check until now.
new 5df0974 Remove FORTRAN from CMake dependencies. (see r7124)
new 0b66d60 fixed bug in naive code, wrote I/O for main, started on permutation-free algorithm.
new 3c93532
new 5c1c0a1 Series expansion should be functional, but really need to go through and verify and debug.
new 7619ae1 Don't modify CXXFLAGS at a lower level (this was causing MLPACK to compile without profiling information).
new 4d197ab l2loss l1reg
new 844015d Bug fix.
new a84a91a l2loss and logistic loss
new 073f943 l2loss and logistic loss
new 7ff700f Counting the number of prunes.
new dfde36f Problem with multivariate gaussian expansion, will fix soon.
new 072d24a adaptive Lipchitz constant
new 4808028 Disabled the Epanechnikov expansion until further notice.
new 4060330 Fix due to the templatization of SphereVolume function.
new d80d828 Took out geometry.c and geometry.h
new 0c06400 Bringing back the distributed kde with series expansion.
new c698d34 Adding in the scale option.
new 8fe5ca7 Distributed kde/test compiles again.
new ad9d06e Parsing error fix.
new 2420940 Timer added to the KDE.
new c9856e5
new d911ddf
new d6a554f Argument parser separated for mixed logit.
new b4084fb
new cba7205
new e26a9f9
new fa44e11 Porting Bengio's method for the finish.
new 45b689b
new 7cc2a9c Added the approximate Hessian update routines.
new 7383a08
new 4b725d0
new 4f76ca5 Added the method for determining whether there are points underneath an arbitrary node in the tree.
new a1baf94
new 2d9884a
new eba4c7a Segfault fix for distributed kde.
new ebc934d More debugging.
new c9fa868 Temporarily turned off non-uniform weight series expansion.
new e666e1a
new 0802c8d
new 294993f
new 465398b Mistake in the series expansion fix, now have to make sure that the rpoints are properly accumulated in the case when the table stores non-contiguous points.
new 815adf8 Minor corrections.
new cefbd27 Changed the AccumualteCoeffs to use iterators.
new a2d6984 Took out a useless operation from kde_dualtree.h
new 6f9e9c5 Found a bug in multivariate series expansion that involves copy constructor of core::table::DensePoint. Must be careful when using core::table::DensePoint since I define assignment operator in a different way.
new 5d1f204 I found out that the series expansion does not work properly under distributed setting, so coefficients must be not being cleared/exchanged. The distributed_kde-test now forces the exchange of entire trees.
new 565d6b0 CMakeLists.txt modified to accept CMake 2.6
new 7721d8e
new b5353a8
new 0a6e200
new fd0c405
new eec6abf
new bfc5697 Now copies farfield expansion when statistics are copied for KDE stats.
new a964f07 Added the copy method for copying the farfield expansion.
new 4bc97dc Changing the test to do level serialization for distributed kde test.
new 214ede4 Now grabs every table from the distributed computation in each stage, might have to threshold this later.
new f59adcd More subtable test.
new c090fc4 Cache size constraint.
new c9a37a4 So there is a problem with the node iterator in the subtable, so I'm fixing. After that everything should work.
new fe5fddf Corrected the subtable iterator test, still debugging.
new 9693968 Bugs in subtable node iterator fixed.
new a5897e3 Took out debugging statement.
new dc31c43 Adding the depth function to GeneralBinarySpaceTree class.
new bc73a72 Compile fix.
new 37665b3 Another fix.
new a804f24 Fix.
new d22888a Final bugs fixed, now have to look at the iterator performance for the subtable.
new a566440 Memory leak in distributed_kde-test fix.
new ee6d0f7 Minor indentation fix.
new 38855c9 Added the quasi random number generator, which needs to be tested later.
new b5a1daf
new 0fa8423
new 312cb25
new 9df432c TEST_DOUBLE_APPROX failed when at least one of the numbers was NaN.
new 15875de Comment updates, unit test, and optimization
new fc6f572
new 770705a
new d85c98c
new 47ed2f6 Should be up to date, now.
new e243890
new 8d94d6f Fix incorrect usages of std::pow introduced in r6231. I can't believe how long I have spent tracking this down.
new b5fa12e
new 68f3d03
new a12ab01
new 5d71e2e
new b91e19f Probably need to change the quasi-random generator with QuantLib.
new 6ca4283
new 511d36a Add mode option and display number of pruned nodes.
new ea9e6d4 Added io.cc and optionhierarchy.cc io.cc Future replacement for the FX subsystem. This version is currently just a one way wrapper for program_options optionshierarchy.cc This class represents the global namespace of options in a path based manner.
new 40b064f Don't include Makefile in the repository, it is a build artifact
new edb48c7 Don't include Makefile in the repository, it is a build artifact
new 3fd1afd io_test does not exist in the repository yet; commented out for now. Also fixed a missing IO::.
new f1daf70 Fixing the problem in distributed kde where multiindex mapping was computed multiple times.
new c73ad6a writing body of matcher and node_tuple
new 0c89fd3
new 60d574d finished writing permutation free version
new f4161b9
new 632e360
new 0bcfd70
new a011591
new c750ff2
new 5003f11
new e15c96c
new 7cded39
new 597b0dc
new 72166a1
new 1378921
new a970868
new 0b60583
new 0212c6d
new 46f2f97
new 2222da1
new ebba0ce
new 0bbcea0
new 83d84e5
new 4c4d6c0
new aad2e73
new 0572a93
new a98ddbd Fleshed out IO interface, integrated OptionsHierarchy into IO. TODO: Make IO more robust, allow printing from non-root nodes Debug
new 51e43be
new bf524aa
new 219c589 Do not attempt to continue if the dataset did not load properly (#32).
new bc4c79f Comment out function that was defined twice.
new 12bad07
new 1a4152d Monte Carlo scratch space for MCMM is allocated only once for distributed version.
new 71756c2 finished perm free alg, fixing bugs
new fb554fe
new 1713ec0 Link against armadillo too.
new 9feb681 Finishing Bengio/Smola expansion so that I can write my SC paper.
new 09c5d5c
new 7ed6eeb
new e217a4b
new 5ab3731
new 814bac9
new 38c4077 Finishing Bengio.
new a3231fd
new 8152cc5
new 616cfde I will continue today.
new a2286ad Getting there.
new 132da1b
new 45380e0
new 318419c
new 918d487
new 3624dd5 Getting there.
new 21a3d35
new cc93eeb
new 86a92b9 Reshuffling should work for weights theoretically.
new 265d216
new c6385e4
new 313296a
new 6829fe6
new 1317d35
new 5dd2e94
new d348673 Weights are now retrieved from iterators in FMM.
new 12349f3 Renamed the files.
new 43216db Getting there.
new 1989822
new 4c2517d
new e2b5dc2 Getting there.
new 189e029 I think almost done.
new 289ec4a Eliminated a useless function.
new c22a4a7
new c03f902
new f711b25
new 5f667be
new 270f471 Quick fix in arma::submat use.
new 723cf1f IO is functionally complete. Will begin integrating with the rest of the library upon discussing a few particulars with Ryan.
new 9e8ca0f Added io_test.cc to the repository.
new 3bb746e fixed bugs in perm free implementation, now naive, single, and perm free are correct on 2 and 3pt tests
new a78fe97 Remove FORTRAN from CMake dependencies. (see r7124)
new 042570b I lied before, but now perm free is actually fixed and passes 3pt tests
new d5679c8 Plugged in quasi newton updates.
new 3b9c38e
new a700828 Plugged in the distributions.
new 0125a53 Getting there.
new dc4f0f3 Correction.
new 11e1ab6 Ready to start the test driver for mixed logit tomorrow.
new 9628cc3
new c9c7952 Starting the mixed logit test.
new 2388665
new 12d9086 Refactor AllkNN entirely.
new 28c2cbd Test compiles, now have to run it.
new c1099a8 Better implementation of MinDistanceSq(DHrectBound& other).
new c4f0710
new 317e04e Oh dear God, I've forgotten a space!
new a8b8ebc Getting ready to run the test.
new 5823f03 Almost there.
new 9fe2409 Typo fix.
new 90e5ddc Bug fix.
new 86d7904 Code formatting fixes, mainly.
new 66398d1 Refactor allkfn.h into allkfn.h and allkfn.cc. Then, remove Init() and Destruct() functions and replace with constructors that are functionally very similar to the AllkNN constructors. Update the main executable and the test executable to use this new syntax.
new de7a28e Move AllkFN into mlpack::allkfn:: namespace. I find mlpack::allkfn:: very difficult to type today, but I think it's just me.
new dfc0307 Add additional pruning; not necessary but I think it gets us a speed boost (I could be wrong -- I will need to check).
new e2f3ea8 added timing stuff to n_point_main
new 10cd100 Don't use std::vector<std::pair<double, index_t> > to store lists of furthest neighbors. It is extremely slow; this new implementation is more than an order of magnitude faster. See #64.
new dcce4aa More fixes.
new 703e2b9 fixed a pruning error, wasn't catching bad symmetry cases
new 6fd5d55
new 69f8d03 Fixing.
new 5a108f7 Still crashes.
new a82bc45 It runs, but I have to check that it terminates.
new 893295c Boost exceptions are not actually being used and this header file does not exist with every version of Boost (it is not in 1.39).
new 7f2d179
new eea5e67 start building wrappers for Numerical Recipes
new 01c02c7 moving the directory
new c912df2
new 342a9bb
new c537dbd
new 32359f3
new 9d1befe
new 15f6015
new b6b3a13
new 2caaeac
new 533c4bb
new 6df28a4
new 0cc9401
new c0108aa
new 9ba025f
new 59caf35
new 4964492
new f79ec78
new 72a603b Some correction.
new c344716 Adding debugging statements.
new 820e0ee More messages.
new d821759 Almost.
new 4281bc3 continued after dinner.
new f926f26 Fixing the memory bug.
new 56e02a3 Made the destructors virtual, but really need to think about making it a template distribution.
new 586d583 Memory leak fix.
new eabdeb3 Changed the virtual functions to traits for performance.
new d1cbdf6 Compile error fix.
new da73a25 integration sample size for multinomial logit fixed to 2.
new 27e6b90 Working.
new 27a11fc Something runs.
new cca5625 Edited in timer support to IO. The timers work, in the middle of integrating timer support with globalValues.
new 940bbb5 Going.
new 50cfd54 Fixing.
new 99db201 Almost there.
new bdc7e27 Minor comments.
new 5dfe52e I think I derived how to evaluate the dictionary compressed far field moment expansion.
new c4c461c Going.
new 07fedfd
new 11cb458 adding directory of numerical recipes' code
new 4cc69a2 Starting the F2L translation operator.
new ddc057c Slowly getting there, too tired.
new 60a8fb4 Code restructuring in Bengio FMM.
new 7390224
new f90f371
new 9955187 Remove Nick's implementation of an augmented Lagrangian which uses L-BFGS, which is not actually L-BFGS and is improperly named. We will slightly modify Dongryel's implementation to replace this with a true implementation of L-BFGS.
new 0e06670 Copy Dongryel's implementation of L-BFGS.
new faecd5d Update CMake configuration.
new 58cb992 Finishing up F2F translation operator for Bengio so that I can start writing.
new 9d092a4 Seems to be working, now have to plug it in.
new 8c60cde It seems to be working.
new 11fbbb4
new b8c4951
new bcf5794 test file for numerical recipes.
new 0cb745c added 'pagarwal' directory.
new 7e9766e developing optimizer wrappers from Numerical Recipes.
new 578d6e5 Comment out pagarwal directory until CMake configuration is added inside of it (CMake crashes otherwise as it is not smart enough to do nothing upon seeing no configuration is given).
new 705f363 test if NR is working and start quasinewton optimizer
new 3d6ec2b Fixing the CMake.
new a11c99b Fixed a bug to make sure that the weights are serialized as well.
new 9ab2338 Bug fix in monte carlo kde.
new 24df9a4 A utility function added to GeneralBinarySpaceTree.
new bd5a88a Bug in the max prioritiy queue fixed.
new 9161562 Some changes.
new 240eeed Prioritization added.
new ab6ad4d Memory corruption fix.
new 42d1d0c Fix.
new a962042 Fix.
new d43947d Fix.
new 24f9dff Changing to kdtree.
new ebed20d Changing to sample based tree builder.
new 7faad3e Fix.
new a2123e7 Fix.
new 634081c Fix.
new 45dd174 Tweak.
new 59339e2 Going.
new d2637ea Implemented timers, should probably implement a method of printing certain values to console. That should basically be it fofr IO.
new 3b79e81 Tweak.
new 455a24d Fix.
new e9a68c6 Warning fix.
new d61f12a Fix.
new 563424c Another.
new 141e25a There is an load imbalance.
new 4c1a5a4
new bafab38
new 020224e
new 00cae4f Do not use local include
new 6b19e3e Adapt L-BFGS method. Wrote test function (RosenbrockFunction) and will adapt Dongryel's ExtendedRosenbrockFunction and WoodFunction. API has changed slightly. lbfgs_test is the thing to compile to test it (it works).
new 592c9ac Don't compile optpp directory (it does not work).
new 1597f04 Add WoodFunction and GeneralizedRosenbrockFunction (adapted Dongryel's implementation) and expand test suite. At this point I think we can conclude L-BFGS works well enough for me to continue with my work.
new 9c14a6f
new f030d57
new f3d26ea
new 8e0ddf6
new b2d854b
new 029acfe Extrinsic prune added for kde.
new 0d66942 Trying out new things.
new c2323c2 Fix.
new 82fd08c Bug fix.
new cdccbde Some restructuring.
new b75d42e Fix.
new 72a07b0 Getting there.
new ffafbfb Hopefully this fixes things.
new 5488a19 Change.
new d34b536 Final.
new a95a78a
new 3b86f9b
new 98462c2 L-BFGS fix.
new d01d6b6
new 60ffa49 Adapt L-BFGS implementation to optimize matrices instead of just vectors (this is a generalization).
new 5d652c4 Simplified the design of distributed dualtree algorithms.
new 8dfb03f
new 2d03caa Fixing the test.
new 7c3524a Bug fix in distributed kde.
new da9da3b Took out debugging statements.
new 9a827a1 Another debugging statement.
new 4da3a22 Going back to the previous.
new e9ad92d Previous.
new b26dc48 Bug fix - self contribution is now subtracted only once.
new f226cde Seeding added for distributed computation for extrinsic prunes.
new 6f5a8a6 There.
new d49a23e
new 5c1e5ae
new a6abad7
new a6efa48
new 4b74732 Implement r7435 changes into this implementation of L-BFGS. Also, for convergence of the Wood Function (in the test), it was required to increase the maximum number of iterations for the line search.
new 91f1273
new 00ed819 Monte Carlo fix.
new 5c03a99
new 2f75104 Fix errors: missed conversion of arma::vec to arma::mat in a couple of places.
new d81a3fd Add a test function with a matrix to optimize (to make sure that L-BFGS is correctly optimizing matrices and not just vectors).
new beaac15 Remove L_BFGS::Init() and use the constructor instead (in accordance with MLPACK design goals). Also keep the function internally as a reference, not a pointer (it may be that we do not even need to keep a copy of the function, but I need to think through all the use cases before I make that change).
new c56ecab Do not provide a GetDimension() function; the user should get that from .n_cols and .n_rows of the returned arma::mat with GetInitialPoint(). The real reason for this is that we now support L-BFGS on matrices, where the dimension cannot be described with one integer, and passing a std::pair<int, int> back would be needlessly complex.
new c6a9e4d
new 60f778c Hopefully this fixes the out-of-memory problem for 512 processes.
new 0373a26 Bug fix.
new 58a595b Buffer size is fixed now.
new 87f5a38
new 8e707b4 Starting random feature.
new edc71b3 Performance bug fix.
new 7e318eb More progress on random feature.
new bfb851c Compile fix.
new 614dfcb Random Fourier feature seems to be working.
new 0669210
new 56105c9 Fixing Rahimi.
new 73be832
new 8cf4f7c Fixing the series expansion test.
new b232ea1 Bug fix in RandomPick.
new 19a81f6 Fix in Monte Carlo.
new 0e8b8de Added the probabilistic prune counter.
new d421fdf More fixes.
new a5edbf9 Changing default option.
new 3e895dc Obvious monte carlo fix.
new c17525c
new b683d70 Another fix.
new cc3b6f2 Compile fix.
new bc955e0 Minor.
new 1cf0392 Now reporting prune statistics for distributed kde.
new df0f9e9
new 4e4e86b Monte Carlo problem fixed.
new 9da7971 Adding unithypercube scaling options.
new a935490 Prints the initial frontier size.
new c64effb Changing to kdtree.
new 29895a4 Bug fix in distributed kdtree building.
new 681df67 Tuning.
new eb54666 Warning fix.
new 72cd5a8 Changing options.
new 525dbd6 More tweaks.
new 7151eeb
new ed9fff6 Some changes.
new c558f22 Adding extrinsic prunes on the global scale.
new f43f4f7 Adding default absolute error.
new ccda5b3 Prioritization on the global scale added.
new 149db7d Formatted.
new fa3450a Slight change.
new 5e745f3 Cleaned up IO, began phasing IO into allKnn. Also took a look at WITH_SPARSE=ON bug. (No solution yet)
new c7778dd
new 3a1f62c Finished integrating IO into AllkNN, AllNN. TODO, figure out SPARSE issue, continue integration, work out what Ryan wants as far as Output is concerned.
new 9c7338f Compile fix for KDE.
new a61ea02
new 1e9506e Turning off scale for distributed kde.
new a92684f
new 88c800a Starting distributed kpca for SC paper.
new 73bf30d Doing distributed KPCA.
new c21c02f Going.
new 082eb6d Getting there.
new e64c7b0 Continuing at home.
new 8311fde Continuing soon.
new 81721be To be continued. Will finish today.
new 248bcec
new bd3c22f Getting there.
new 6f30973 Getting.
new 6b87ab3 Getting there.
new 4f773f2 Close to graduation.
new 4f9255e
new 5c7125d I think it works.
new 83e10ab finished with rough version of Least Angle Regression (LARS)
new 7d189a8 changed CMakeLists.txt to include lars
new f4eb04b I think it works.
new baf1c7d Lars class now stores beta path and lambda path results
new 68a0ebd
new eeda162
new 62bc6af
new 02d1082 Getting there.
new 54ca82f Warning fix.
new 4aa970d Another warning.
new 0c358a1
new 68a471b
new c48a001
new 3871dee Bug fixes.
new 628b516 Need to fix compile error.
new 77e8711 Compile fix.
new 68151d9 Bug fix. Normalization added for KPCA.
new d047845 added LASSO modification to LARS
new 4aa41e4 fixed CMakeLists.txt by removing test_new_fastlib
new 92492bb Different outputs for each process for KPCA.
new fe04a08 Minor debugging statements.
new dcf2e1e Don't build LARS by default
new cb220ba Don't build contrib stuff as it has not yet been converted to Armadillo and stl.
new 3a9d4b9 Started working on template magic to make easy parameter registration. Don't use these just yet.
new efba9f5 Gradually moving toward sampling both in data space and function space.
new 467410b finished coding version of LARS that uses Cholesky factorization rather than Gram matrix. Still need to test and tweak
new 23ef968 Crossing fingers
new bb1409e Fixed.
new e646fca Fixing.
new aff8ab0 Bug fix.
new 3d1d488 Starting KPCA distributed computation part.
new 007eee2 Will continue later today. Almost done.
new adc2cc7 made some variables private. improving style and modularity of program
new 5110bb2 done with LARS and LASSO. need to add modifications for elastic net
new 1998d7c Slowly finishing.
new bc1671a KPCA step almost done.
new b60ff9a Getting there.
new dd1b0c3
new 6cb88a7
new 350a2d9 ALmost.
new 199bfd6 Almost there.
new c71b9cf Cleanup.
new 08fb597 Just need to finish one part.
new 5fac10a Added the copy constructor/assignment operator to MeanVariancePairMatrix.
new 52b3518
new ee45393 Working on the output portion of IO. Finished the registration at compile time feature.
new d13672e Getting there.
new 1dcccbd I will continue soon.
new 9d70129 Make all error/warning/info prefixes 5 characters wide (NOTIFY -> INFO). That way it's formatted a little nicer as output.
new 20e8e0a
new 057bdb5
new 15a5817 Should be ready to run on the full KPCA mode.
new 030673d Getting there.
new a311b11
new 982698c Almost runs.
new 009413c Memory leak fix.
new 98abc8f Almost done.
new b86f14b Almost there.
new 1fe8c12 Getting there.
new 8883c26 Fixing the KDE mode bug.
new 32f1f89 Almost done. Now adding the centering.
new 52de112
new c412756 in process of making modifications for Elastic Net; have modified CholeskyInsert
new 9bfc4a6 in process of making modifications for Elastic Net
new 8f6d5a1 Starting the centering.
new 044353d
new a7a478e Restructuring.
new 99fc232
new d96f602 Almost there with the centered KPCA.
new 76152d1 Almost there.
new febd5bd elastic net code seems to work!
new 8978163 added missing test.cc
new 8866305 Done. Need to debug now.
new fd52eea
new ad659ea Adding KPCA component vectors normalization.
new 2f268ca More bugs fixed.
new 6cf0e18 Getting there, almost.
new 5820223 Adding the naive mode.
new 03a3e00 Good news is that the naive seems to match.
new 1e733bd Add augmented Lagrangian method. No tests or implementation yet.
new 059af32 fixed a line of code in CholeskyInsert function, related to solving linear system; now a massive bug has been fixed!
new a976d6f Bug fix.
new e3cce8b restructured program into lars.h and lars_impl.h and created library
new ce8ba26 added project directory for discriminative sparse coding - code is pretty much an incomplete skeleton so far
new 84971f3 file renaming and class renaming, and added disr_sparse_impl.h
new 52e4534 updated CMakeLists.txt
new 8f1e158 Lots of bug fixes, almost there with distributed KPCA.
new d660adc more code reorganization
new 53215a8 fixed DiscrSparseCoding compilation errors due to class renaming
new ee2b988 added accessor for active_set() for LARS, and changed the check for LASSO early exit to strict inequality from mere inequality, to ensure correctness of active set upon program exit. This last thing requires some testing still.
new e1d151b Continued work on IO output. Added system for automatically printing output without further programmer interaction. Working on formatting output.
new 3635d4b file renaming and stuff
new 919934f file restructuring
new 4fb56b9
new be479da Fix formatting error.
new e1b0f5f Fix several errors inside of AugLagrangian.
new c27622d Add test function and test for AugLagrangian. Compiles, but does not yet work.
new 39cd250 Update CMakeLists for new AugLagrangian test.
new cec87e4
new c88e61a
new 789863f
new 2d105f3 made cholesky factor a class variable and now am able to return it
new b550be5 file reorganization
new 3113af4 fixed some minor issues so code compiles
new 08bb18b added discriminative sparse coding to CMakeLists.txt
new c78297e
new f3c030a Bug fixes, should be ready to start running by Wednesday.
new f1f1446 Committing.
new 0bfb88d Took out exit.
new d3c5f9d Compile fix.
new b7e1527 finished preliminary version of stochastic gradient descent for local coordinate coding
new 2e2ba34
new c772ecb Small parameter tweaking.
new de31966 Should be ready to run the experiment.
new 333ede2 Almost ready.
new 6ae0efc Critical bug fixed in KPCA centering case.
new 6e1de19 Warnings fixed.
new 9d3a9dc Debugging statement taken out.
new e2947b2 Last change.
new 9faa862 Fix Lagrangian calculations (I had a sign wrong) and terminate when little improvement is found.
new 3e2171f Make AugLagrangianTestFunction work, and also create new test function (which works).
new 4a89a3a Reduce gradient norm check value, and add some useful output (as comments).
new ba870c0 Took out a debugging statement.
new b0f530a Adding threads to distributed KPCA.
new 461d1d8 Fixing silly mistake.
new a1844ac ANother error.
new 7cb9ec9 A bit of restructuring.
new 7bd7e7b More stuffs.
new e407f34 Added threading to the convergence check part.
new 7f09fda Adding the new convergence check file.
new f3f7a1f Crucial bug fix.
new 3df7ef5 All done, some sanity checks are in order.
new 0df45c0 Memory leak fix.
new faf898f Another bug fix.
new fbb3a82 Now turned off the random generation mode.
new 8137c9a Going to refactor optionshierarchy, it's basically not extensible. Also, IO seems to not like having singleton declared as a non pointer type; I will make it like non pointer types.
new a8e1bf0 Fixing an error.
new 198b7e2 Another mistake.
new 91fdeb9 Seems all bugs are fixed.
new 66c3037 Be more stringent with Armadillo version checking; fix regex for checking if parsing was correct.
new 91c5505 Should be able to read one file across multiple MPI processes.
new 8b9f96f Now outputs to different files.
new fc14ff7 Bug in the driver fixed.
new 296f172 Postscaling added.
new 07a33c5
new 9f2138e Minor change
new 69dbe8f Changing.
new 3035b24 some trivial change to main.cc
new 057f899 A little tweak.
new 27b6b0c Another tweak.
new 27939fd
new 008b69f bug fix in lars; if all variables are active and we are kicking one out due to LASSO, before we would stop, but now we realize we need to keep running interations, since not all variables are active anymore
new 754a054
new 7fde9a4 Finished auto-output for int, bool, string, and timeval types. Adding more types will be trivial. For w/e reason, converting the singleton variable to a non-pointer type makes the compiler cry. I will wrap it in a scoped_ptr next time.
new e2dcb8e Is it working
new fd14670 Going Pthreads.
new 505866e Changed all calls to pthreads.
new ab62cc8 Hypercube scale fixed to prevent division by zero.
new 940e655
new 7a3e309 Now has the option to take a real dataset and grow up to a prespecified size by adding random gaussian noise.
new 4ae30e8 fixed a stability issue; no longer using clever update of maximum correlation. for stability, it looks like we have to compute it by doing an actual max operation over the correlations!
new f6f7397 removed mlpack from library dependencies for lars
new 1d3ea27 swapped out solvers; now using triangular solvers, and using a function I made called solve_trans; note that solve_trans does not exist
new a2c5092 A quick fix to make sure that growing the file is done in parallel.
new 3f005b4
new 7449d6b added preliminary program for experiments on MNIST
new e031947 added mnist_main.cc, oops!
new 9fa6100
new 028654d
new b7b038e trivial change to CMakeLists.txt
new ef73f1c
new 0f8b4c3
new 2ffaaf3
new d14a548
new 2af47bc
new 95b54ad
new 31883e5
new ed160ac
new fd31afe
new 92ce9ff
new 3a925f2
new b9640f6 added local coordinate coding - awaiting testing
new 3cc3419 added local coordinate coding project to CMakeLists.txt
new a9c19a3
new d1f421c fixed but where in the case of initial maximum correlation being too small, we still ran algorithm and ended up returing wrong solution. instead we can return immediately without running alg!
new 39f8055 commented out some debug printf statements
new de6c2b5 I like it when my code compiles
new 5a2ed5f Cleaned up io source, got trolled by ryan and left camel case.
new 344f3fd
new d367dfc
new e139292
new e154fe8
new d69fb97
new dbb36b6
new 222e269
new f1bd140
new 4e94883
new 2cd35f3
new 7ec2872
new 6521109 added CMakeLists.txt file, sorry Ryan!
new 2e369f5 some changes to driver main files
new b1e6edb added local coordinate coding to CMakeLists.txt
new 9b45922
new ac60a12
new 67d8809
new c6a4937
new 8d0dc7c Quick bug fix in naivekerneleigenvector in non-centered case.
new 5212880 More numerical stability added to the centered case.
new 1f67fd7 Fixed the centering bug in KPCA.
new f5b88f8 Changing the perturbation.
new 15eb892 Should run faster.
new 205b052 Serious performance bug in threaded code fixed. Now the main thread goes after the children are launched.
new 6175cd2 OpenMP-ified.
new 455d15b Cleaned up code to better conform to standards, edited vim configs to help out with that.
new f73bfbc Bug fix in openmp part.
new 87ce658 OpenMP retake.
new 0afdb30 Take out Numerical Recipes from the repository and save the lab from potential license violations! :)
new 812ec5b Should read in faster now for KPCA testing.
new e67276f
new 87afba6
new d4d6004
new 5e0548d
new 6a624f1 Dataset reader compile fix.
new 788b046
new d738dfb
new 72b0816
new b05fb14 Adding the training error measure.
new cdea05b
new c838af9
new 2f58f6f
new 76e4dc8 Continued later.
new b2c2c96
new 0b0c76a
new 7b54c52
new 2791839
new d0d91a6
new ae2eb06 Splitting file optimized.
new 2cb36eb Timer added.
new b6e040c
new 28bfdb2
new 77cea67
new 52b4cf3 To be continued tomorrow.
new 5ace004
new 0e26db4 Getting there.
new b0bcd12
new 1d7d340
new 58993d5
new 4ab5ada Fix.
new 3a12357 Fix.
new 22ca8db Format.
new d855195 Bug fix in random combination generator. Added the option to clear or not clear.
new 0eec30a Format.
new be0be91 Turned off probability allocation for three-body.
new eff28a5 Fix.
new de69db6
new 1a45a9d Bug fix in three-body Monte Carlo.
new 1199a90
new bcdb9bd
new 11275c2 Fixed a bug in IO. Replaced FX functionality in allnn/* with IO functionality except where such removal would effect other parts of mlpack/fastlib.
new fa75ed2
new 7818593
new 6a1ab6f
new 39bda4a
new 2b8bc99
new f4b84d9
new 2f19e7e
new 6f865fb Fixed a few bugs, still working on one in IO::PrintAll (boost any cast is returning null, sometimes). Added cout like functionality. In order to prepend [NOTIFY] to output, will need to capture <<. I will get around to that when I get back.
new 428659f
new 6f78a23
new 3b167a2
new 2f1fc8f
new 69d005e Adding local regression.
new 25bc6c5 Fixing argument list for mixed logit.
new 10d6059 The test sets are now read in.
new 0072a77 Tomorrow.
new 66787a8 Changed to use boost scoped array.
new 9f68784 Should fix the numerical stability problem. Will debug tomorrow.
new b66f21c
new 0284d09 Took out exits.
new db2ec97 Bugs fixed.
new 813c8a7 Another bug.
new f0ad17d Test.
new a359fc0 Bug fix.
new 9970202 Another.
new 56c0acc Bug fix.
new d72a743 Fixed.
new f452e9a Still debugging algorithmwise.
new 30235db
new f410cfe
new c856f44 I think constant distribution is fixed.
new 08c5554
new 2e9cb25 Main driver.
new cccc223
new 609bd39 added mnist programs
new f05657d
new 55f90e5
new 2b82931
new 06a00da
new 056acb5
new 4c2006d Return a bool instead of an int (this is C++, not C, so we have this nice type).
new d167430 Took out the statement.
new 59bded8 Remove stringification from macros (users should pass in strings in quotes instead, which is a more intuitive interface).
new da40ec8 Transition to IO in a more complete manner.
new 77971fd Comment out IO parameters for now. We'll come back to this later.
new ec2e982 Document PARAM() macro and add PARAM_*_REQ() macros. Documentation should be expanded on a bit, but that can wait for now.
new 50189c1 Make relevant parameters required.
new 8cf102d Well of course, I forgot to check something in and I broke the build...
new 5803fa2 Make iostream-based output system. I still have a concern, though, which is that something could try to use one of the streams before they are initialized (this is possible), which causes a segfault. This can be solved, but it needs thought.
new 429780d add dense version for pole
new 1e74f07
new 12ca3d5 Some optimizations.
new 7cb5549 Don't add std::endl at the end of output (this doesn't work right). We can remove the Print*() functions.
new 80b6b31 Remove Print*() functions from io.h and change internal IO calls to now use the stream-based solution.
new fa5a033 Adapt to new IO output API.
new 2c4bb99 No using directive in header files, this makes angry worlds happen.
new 421b24d Grammar Nazi strikes again
new 5281283 Remove extra unnecessary newlines, even though this class will be going away soon.
new 7900ea5 Don't show missing required option warnings before giving help, and make those warnings fatal.
new 4f57d4b Added the diagonal gaussian distribution.
new 07e547b Missed all this stuff and broke the build. Adapt output to the new IO API.
new 83212c1 added tools, which currently only contains a function for efficiently removing rows from a matrix (creating a new matrix)
new 1046aa1 cleaned up LCC code, it seems to work now
new ed2e0b9 fixed CMakeLists.txt
new a24b0b9 fixed CMakeLists.txt
new 1537b59 made lcc main.cc concordant with fx_init; we now accept parameters
new 24e0bb5 added speed test to main.cc for tools
new 35ba398 switched call to lars to use cholesky
new 3f973be modified LARS to optionally accept Gram matrix as parameter
new 22d65b9 removed a debug printf
new 8d8c1b8 modified LARS init functions so that they allow reuse of memory that originally stores input data
new 2952b2c changed random initialization of dictionary to sample from unit normal rather than unit uniform
new 3dd1f8f
new aeca020
new cff0e3b cleaned up test for removerows
new 8a81c30 Compile with optimization when not in debug mode, and prune arbitrarily long line.
new df220e3 Don't overwrite CFLAGS and CXXFLAGS.
new 2d3804b Back to distributed nbody and adding OpenMP parallelism to finish all of it.
new 114786a Changed the function for grabbing subtrees so that the size is limited.
new 1303fff added mnist experiment executable for lcc
new eb0db8d More changes.
new be849d3
new 2dacee5
new 03ff13c moved existing lars implementation into old_lars, due to possible issues
new 0158394 added newly coded lars implementation
new 3b836c8 moved old lars implementation into isolated subdirectory
new d323c29 fixed some #defines and such in lars
new d6235b1 fixed include file name for main.cc
new cda8cd2 minor changes to mnist_main and some changes to lcc_impl.h to handle multiple iterations of the optimization algorithm
new 95b5ff6 added GetCoding function to lcc class, and created executable for testing synthesis quality of a dictionary
new abf4a51 forgot to add executable for testing synthesis quality; now it has been added!
new ee541d9
new 2fe24a3
new 28f646a Add contrib directory and the code I have used to learn a metric for AllkNN; I will be submitting the results to MLSP 2011.
new 4377c65
new 4dc024b
new 205122b OpenMP shared memory parallelism added to distributed GNP.
new 28e94ea Bug fixes.
new 1400208 Number of threads option added.
new 055af0e
new 9e48961 Bug fix in KDE. Still need to fix more.
new 1d7ed22 Bug fix in the dualtree_dfs_dev.h. Compute function needed to consider pairwise distance between query_start_node and reference_start_node.
new ff2d1d5
new 671b659
new 7a93163 Fixing mixed logit sampling problems. Still need to look at more.
new 6e3c312 Some optimizations for mixed logit.
new 6f6d88b Default option is now bfgs.
new 3e740ed Optimizing.
new 623ab0f
new 8bebd9c
new 73bf98d changed lcc implementation so that DoLCC does a final OptimizeCode step so that, at termination, we have a learned dictionary and the correct coding to that dictionary
new dff313e Bug fix in diagonal gaussian.
new 765b482 Changes.
new d1efd4f Another bug in diagonal Gaussian fix.
new 90060a1 Some fixes.
new 1363f80 Dividing up code.
new 524e0e5
new 7fb5948
new 20ca375
new ff798ed
new 2d1cb7d Specialized so that the integration samples are always 0 for multinomial logit case.
new 57132ce Some fixes.
new 26af859
new 66097fb Getting there.
new 421845c Getting there.
new 6d6524e
new 2507b28
new 10a4498 Some changes.
new a691517 Now reports the maximum number of integration samples in use.
new a3694ab
new 675c249
new c290e56
new 4093852
new 4a009b8
new def18f8
new f48b105
new 7bb7f34
new b161afa
new 92d598a
new c2f9433
new 0e8d4d5
new e882797
new 9190a44 small changes to mnist_main and changed local_impl.h so that it correctly outputs percentage sparsity (forgot to multiply by 100 (!))
new e39006e Compilation error, ptrdiff_t not defined, add #include <cstddef>
new 3db7556 Found another ptrdiff_t problem, added #include <cstddef>
new e99fa92 Turn sparse off by default (because it doesn't work). Require optimizers for MVU.
new b184b84 const IO::IO& other didn't compile with g++ 4.6
new 8f9328e Putting back in the gradient error computation by formula.
new 175cccc added executable for discriminative LCC for MNIST
new a0a5ce5 fixed bug in ProjectW
new 932d758 added code for Pegasos algorithm. have not yet implemented mini-batch version
new b857d7a changed list of bugs. now there are no known bugs
new c2a4645 added pegasos to CMakeLists.txt of niche
new fca4938 Transitioning.
new 2e16352 Added the function to return the set of sample mean variances in meanvariancepairmatrix object.
new baac055 added mini-batch to pegasos
new 8fd1ccc changed mnist executable to use pegasos
new 5f42151 Limits the integration samples per person.
new 534231e Revert r7929, which I think was an accident.
new 0d60962 Commit the change that I think r7929 was supposed to be: fix compatibility with gcc 4.6.
new 4beb572
new 1fde152
new 4c80d0a
new 628bfa4 branches/fastlib-stl: fix #63; remove several warnings
new 9fd5332 branches/fastlib-stl: undo the insertion of Wall until I can address the additional warnings
new 3d34ec1
new 95782e5 Getting there.
new 9e02dbf Updates the approximate Hessian in every iteration.
new 4cfa425 Compile error fix on no.
new 75af52f
new bb39850 Adding weighted Lmetric.
new b9ec109 Trying to revive the kde crossvalidator.
new 5bb41bb
new 1054663
new a8571fd
new 6c81d54
new 97221c9
new c1f1d92 Starting local regression.
new 4458195
new 9223147 Update distance learning code; more documentation on parameters and use FDSA for gradient estimate. I could probably use to clean it up a little more but I'll postpone that until after the paper deadline...
new e1a0845 Add support for 64-bit types (u64, s64) to our little Armadillo extension collection until it gets integrated into Armadillo itself.
new b3dcf8e Add arma_extend.h to fastlib.h so that a user does not have to try to include it themselves.
new c569999
new d4c864d
new bd8a5db
new f476493 Added formatted comments, will add them to cc files after unit tests are finised and correct.
new 1200089
new 1307af9
new 3db9b5f
new aa94ab0
new ef9677c
new 941b668 Unbreaking the build server.
new fcb239b
new e249822 added function to discr_sparse_coding to set w, and changed mnist_dlcc_main to compute svm loss via a function
new 240bba9 changed frequency of iteration number output
new 2d5a2df uncommented projection step
new e34fd37
new 49b89e9
new e4cdbab
new 860f8f8
new 42f3c33 changed prototype for LCC::SetDictionary so that passed in mat is const&
new 7b351fb changed mnist_main to allow specification of initial dictionary
new d7eb455
new 4a24d97 switched two usages of fx_param_int_req to fx_param_double_req since the latter allows the use of scientific notation
new 5321924 switched a few usages of fx_param_int_req to fx_param_double_req since the latter allows the use of scientific notation
new 71bbfbe fixed a horrendously inefficient minibatch implementation. now the cardinality-k-index-set sampler (sampling without replacement) is very efficient
new 68e9c43 changed neighbor_counts to uvec
new bdf0169
new 8e36527 A little fix in the distributed dualtree to maintain one computation frontier per each MPI process.
new 726a868 New local regression in progress.
new e65d920 Filling out the dualtree stub for local regression.
new 273cbb6 changed display of loss in mnist_dlcc_main, now store loss results via fx_result, and slight tweak to SGD learning rate
new be1103c Fixing local regression.
new e40072c Fixing local regression part 2.
new 0e21ce6 Additional argument to the mixed logit code for deciding how to compute the errors.
new ae4c47e Moved the serialization of arma::vec to core::table. Added the serialization of arma::mat.
new f611272 More stubs filled out for local regression.
new 872c337 More.
new 22165dd Finished unit tests, finishing up documentation in the cc files, general cleaning up. Will come up with a few more unit tests (negatives, etc).
new ac91fb1
new dbbfe06 Compile error fix.
new 4b0e5ca
new 4868850
new 8205e59 Did some more cleaning. Working on making output streams more robust. Tried template specialization + helper class but that's not really going to work it seems without overloading for every conceivable type. Will try extending ostream next time, that should help with the excessive overloads.
new e025bb2 Will be back.
new 36e58be Compile fix.
new 7004f92 More.
new 2321ff1
new a70a4fd It's not used, it's bulky, useless, and bloatful. DELETE
new 224eeb6 Their eyes were bright and optimistic as they implemented a complex parallelized n-body problem solving library, but as the years passed, optimism faded away and free time disintegrated. Slowly, the code became untouched, and slowly, the original maintainers passed on into the next world and the knowledge of the lofty goals they once held faded into nothing. Now, in the present, we have an artifact of the past; a piece of history. But without the knowledge of how [...]
new dc67f20 We don't need a ComplexVector class; we can use Armadillo just fine for that.
new f5e6b1b Don't include the file we deleted...
new 30daccc Don't include a file we deleted...
new 740fd19 #17: remove horrifying object traversal library.
new 4b867a2 #17: Remove object traversal madness from base FASTLIB classes where necessary.
new cb231a3 #17: Remove object traversal madness from MLPACK methods.
new 17c0a7d #17: Remove object traversal madness from something on contrib/ which something in mlpack/ depends on.
new 773f28d Clean up includes for NBC
new ef19fab Remove last references to object traversal.
new 5a15071
new 5b773a7
new f9e739d Remove ccmem.h and ccmem.cc. No more mem::. Glory ensues.
new 3105f1a Remove RangeSet, DenseIntMap, and fast allocation routines. They were not used anywhere.
new d6c45e5 Nothing in par/ is used anymore (with THOR gone). Remove it.
new 30e064c Update header files for removal of par/.
new 4e5c32f I don't know why this test was never included. Anyways, it works fine.
new c85a0a2 Continuing tomorrow.
new 4cba48a Minor useless change to see if Doxygen is being regenerated on commits.
new cdc42a9 Another useless checkin for testing Doxygen regeneration.
new 6d5aa8b Update includes, do not use fastlib_int.h.
new 3380fde Don't use fastlib_int.h.
new e4244a1 Will be back after lunch.
new 0120ca4 Remove fastlib_int.h.
new 499618f Remove deprecated.h (hey, it's all deprecated, right?) and an unused macro or two in compiler.h. Update CMakeLists.txt accordingly.
new 09620d3 branches: fastlib-stl: fix #70 (for now, with hopefully minimal damage...)
new 0b821bf Always make sure you are properly fed when you code. Otherwise, you risk writing ridiculously simple memory management errors. Bonus: the textfile_test still passed like this. Anyways, it's all going away soon...
new 92741b8 branches: fastlib-stl: commit a few space changes and function replacements
new a8edb7c Compiles, but need to make another pass.
new f315bd2
new 76c0aa4
new 8d6910d
new 765d5aa Compiles finally, but still debugging.
new eaf2a59
new 882bcf4
new b11d344
new ea354ab
new 27b9913
new 47f2eb9
new ff4bbf5 Fixed the parser for local regression.
new 334ce37
new 66bc687
new a10a7a3 Segfault fix.
new ac0bd35
new 729b635 Some bug fixes, getting local regression to work.
new c9a1641
new 09ca001 Switched the initialization order of query tree and reference tree.
new c55e1d2 More fixes.
new a1bd1d7 Dualtree modification for query result initialization.
new bafe80e modification for query result initialization.
new 8ac9736 changed discr_sparse_coding files to fully implement discriminative sparse coding, but not discriminative LCC. previously, we mistakenly had implemented some weird nonsensical hybrid between the 2!
new 78cbfd8 added test files for dlcc
new ed97501 added everything for sparse coding
new 27ac11e added sparse_coding to CMakeLists.txt
new 9df3123 changed InitDictionary(filename) so that it accepts fullpath of dictionary and does not assume some directory exists
new eb18614 added mnist lcc test files
new 7b622a1 Prints out the number of dimensions parsed.
new 3789b75 Adding the test mode for mixed logit.
new 33c220b Mixed logit adding the test mode.
new 864bdad Implemented output to specifications. (Re)implemented debug output/null output in similar manner.
new 20cdca0 Fixed that bug.. gotta watch those references.
new 1a73888 Slowly adding in the test mode.
new 6ee7a1e Compile error fix.
new 57efceb Modification to the dualtree generator.
new 05fca4b Modification to the local regression so that it computes the final regression estimate.
new 31bb4a9 Mixed logit test compile fix.
new c2db95e Writing the local regression results to the file.
new 1d409ec CombineWith function MeanVariancePair is fixed such that if the incoming pair is empty, then it returns.
new 8afbc67 More edits to local regression.
new c38a7bc Added the method for downdating the Monte Carlo sampling.
new e3a3289 Changed so that coordinates are non-negative for local regression.
new 1c18a60 Nonnegative transform added.
new 57e21d2
new a728215
new 6807d03 Adding the Monte Carlo test.
new 606767a
new 809a06f
new 0f8d1a2 Local regression being fixed.
new 733c4a2
new bf1ca98 I think it work finite difference-wise.
new b004e06 Adding the NWR mode for local regression.
new 3b0092c
new 902c830 Modification to dual-tree generator to support NWR.
new dd4f3a2 NWR should work now.
new f82034b Bug fix in local regression post-process.
new 840bb78
new 33d0d41 Bug fix in local regression. Still debugging.
new b078364 Ready to test NWR.
new 7a970b5 Table class changes to add method for returning point weight.
new ab9c875 Adding the local regression test.
new 29b83a4 Local regression test added.
new 6e8c916 There is a bug in the table which needs to shuffle the weights as the points as the tree building is done. Will fix now.
new 8d7586c
new 31d4a55 Fixed the tree building to shuffle the weights as well.
new 43816c7 Fixed the local regression test.
new 3a7a103 Trying to pass the local regression test.
new bbc459a Bug fixes in local regression. Gaussian case works now, have to fix for Epan Kernel.
new 72cec76 Fixing the pruning rule for monochromatic case, then moving onto Monte Carlo version of the algorithm.
new 3f06f61 Getting there.
new 1a40bf3 Local regression fixed, now plugging in Monte Carlo.
new 1b4c1f9
new 63db5db
new 0140a48
new 29434b4 Weighted metric added for local regression.
new d6544ae Extensions for weighted metric.
new ac601bb Fix.
new 3ae31ba
new 3b89920
new a281b30
new c913d1a
new 5b2fc68
new 32f76c8
new 2584d9b
new e578195 added multi bandwidth to main
new 4728c50
new d9e254e
new c1b3626
new 1b42771
new 70961d5
new 4e2ec66
new f67df12
new d55649f branches: fastlib-stl: attempt to fix #72
new 4bf30fc Half-solution for when __COUNTER__ does not exist.
new 7840a73 Fix to uninitialized values.
new 6e98c71 Fix a minor spelling issue and add a comment noting why we don't have to worry about platform-independent newline characters (because I spent a while making sure we didn't have to).
new d7b6d44 Fix warnings about non-virtual destructors (which didn't actually make a difference in this case). I think these classes may be going away soon though.
new eac510d Make FATAL output stream actually cause the program to die. Update test to arbitrarily die too.
new dc36646 Oops, this isn't included by default.
new 9913415 Half-revert r8133 to use __USE_ISOC99; update CMakeLists.txt to issue -std=c99 in all compile modes. This should fix #72. If it is fixed, we should fully revert r8133 since it wasn't necessary.
new 837bdee
new ec83228
new 7eee59d
new f044e05 nonnegative transform only translates form negative mins.
new e2fe875 Trying to fix local linear bug.
new 5f86cec Local linear bug fixed for fixed bandwidth. Works perfectly, but still need to add Monte Carlo in a clean way.
new dc20999
new 9978b70 Broke the files into smaller pieces for local regression.
new 0b87dfe
new 2db2b1b
new 5777bdf
new bc271f1
new f873aeb
new 53d622e Broke kde into several parts.
new aea099d
new 9755a0b
new 68ee994 Use IO output instead of NOTIFY and related macros.
new aebdc8a Allow PARAM macros to accept default values.
new d1c91fc
new 37bee93
new 6d1d5ce
new 0c4cdbd
new 7a91e8b Add io.h to default include
new e17bd53
new 2d0788c
new bf502bf Set up CMake to use Boost.Test
new 964be4d Change allknn_test to use Boost unit test framework. It works.
new 8b2b64e
new aa74043
new 3e1104f --Converting fx-style output to IO output
new 3d29a35 Pluggin in Monte Carlo for local regression.
new 43be69d Restoring CMakeLists.txt
new dc32929 Revert changes by nkauffman3 to unbreak build
new 5112976 Resolved ticket #75 by retyping leaf_size and 'k' as ints. Modified io unit tests to fatally fail when a required option is undefined, a bit more useful than arbitrarily failing.
new 9261552 Testing class no longer exists, and fix some formatting issues
new c339a46 branches: fastlib-stl: remove some unnecessary whitespace
new 280d6fe Although the C++ reference site gives all these functions as taking a reference, this is not the libc implementation and this is changed to match. The penalty paid by passing objects and not references is trivial in all these cases anyway (and in many it is no penalty at all).
new 2270bdb Removed unused code. Refactored some methods in IO. Fixed allnn into convention compliance. Minor changes to IO unit tests.
new 35b184e Add operator<< support for armadillo objects when using IO output components.
new 52d7e4b branches: fastlib-stl: eliminate a few new warnings
new e1138de Began implementing IO in mlpack's emst and fastica methods. So far, no compilation erros. Currently ensuring I didn't break them in some more subtle way.
new 9302d46 Rewrite armadillo output functions just a little more to correctly utilize the IO output.
new e245759 Sanity check on input parameters.
new 0d24189 Rewrite help output formatting for IO. We needed a helper function to hyphenate (or just split on spaces) so it all looks nice.
new 1699309 Fix odd formatting issues in io.h
new 908d9c4 Add PROGRAM_INFO() macro (and related support, including ProgramDoc class) to allow simple documentation of programs, to be displayed at the top of the help message.
new 4f0bea8 Derpy derpy derp derp hurrrr
new 2194569 Change BOOL to FLAG. Clean up output a little bit more -- sort the types of options.
new bc07731 Change BOOL to FLAG
new 7082951 Update from BOOL to FLAG and remove default parameter.
new 0e98474 Remove default parameter for flags (it is always false).
new 0fdeaa2 Almost done adding sampling for local regression (Gaussian kernel).
new 028b348 Fixed the monochromatic case for KDE, now back to local regression Monte Carlo.
new 5b930a7 Bug fix in distributed kde test.
new 679e19b Getting there in finishing up sampling based local regression.
new 1dae219 Will debug later. Almost done with Monte Carlo sampling in local regression.
new 6b19cd1 Almost done with Monte Carlo local regression.
new 156a06c Getting there. Should be ready to run the mega-scale experiments in a month.
new c5e8e46 Fixing the compile errors.
new 0591c3c Fixed the compile error for local regression, now just have to debug/verify.
new 6564995 Starting the CUDA version of KDE.
new 8c59280
new 867f006
new 720df6e rewrote perm_free node list updates, starting on multi bandwidth reimplementation
new 0efc45a CUDA fix.
new 6dd1f7d Allow newline characters in hyphenatable strings.
new 8553d0f Update program documentation.
new 19d48bb Replaced FX with IO in HMM, Kalman, and Infomax today. Worked on some IO stuff, which will require more thought.
new 2de86a6 Modified PrefixedOutputStream's behoviour (sp?).
new b3291ff Adding the CUDA kde driver, now starting naive CUDA kde.
new 4338fa6 Convert L-BFGS optimizer to use IO-style output. Also change test to use Boost.Test framework (and update CMake configuration accordingly).
new e07368e Update AugLagrangian to use IO-style output and use Boost.Test framework. Update CMake configuration accordingly.
new d9b2b7f Add IODeleter class to ensure that the singleton actually gets destroyed someday and that the memory doesn't leak. Using this, we can display all the passed options and timer information using the destructor of IO (this is what the --verbose option is for).
new b7c08b6 Remove Printing classes because they are no longer necessary (see changes in OptionsHierarchy::PrintNode()). Now, when --verbose is specified, the program will print all of the execution parameters at exit (using the IODeleter functionality). I am not sure entirely how this will work with timers yet.
new fb1adb7 Fix includes for PrefixedOutStream and NullOutStream.
new 800d690 Fix more includes for IO; remove some unnecessary includes from io.cc (since they are already in io.h)
new 707a948 Reintroduce needed TYPENAME() macro.
new 183629b Update AllkFN test to use Boost Unit Testing Framework. Also switch to IO timers since FX timers seemed to segfault and it wasn't worth investigation since they need to be switched anyway...
new a955692 Finally linking CUDA, but still in progress for naive GPU KDE.
new c064f9c I will continue tomorrow.
new f55dee8 Now running local regression to verify Monte Carlo.
new 72d0cd2 Compile error fix.
new 5d09e08 Added the probability argument for local regression.
new 9f5782d Debugging Monte Carlo sampling in local regression.
new 2c3abea Monte Carlo seems to work.
new 0058f93 Almost done setting up CUDA kde.
new dd5dcb4 Write exhaustive check which provides a lot more coverage of the functionality of AllkNN than the other three tests do.
new bba9eab Make same optimization change for single mode optimization -- don't use std::vector<std::pair<double, index_t> > to keep track of neighbor lists. Refactored the optimized form into its own method, InsertNeighbor(), which is now used by both the dual-tree and single-tree recursion.
new 8eec562
new 5b937eb Comment recursion a little better; fix bug for corner case where the number of points is not a factor of 10 (pass ind instead of i to the recursion point number).
new 7646b6c CUDA kde almost done.
new 3b42d67
new 0e493fa
new 241bf11 I will test on the GPU now.
new d728f1a Getting there.
new 8a325bb Fixing the CUDA KDE.
new a16a35f branches: fastlib-stl: remove Dataset and Matrix dependencies in nnsvm
new b7821e9 branches: fastlib-stl: mlpack: nnsvm: reorganize the code slightly
new cacfe80 branches: fastlib-stl: mlpack: nnsvm: adjust some spacing
new 5be642a Bug fix in CUDA kde.
new fd4e947 Debugging.
new 8e6b6c2 Debugging CUDA again.
new 568f777 Getting there.
new 67fd5c3
new f845438
new 0e2957a
new 5354a19 CUDA KDE works.
new d30a047 Bumped up to 512 threads for CUDA kde.
new c5db902
new 129a081 I sat down to make a SetParam() method until I stupidly realized that GetValue() supports this functionality. Made a note of it in the documentation for the non-clueful (like me today).
new ae35b9b
new 12690a9
new 34d4c2b Uncommit another repository from within this repository
new 9078c7c Relaxed the pruning rule for NWR.
new 3b160cf --Convert FX Style Output to IO Output
new 4ece24d Adding the distributed local regression driver.
new b38999b Undo r8255 since the changes to IO-style output were already done for these two classes.
new 26b0542
new a6fdc92 Bug fix in distributed tree in progress. One more bug to fix there.
new 8b979db Resolved a bunch of tickets. Renamed GetValue and CheckValue to HasParam and GetParam. Also modified the behavior for flags.
new 679475b Possible race condition in distributed tree building. Barrier before refreshing the number of points.
new 4959642 Fix in the distributed tree building. Should return false when failing to split points.
new eb7fca8 Distributed tree building should work more or less.
new 3087a44 Went through all the files in kde and replaced fx with IO. I will need to go though them again and make sure the default values are all set accordingly, as this code has several default values for any given input.
new 174f304 --Convert FX Style Output to IO Output
new 1018104
new bcf6c90
new fb9d54f Added the multi-threaded tree building. Now onto GPU-based tree building.
new c5dd5d2 Fixed omp for to omp parallel for.
new 01f3cc1 Distributed local regression compiles now.
new 2328bf6 Warning fixes.
new b221811 More warning fixes.
new 3860334 More warnings.
new 0f2ac2d More warning fixes.
new 40c5b72
new 23c3ca8
new 0e4d512
new 3575be5 Unmerge svn repo-in-repo, 2nd time.
new 1ee427c
new 8183b4d
new c9bb3f3
new 1410620
new 5a87c83
new 48010a1 Finished cleaning up KDE. Apparently KDE is not currently part of the build process; Attempting to compile a pre-IO KDE resulted in build errors.
new 832e6f4
new 886b775 Multithreaded tree building enhanced.
new 57d7e41 Testing the distributed local regression.
new 00b583f Compile error fix.
new a40922b Another fix.
new 3c5ac79 Fixing the subtable test to compile.
new e35b926 Entirely refactor AllkNN into templated NeighborSearch class. This allows separate distance metrics (or kernel functions) as well as sorting policies, so both AllkNN and AllkFN can be instantiations of the NeighborSearch class (as well as many other similar calculations).
new 5911029 Add core/kernels directory to start work on #78. Only one kernel for now (L2SquaredMetric, which maybe will be renamed), but it's a start.
new 6fe51d8 Don't compile mvu; it is not necessary for now (but it is under development and not yet checked in). Remove allknn and add neighbor_search and core.
new 52a5b6a Update instantiations of AllkNN to reflect constructor changes.
new 9bf3b96
new 1b502ea wrote generic multi bandwidth code, still a few bugs, though
new 47ba73d AllkFN has not been transitioned to NeighborSearch yet.
new 77bbefa Debugging distributed local regression.
new f25ffa1
new 8b6fc66 [svn-inject] Creating jenkins/tags/ directory.
new 346070a Creating trunk directory
new 0a6b8bd [svn-inject] Applying Debian modifications (1.415) to trunk
new f94b207 update jenkins package rule get-orig-source to put the tarball in the tarballs folder if it exists
new 9c04d01 original source tarball for packaging jenkins
new e81ed92 comment out unused file installation
new ce74b69 Oops, I made an unstable test (fixed).
new 3388910 added better output, fixed bug in indexing
new 4ecc4c6 Ultranaive for local regression factored out.
new 95d96db Re-factoring the test driver for kde/distributed_kde.
new ab1f120 svn-bp:origDir property allows svn-buildpackage to figure out where the original source tarball is found
new 5039d4e Bug fix in multi-threaded tree building.
new 0148b94 Multithreaded tree-building fixed.
new 7145739 Need to fix distributed local regression, then back to CUDA.
new 54f1c82
new 34a2df6 [svn-inject] Creating armadillo/tags/ directory.
new d339a9e Creating trunk directory
new 1243d46 [svn-inject] Applying Debian modifications (1.2.0+dfsg-0ubuntu1) to trunk
new 7f23954 Fix in the distributed local regression.
new 2a768eb Distributed local regression test runs, but does not pass yet.
new e3d2507 Duplicate option in distributed local regression cut.
new 1285625
new fab884e Fix dmangle to properly convert the local version of the package to the upstream version format
new 53d4f01 Remove allkfn because it is now a part of the neighbor_search class.
new b8d3243 Expand NearestNeighborSort SortPolicy class so that the NeighborSearch class is fully transitioned from nearest neighbors to anything-neighbors.
new 7bad0ff Transition AllkFN to NeighborSearch, adding FurthestNeighborSort policy class so it works correctly.
new 8052bcb Convenience typedefs for AllkFN and AllkNN.
new 83bdc98 Update CMake configuration to remove allknn, allkfn, and allnn, using now NeighborSearch instead. Add AllkFN executable and test to NeighborSearch CMake configuration.
new 84599a4 AllNN is no longer necessary; it is simply AllkNN with k = 1.
new b0a4117 Clean up code, adding some comments, and make names of variables truly agnostic with respect to the sorting policy. Make the QueryStat class a lot simpler than it was.
new 6ec4128 Update README for debian packageing to reflect the correct way to call svn-inject for this repository and add a note about how to make obtaining the original source tarball easy.
new af0ac66 Add exhaustive test for AllkFN. A lot of code duplication...
new c813095 Distributed local regression test still does not pass yet.
new da549dc
new a2bccfc Distributed local regression test passes now.
new d35c8c4 Add tests for sort policy.
new 1a1b79b ifdef added for OpenMP.
new 0f905f5 Fix.
new 886fb6a Fix.
new 916938a Integrated IO for the remaining parts of mlpack. Will go through and make sure nothing's been missed.
new ad6d5dc Glaring typo fixed
new 7078769 Move LMetric class to kernels to replace L2SquaredMetric with something more flexible. Update CMakeLists.
new 5d910b9 Add test for kernels and remove L2SquaredMetric
new f5eb603 Update tree code to use LMetric which is now in mlpack/core/kernels/.
new f075254 Change from L2SquaredMetric to SquaredEuclideanDistance.
new 67cec88 Update from old LMetric class to new one in mlpack/core/kernels/.
new 7445cf8 runTestBins.sh runs all the test binaries, finds boost test results, then renames those results for jenkins to pick up for test result reporting.
new b55f4a0 Boost anycast error fixed for dist local regression.
new 3e5b217 Fix.
new 837ebb1
new 6c91b0b Fix.
new 1a5ce19 Fix to the subtree size so that more cores are utilized.
new 948bcd1 Change so that multi-threading assigns a unique core to each query subtree.
new 6f6a7bd Fix so that division by zero does not happen in NWR.
new fac3342 Fixing the distributed tests.
new 804003a
new 51d1f62 Add MahalanobisDistance kernel and corresponding tests to make sure it works. I am not sure I am happy with its speed (it is not incredibly fast) but it does provide convenience.
new 1414ffd
new 8a244b5 MinHeap? More like MinDELETED BECAUSE NOBODY CARES
new 12d64e1 What is this crap and why is it here? This is not the place for it...
new 83c710f fixed bugs in the multi bandwidth version, writing new I/O
new e7f93f3 Remove svn-buildpackage artifacts mistakenly committed to the repository
new af3a50e making the constructors uniform
new d496cc7
new d7a8087 Undo r8363...
new aa5ac1c --Trivial Remove Copyright Notices - ticket 84
new 922c465 Update watch file to use new jenkins war file packaging script
new 9176d0e
new f0066c2
new 95e6f27 Modified jenkins package changelog to reflect our packaging situation
new e55fcec update maintianer address in control file to comply with debian standards
new 65b26de update maintianer address in control file to comply with debian standards
new df0917e --Ticket 85 -- Convert tests to Boost Unit Test Framework
new 94724f8
new 57a0bf6 Starting the randomized range finder from Halko's paper.
new ba3efa3 Added matcher generator, passes basic tests
new ad06368 made sure that multi bandwidth computed results for the upper limit of the input as well
new e6b505f branches: fastlib-stl: remove a couple new warnings
new 8b211f2 Use explicit floats for older versions of Boost UTF
new 1034fc3 Fix error which only appeared on gcc < 4.3; the __COUNTER__ macro is not available before that. This appears on RHEL5 systems which use gcc 4.1.2. So, we need to redefine the PARAM_FLAG macro to call out to another macro which properly accounts for whether or not __COUNTER__ exists.
new c38884f Explicitly specify floating-point numbers for BOOST_REQUIRE_CLOSE().
new aadc929 Move parameter options around so conflicts don't occur when using gcc < 4.3 because the __LINE__ macro is all that can give us a unique identifier.
new 8cd1a5d
new 5b8d36e branches: fastlib-stl: mlpack: nnsvm: add initial testing support
new d292979 Finished adaptive randomized range finder, now have to test it.
new f8bd847 branches: fastlib-stl: nnsvm: commit the latest changes for RC to examine
new 0b3f3b5 Aha! Found it. This fixes the segfault.
new a5682f4 Add PARAM_DOUBLE macro just in case someone wants it over PARAM_FLOAT. Really, it doesn't make much of a difference which you use, but whatever.
new 7865502 Testing the random linear algebra stuffs.
new 8c0ecb9
new f247f07 -- convert to boost unit test
new af480f1 -- convert to boost framework
new 2acf68d
new 9c77e9e updated single bandwidth main
new 5f5e529
new d8b06fa Update jenkins packaging to more closely match upstream packaging
new a78eaba Halko's algorithm completed, now ready to plug into KPCA/GP.
new c09c7f7 Tagged from Package-Jenkins #27. Jenkins package is successfully being built but still has some lintian issues. Does not grab the plugins yet, nor does it automatically build a new package from a new upstream release yet.
new 0404468 rank-approximate NN files added to new branch
new 2668ee8 making appropriate changes (hopefully) to the CMakeLists
new 4337699 -- Convert to Boost Unit Test Framework
new 2521bf7 -- undo changes from last build
new f4fc093 --Conversion to Boost Unit Test Framework
new 0c93aca
new 3a55457 -- Try to unbreak build
new 32c1954 -- FX Conversion to Boost Unit Test
new 21e0a2b
new bb15311 --Conversion to Boost Unit Test
new 6510d55
new 12ce0bc -- Convert to Boost Unit Test FrameWork
new 82be325 -- Convert to Boost Unit Test Framework
new 233ff55 --Convert to Boost Unit Test Framework, Still Needs Macros Removed
new 71138ed To be continued tomorrow.
new 91b29b0 Randomized power iteration works.
new ef851aa wrapper script to convince jenkins not to mark the upstream source checking build as failed because there are no new upstream changes
new 35d85f1 forgot to make uscan-wrapper.sh executable
new e2b2ede
new 8c60829 SVN crapped out on me, rechecked out blah blah blah.
new 4790339 Don't include FX in weird contrib file which is included in MLPACK
new d86c2e2 IO test should not display output because this breaks the build server... commented out for now, but we will fix it for sure later.
new 91f9d44 Reverted change to io_test. I think I was killing the server by printing text during test. Oops.
new bb75f9f Fixed a bug, where options like '--help' and '--info' would be prefixed with the default path even though they are special.
new 25c53f9 Reverted part of IO's default modules logic.
new 37f6066 -- Conversion to Boost Unit Test
new 79ba3c4 -- Convert to Boost Unit Test Framework -- this might break build
new ba667d9
new 134875c Update test, which was incorrectly written to test Center() on matrices which were transposed (in our context). Anyways, that sentence doesn't really make sense, but it's fixed now.
new 0a57e96
new 3678041 Test.
new 69e0278
new c0fb4e4 Starting the GP regression driver.
new 6273861 Deciding on the final algorithm formulation for GPR.
new 454f8d4 Starting ADMM distributed optimizer for GPR.
new a57d69f updating files for dtree without updating the CMakeLists
new 51b7cde Implemented default modules, hidden Info except on verbose. Working on debuggable output streams.
new 6b20f41 I would like ten million output for debugging the build server please
new ce6aba7 branches: fastlib-stl: hide code that generates warnings
new 73d6f67 Revert r8434 because it introduced a bunch of errors and now I can't use IO the way I should be able to.
new 29e97ee Revert r8434
new 33de468 Strip non-XML compliant charachters from the test result files before xUnit pukes on it
new 85b2a7d Remove non-sed compliant option from the regex string
new 4a67552 Tweak script output to make determining Unstable build condition more reliable
new 07a3343 Replaced sed with more appropriate tr invocation
new ffdcf2e another fix for uscan-wrapper
new e494642 Fix assignment of delta_f in CalculateDF_(); it was using w_square_sum_, which was until that time uninitialized. This will solve the elusive build server error, which is only present on 32-bit systems. An uninitialized double has a much higher probability of being large on a 32-bit system than it does on a 64-bit system; so, the problem still existed on 64-bit systems, but the probability of it causing a failure was absolutely tiny.
new 65eb8c9 I am unsure about the validity of my changes, but fix small differences in the test output so the double comparisons are within margins.
new b27d9ef Add new methods/ directory, where we will move all the MLPACK methods to eventually. Also included is an implementation of Neighborhood Components Analysis. The formal test has not been written, but it is informally tested. Boost test is forthcoming...
new 7e044c5
new c98546b
new f25b5cf
new 6bc4de0 No more notification for debug builds using this mechanism.
new 73c0037 Have IO output information if the program was compiled with debugging symbols ...and fix a spelling error.
new 4eb51eb Add a few introductory tests for SoftmaxErrorFunction.
new c4c1bbf Make debug output only show if IO was used to parse the command line; this way, output is not given for Boost tests, which should be silent except for the Boost output.
new bcc9a22 Fix a few warnings I caused, and remove some unnecessary warning output (it doesn't need to be a warning because it's not really dangerous).
new aee519d Remove some IO warnings that aren't actually dangerous and fix some build warnings I caused.
new f61fa8a Add tests for the evaluation of the objective and gradient of already optimal datasets.
new b0ac6ab Add test for the NCA algorithm. Needs hand-calculation of optimal output matrix.
new 63674e2 Remove these files because they are not part of the L-BFGS optimizer. We may choose to add them later, but in that case it will be better to re-fork from Dongryel's implementation.
new 057f29f Transition the L-BFGS optimizer to use IO parameters. Now for things that use L-BFGS (like NCA for instance), we get documentation and configurability of the L-BFGS optimizer at the top level.
new d77522b Fix error in L-BFGS test. [] only takes one argument and will ignore the other...
new 3758e95 Clarify documentation slightly for the L-BFGS module.
new 10b783e Uh, I mean, don't break everything forever. How did I forget that...?
new 5809f25 branches: fastlib-stl: remove a couple constructor related warnings
new c9ff7c3
new 659fde5 Fix some grammar and spelling, make documentation wrap correctly for modules, and have it display [double] instead of [value] for parameters of type double.
new c77ec09 [auto-packager] updating packaging to reflect new upstream release
new 273cc10 -- Convert to Boost Unit Test Framework - Ticket 85
new a6aa309 We can't know the final optimal matrix because it is not necessarily unique, but we know the gradient norm should be close to 0.
new f61cc88 -- Convert to Boost Unit Test - Ticket 85
new 9bda9f5 Fix update made by buggy script
new 523df58 new automatick packaging updater script
new 5738a55 -- Convert to Boost Test Framework - Ticket 85
new ac18e1c [auto-packager] updating packaging to reflect new upstream release
new 45e6b99 Tagged from Package-Jenkins #33
new 89a9589 Fix some lintian complaints about the packaging
new f475c4d Warnings all the time for all build types
new c82e697 Fix unused variable warning
new 24c8a65 Symlinks? Really?
new 19a9119 Remove disk_allnn. It was never used, it will never be used, and it can be done in a smarter and better way.
new 97be867 --Convert to Boost Unit Test Framework -- Ticket 85
new 73d857a This simply isn't used anymore.
new 7a45f8d --Convert to Boost Unit Test Framework
new 0fdafae --Able to build, but running test case throws : run-time error: qr(): need LAPACK -- on my machine. Want to see if this fixes build (meaning i need to update lapack)
new a874d7f -- Undo infomax changes --- will redo tomorrow
new 9d73c7e --Undo changes for kernel pca -- will fix tomorrow
new 939a2c4 -- undo ridge regression changes -- will fix tomorrow
new 1802351
new ff0a19e Actually revert Noah's changes to ridge regression.
new 810aa5e Actuall revert Noah's changes to Kernel PCA.
new 82a2b60 Actually revert Noah's changes to Infomax ICA tests.
new 55cd362 Actually actually revert Noah's changes. I blame exhaustion.
new 2a1bd16 Write the NCA softmax error function in a more computationally friendly way.
new 761be1a --Convert to Boost Unit Test Framework, Ticket 85
new 9e7e5a1 --Convert to Boost Unit Test Framework -- Ticket 85
new 57ad3ca --Convert to Boost Unit Test Framework
new 446e3ad -- Convert to boost unit test framework
new cf5b6a1
new 80b8c84 Do not use these small CSV files; hardcode the values into the test program.
new e5d9f17
new 2bdfe2a script for generating the sloccount results
new d80e349 fix output file
new ef85fdd Fix compiler warnings by converting from fprintf()-based file I/O to iostreams-based file I/O.
new 09217b0
new 9b24f06
new cf2465b
new 1d4ad7b
new 8a4bc5a --Convert to Boost Unit Test Framework -- Ticket 85
new 3ea433c
new a7e0a8c
new a0e6ea5 Fix #91: newer versions of Armadillo require a different style of magic to correctly work with u64 and s64 types.
new 625a62e only run sloccount on the library, and not the contrib
new 25ecf9e remove line that was meant for testing only
new cebc684 new post commit hook to notify build server of repository commits
new bb6d209 fix report directory collisions
new 876bd05 removed deprecated fx stuff
new 4820f27 fixed PARAM info
new b445d1e auto-packager updated to use a secret file on the build server for subversion access
new 242f2dc remove debug lines
new 73af39b next rev for jenkins package
new ec636fb
new 5b83261 Tagged from Package-Jenkins #35
new f8097c6 added PARAM_FLAG() etc. to multi bandwidth main
new 227e792 Output doubles too
new 056afa9 Retool IO a little bit to allow the output of timers. This involved modifying PrefixedOutStream so that it would accept stream manipulators. That modification may make all of the specializations in prefixedoutstream.h unnecessary...
new 009737d Oh no. We cannot forget this space. It is very important. Otherwise, the user may get confused.
new e197557 fixed PARAM stuff
new 9522f4c g++ 4.6 wants #include <cstddef> when using things like ptrdiff_t
new e9c1acf Give convenient divisions of timers so users don't have to do the division themselves.
new b81b70b Don't use NOTIFY. Wow, that is a horribly written test, by the way.
new 29b3714 Don't use VERBOSE_MSG.
new ba44fda --Convert to Boost Unit Framework - Ticket 85. Code is causing issue with new test cases that do not use pointers.
new c7fe760 Let's try not leaking memory everywhere.
new 6190a1d --Convert to Boost unit Test Framework -- Ticket 85 - will remove test_infomax_ica.h in a sec
new fbd8a6d No more VERBOSE_MSG or VERBOSE_GOT_HERE or VERBOSE_WHATEVER. Transition to using IO where possible (although I just dumped some of the clearly debugging-only messages).
new 5c3f8a6 Remove NOTIFY_STAR, NOTIFY, VERBOSE_GOT_HERE, and VERBOSE_MSG.
new 56fcbc9 Don't use NONFATAL or FATAL.
new d79a548 Remove some odd code...
new 299d05e Stop using NONFATAL and FATAL.
new 84835da Don't include base/test.h.
new e225898 Don't include base/test.h. And remove base/test.h.
new 32cbad7 Remove uses of DEBUG_WARN and DEBUG_ERROR macros.
new a809ce7 Specify mlpack namespace
new 706d8ad
new 46cac0d
new d81a0b2 increased script robustness
new db769eb fix authentication problem, i hope; it worked fine on my machine.
new fd2e3b0 fix issues with interactive prompting in a non-interactive script
new ab79561 fix another issue with interactive prompting in a non-interactive script
new 20334c7 fix typo that broke the script
new a464de7 Only try to add new things to the hierarchy if they are timers. This helps the documentation not get overwritten...
new 399222c Sometimes splitpos gets higher than the length of the string, and we don't want to add a newline in that case.
new 7ca4188 Fixed a potential bug where documentation would be overwritten at runtime.
new 6376d65 Add a little bit of documentation.
new 192ae70
new d7b3bc2 Adding in sender-initiated asynchronous distributed GNP engine.
new 372fa15 don't fail out of svn-upgrade ust because it can't perform its own _svn up_, because the script just did that
new 1855440
new ad7c0ac
new 7a5fdbe
new d91e93d
new d8978e0
new ed30b44
new 7ff2916
new 3c0d2ec
new 7b977b8
new 37367b0
new 72bdf08
new feded43 More.
new 6bc541b
new d697425 Add some notes and changes, functionality does not change but I can debug from another machine
new b68e0ce
new dd7d04d --FX Convert to Boost Framework - Ticket 85
new 75b976e --Convert to boost unit test framework - ticket 85
new e49085d --convert to boost unit test framework -- ticket 85
new f5a23a3 --convert to boost unit test - ticket 85
new e619af2 --convert to boost unit test -- ticket 85
new 30196f8 --convert to boost unit test framework -- ticket 85
new 56a4763
new 6fc05cf
new b9bb097
new 0d7d497
new f86fe04
new 055e543
new f354512
new c0a5f8e
new d7988f7
new 5ee5f14
new fc20ce0
new be5c796
new 03320c2
new cfd849d
new e2c66bf
new 7663a5f
new 4bf4828
new 776eb2e
new c3057f4
new 23a0e0c
new 2247a6c
new a5304f9
new 9f1f03c
new 2b7c032
new 1f4cb3c
new 6c8b3c9
new 9ec2c07 convert to uscan/sed/awk/dch instead of using svn-upgrade
new 02de01a make the rquired directory if it doesnt't exist
new 54563f5 add forgotten $ symbol
new be01610 fix build hang when calling dch
new 200198f allow auto-packager to update the repo, now that it appears to work
new a294f1a [auto-packager] updating packaging to reflect new upstream release
new 43c8d5c Tagged from Package-Jenkins #47
new ba4dbea
new a28fea3 N-body engine now uses asynchronous communication so that computation can be overlapped better.
new cbeeff0 Moved distributed engines to core/parallel.
new a7e8711 Now have to fix the load-balancing issue, and done with 2-body distributed GNP.
new 3b5c8ef
new e3471ec [auto-packager] updating packaging to reflect new upstream release
new 8a087d8
new 2c601d5
new dc1e169
new a6cd97c Tagged from Package-Jenkins #48
new 7b0d30a Need to fix the load balancing issue.
new 2805a1b Bug fix which resulted in non-termination when extrinsic prune occurred using the global tree.
new 482a359 Tagged from Package-Armadillo-stable #10
new 04dffb2 Update to upstream version 2.0.2
new 283ee37
new 26eeb63 Adding the dual-tree load balancer.h
new bc2d50c Compile error fix.
new f716f3f Parallel METIS cmake finder.
new caa17f5
new 0e762a1
new 2c2d44c ParMETIS works, now have to use that to do load-balancing.
new 9b5860e Fixed some missing IO parameters for SVM and incorrect types. Created a unit test - svm_test - tests svm_c with linear & gaussian kernels. svm_r seems to loop until n_iter when it shouldn't, so the unit test has the verify() call commented out for those and n_iter is set to 10000.
new 5226eb9
new ca543ad ParMETIS edge weights are always positive integers.
new fcc9af3 It helps to attach the new file..highlight.
new f2466e8 Actually use the DATA_DIR after making it
new dc6ae16 --Convert to Boost Unit Test Framework - Ticket 85
new 5d58760
new 31184a3
new 836d895 Giving up on ParMETIS since it segfaults, doing naive load-balancing.
new a8f9d81 Limit to 10k iterations as opposed to 10M for the test.
new 0f4e904 Force lambda to be updated immediately at the end of the first L-BFGS optimization.
new e133109 The code is incapable of running the first test, so comment it out entirely. The second test fails anyway.
new fe9b6ac Naive load balancing.
new 33b7fe1 Slowly transitioning to the load-balancing scheme.
new 9665bc6 Don't use external files for the test. And clean up some odd formatting...
new f136ff0 Copy ARFF files to correct place for Naive Bayes tests.
new dfd093e
new 237922c
new fea8843
new ce558b2 Bug fixes.
new 2b2ed87 Ditching the static load balancing and implementing the receiver-initiated load balancing.
new fa1849f MPI timer measured for each MPI process.
new cee13ca Slowly transitioning to the receive oriented load balancing scheme.
new 4338f56 Eliminated useless variable from TableExchange.
new 7199068 Adding new messages.
new cd9681f New file.
new 11f90e5 Slowly getting to a smarter communication pattern.
new 11486bf Compiler warning fix.
new 70ec3c7 Adding a new file for distributed local task list for better organization.
new 72547b4
new e840b5f
new d0de30e
new 2ed811a Now need to plug back in the distributed termination and work stealing among the cores.
new c025363 Renamed the Task to TaskQueue, now adding Task class.
new 7df8ea5 Slowly making changes to load-balancing.
new e06c268 --Convert to boost unit test framework, ticket 85; replace reserve with resize()
new 9084e9e
new dfd3717 --Convert to Boost Unit Test Framework, Ticket 85
new 3308087 Adding the task stealing among cores.
new 59286ef [auto-packager] updating packaging to reflect new upstream release
new aa9fe13 Multicore work stealing should be working.
new 7075288 Some fixes.
new 3aff1f8 Getting there.
new 9ea3ce4 Memory leak fix.
new 4c904ae There seems to be a deadlock, need to fix in the subtree split part.
new 9847d98 Fixing the monochromatic problem.
new 97f91ed Another possible bug fix where splitting was requested whenever it hits a subtree that is locked.
new e9f4838 OMP critical added.
new 759d12d Some fix. Still debuggin.
new 60af244
new 9437f3f Moving the termination check.
new 64aeb29
new f46919f
new bfb6943 Should fix the deadlock.
new aedc15f All fixed, now moving onto load-balancing.
new 472b0c5
new e840930 Starting the routing algorithm for distributed dualtree.
new 8b48c92 Starting the e-cube routing algorithm.
new 37fd218 Now have to change the termination condition.
new 0c73173 Implementing the routing.
new b3d7b0c
new 1d8cd14
new 0509a0c added support for DDR-type counts
new 62d3e7e
new 81428fa Transitioning.
new 31963fe Fix.
new 218f2e6 The changes should have fixed the monochromatic problem.
new 5fc8ea3 started implementation of specialized case, wrote most of algorithm class, wrote point tuple comparison for matcher
new f5f3a81
new cbfa800
new f92f98b
new d6f5848
new e1c7643
new a3f347a Adding the random seed option.
new c8fd0a3
new 936028c
new d185878
new 6864fdf
new 1208fe1
new f3ea981
new 0b39b3d
new 3a1dfa7
new 83a2437
new 1bc98bb finished up angle implementation
new 30d51d5
new 3e500fa
new b597300
new c570a51
new 439f8f5
new f7fea73
new 422ff12 [auto-packager] updating packaging to reflect new upstream release
new 5f34aa8 Tagged from Package-Jenkins #50
new 6f02f8e Fixed so that the rank is fixed after distributed tree building.
new 6f97bcb
new e9b2909 Fixing the subtable test to compile.
new 8f28e38 Taking out parmetis.
new 2043bef
new 6b074db Fixed the subtable serialization bug, where the loaded subtable is saved and loaded again, did not result in a valid subtable.
new 681c0a6 Renaming files.
new 77ed071 Remove.
new a524563 Fixed so that it uses recursive doubling, now need to fix TableExchange.
new 48f0017
new b2c21c1
new 4f37a06
new 14bb4b3 Recursive doubling scheme started.
new 6c52b96
new ab1718a
new 9b73ab4
new 21cf569
new adf3680 Added a method to test the ID of a subtable.
new da17e0c Renaming.
new 9e7993c Renaming.
new 7957e0f Cmake change.
new c133384 Compile fix, transitioning to recursive doubling scheme.
new 754cc1b Compile fixes.
new 83c72c3
new 1a1002e
new c9e93f3
new c13f5bf
new 9773ae0
new 5bd6c41
new fb66737
new 6e05773 Fixed so that MPI_Iprobe is done on a smaller neighbor. Now have to fix so that the subtables are coalesced before sending out.
new ad6a4e5 added some mostly empty files for sparse censorship
new 43b3ef7
new d881b33
new b14368b stub
new e62ef98
new 7341680
new 03a2988
new 3b8b34d
new 9cd4bee
new 79aa741
new 5a1b847
new 5d5043f
new 7bc76aa
new 3c7d41b
new 08c0568
new 30b92dc
new 73b7f4a
new 397eb6d
new fe78338
new 8c9f598 Kind of works, now need to put the asynch barrier only once.
new d5d504f Fix.
new eb9521b Trying to debug.
new 9c105c7 Fixing in progress.
new ade5fb6 [auto-packager] updating packaging to reflect new upstream release
new 6d146ae
new c4fd62b
new 222d7fc Patch so that STL vector is not used in all gather.
new 853f203 Formatting.
new e16dcf4 More bugs fixed, but now have to deal with deadlocks.
new d0802d3 Mainly formatting.
new 28481d3 Aug 9, 2011 - mmtrees code added
new 44999eb Compiling somewhere else.
new 50525d4 Fixing now.
new ea9c9f8 Style
new 748fd24 Style.
new 201d5aa Style.
new 5851496 Debugging
new 2a4327b Bug fixed, now have to put back in the termination propagation.
new 125f101 Bug fixed. Now have to fold in the termination condition.
new 0c61aa1 Hopefully the last bug before termination detection.
new 44ed713 Style.
new b390473
new fdb3acd Cleaning up and merging termination detection.
new 59e8ef4 Minor change.
new 9f43242 CMake change.
new b1525d3 Reformatting.
new 6f4e32d In transition.
new 46eb6b0
new 3dd8bf0
new d0e4cc1 Implement Lovasz-Theta SDP, but it does not work and pass the test yet.
new 0a75910 Debugging output, probably temporary.
new 3fb6912 Bug fixed.
new f47dc51 Default argument revert, since distributed 2-GNP is stable now, now have to do the load-balancing.
new f10c06b Memory leak fix.
new 58cf62e Fix.
new a01595d Removing an obsolete file.
new dfb7fd2 More code cleanup.
new 42416b0
new 0a0bc25 coded update for variational parameters for q(z)
new 3a2a401 corrected E step (computing variational parameters for q(z)), made it work in log space to avoid numerical under/over-flow, and pushed it into a function called ComputePhi.m
new 8bfcb9a
new e027796
new cb14d54
new 160bc37
new fe73ba0 Splitting among cores put back on.
new 7d95e08 added gradient and Hessian computation for theta
new e7a363f Return true when the gradient norm is too small, because in that case the optimization has been a success.
new cfaf173 added ThetaObjective
new 606939c changed name of sparse_censorship to SparseCensorship
new a479555
new ca5edbd made a start on BetaObjective - need to address issues with storing the Hessian
new 7760d8d Performance bug fix in single node case.
new a060861 Bug fix in multicore.
new 2a5cb82
new f4dd9dc Bug fix in getting initial tree frontier.
new 5cf4894 Temporary patch. Fixing the OpenMP issue.
new 452362e More cleanup in the OpenMP region.
new 1476a94 Table exchange inside distributed task queue.
new 1c0eb44 Bug fix in checking power of two.
new 8fdb9ad Another fix.
new 1a83675 Minor tweak. Now going with load-balancing.
new cfb4f2d Minor format.
new 8227747 Adding a different way of generating dualtree tasks.
new 92df83f
new 31bca08 Incrementally cleaning up.
new e0b4433 Segfault fix.
new 8710128 Compile fix.
new cd54dd3 Need to fix the STL map problem.
new 85f5e8e
new 1ccbf37
new 3f910b7 Use Mat_meat.hpp, which has not changed over Armadillo versions, but arma_ostream_proto.hpp has changed names.
new 59e50db Bug fix.
new 86bc8b5 Added a function to clean up terminated query subtrees so that the searching can be done faster.
new f0a3d5f Need to put omp_lock inside DistributedDualtreeTaskQueue.
new 6ff74a5 omp_nest_lock_t transition.
new 917a515 Bug fix.
new 1f1e34c More active task splitting.
new 1e9efa5 Transitioning to the load balancing.
new 72d9609 Adding a new data structure that is needed for load balancing.
new 1e090df Getting there to load balancing.
new 2e21bbc Getting there by implementing subvector class. Now have to implement load balancing.
new 580691e Update to the MapVector iterator.
new 80065da Uses MapVector iterator for kde.
new 64bd9ce Compile fix.
new 3750aef Fixed compilation for distributed tests.
new 7fd9c69 Bug fix.
new 1631e12 Adding scoped omp locking.
new f2aa882 Getting to load balancing.
new ecf3eec Still figuring out how to add load balance.
new 18ed321 Compile fix.
new f532baa [auto-packager] updating packaging to reflect new upstream release
new 2781557 Const_cast fix.
new 7da1905 Transitioning to load balance.
new 9c367f6 Update the Lovasz-theta SDP constraint conditions, which in Burer's formulations are weighted twice as much (better convergence is seen this way). The extremely simple test case is successful, and most of the debugging output has been commented out but not removed yet.
new f669a48 Remove unnecessary debugging output.
new f927405 Getting there.
new 6d5ec23 Optimizing before load balancing, now need to re-prioritize so that the earlier cache is evicted first in the task priority.
new 9b5c98d More optimization.
new 49fbd59 Reprioritizing. Now have to implement the rest of the load balancing.
new 1e208d3 Bug fix.
new 304c7c6 Another.
new 07d77a7 Priority change.
new b2ff448 Turning off the process rank favor.
new 1a3ef34 added support to for single matcher alg to angle matcher main, fixing bugs
new 6a0729d crusing bugs (and it helps to call Compute())
new e98aef9 Put a few things into the correct namespace, and split definition and implementation of BinarySpaceTree.
new 96c7b28 Update trees because they are now in the mlpack::tree:: namespace.
new ea01fd8 Split kdtree.h implementations out to kdtree_impl.h and put it all in mlpack::tree. Lots of work to be done with these files...
new a17f3ed Getting there.
new 4387282 Use typename instead of class
new 04d3073 Start refactoring BinarySpaceTree. First stop: constructors.
new 6b4162f Rewrite to stop using MakeKdTreeMidpoint() and start using constructors of the BinarySpaceTree. Also this introduces warnings, which will make exciting graphs on the build server but at the cost of making Neil unhappy. I'll fix them later, after I look at the graph... heh heh heh...
new 92a8b8d arma::linspace() fails with one dimension for earlier Armadillo versions. So... don't use it, especially since the need for that vector is going away.
new 24bb503 Added the option of fixing the random seed.
new 9da1ead Easy optimization.
new 3feb55d Optimization: don't set the bounds of the splitting function just does that again. Grrr!
new 746ca10 Change ordering of initialization lists, and initialize left and right members. Fix warnings.
new fd921ae Missed one constructor.
new 84117b9 trying new angle-based pruning rule
new 4db38df Now the query subtree list is converted to the query subtable list.
new fc8349b
new c4a56a3 Transition to shared_ptr.
new 56511f3 Add a lot of comments. And delete unnecessary code in SelectMatrixPartition(), to make it a bit simpler to read. It still functions just the same.
new ba6716e Avoid vector copies. They are bad.
new 39fcae5 Ticket #30. DHRectBound now no longer computes periodic distances, and that functinality has now been moved to DHRectPeriodicBound. This way users of periodic bounds can just call MaxDistance.
new 44fa79d Just some quick formatting.
new f62cc72 Remove unused methods.
new 1db4288 Code restructuring for load balancing.
new d5b6735 Adding parallel random dataset generator.
new 5901e13 Factored out random dataset generator.
new cd61ddf Tests now use RandomDatasetGenerator.
new c5a45ab Fix.
new 1c1f302 Taking out boost thread.
new 2e713a7 fixed bug in angle pruning
new 8c13741 Multi-threaded random dataset generator should be working.
new b85f17d Revert since the test is failing.
new 06e5a22 [auto-packager] updating packaging to reflect new upstream release
new ba0276a Fix.
new 2e63831 Fix.
new 0bb6eda Fix.
new c73eced Test clean up.
new 5e6610c Fixed the random dataset generator. Generating weights for kde made series expansion to think that there were actual weights.
new 1995f3a More comments before transitioning to load balancing.
new 6dc2406 More optimization.
new f0b9db3 Working on map vector.
new 0a3e05a Getting there.
new 753b045 Getting there.
new fec07ad Getting there.
new 959aaf2 Tweak.
new 8699c44 Getting there.
new 10f111f Transitioning.
new dfb393f Turning off load balancing for safe version.
new b05547a Load balancing.
new 97a502c fixed tree stuff and corrected angle based pruning
new 336a79d cleaned up angle code
new 9ab9fa3 Getting there.
new 7dcbf31 Getting there.
new eddd39d Destructor for subtable added.
new 26282ce Add profile option
new 361e4c4 Fix.
new f9f9214 Fix.
new a82f2ef Bugs fixed, now continuing with load balancing.
new 36e1b6b Temporary checkin, still stable version.
new de21c50 Adding copy constructor for kde result.
new 312a5bb Copy constructor for local regression result.
new 065572d Serialization rule for std::pair
new 0bb5ac8 Adding flush request.
new 853d871 Getting there, taking a break.
new d47e839 Back to something.
new 30c6a48
new 1010bf3 Prints out the elapsed time from the master.
new ba41de6 Getting there.
new 21f05d5 reorganized code to take generic algorithm class, results are now stored in the matchers, which probably need to be renamed
new 3639d27 Infinitely closer.
new 02fbdbf Getting there.
new bb0a15a Getting there.
new 6e04f1f Getting there.
new 432732a Will continue tomorrow.
new fe444f1 Going there.
new 484b333 CUDA kde compile fix.
new 9e22b6b Minor correction.
new acafb95 Getting there.
new 8f2313d Transitioning to boost shared ptr.
new 5bc45c7 Bug fixes.
new b85b818 Plugging in the test mode.
new 293056b Getting there.
new c13c6eb Getting there.
new d3139ea Minor.
new dabdca5 Getting there.
new 4d905e6 Time to finish load balancing.
new 4a021e0 Adding true parameters.
new fe4450a Going there.
new c264d43 Getting here and there.
new cf781d9 Getting there.
new 7a5c6b5 Getting there.
new 3d203b8 Getting there.
new f2e0cf7 More commenting.
new 09f7ebc Getting there.
new a8417f8 Add this test case for Bill to try out. We needed to make count_ public temporarily until we get the issue solved.
new 37450ac working on weird tree bug
new a8b7f74 right CMakeList
new 7ec6936 right CMakeList
new fa37a58 Query subtable lock is inside subtables now.
new 8bbbe84 Getting there.
new f9fe973 finished up generic angle version, still not sure what was wrong with the nodes for a while
new f6bd373 Getting there.
new 9a04138 Add the cosine distance. It is not very extensible at the moment but I think that will change.
new 8635428 Actually, we implemented the cosine similarity. If we want it to be the cosine distance, it has to be 0 for an identical vector pair and greater than that for anything else. So, one minus the cosine similarity satisfies this condition.
new fed29f6 Getting there.
new 5db62fe [auto-packager] updating packaging to reflect new upstream release
new 6bbd844 Load balancing added as an option.
new 663d22f Output added.
new 59b60aa Bug fixes in task list.
new 722e27f Another bug fix.
new 0b0d4f5 Replaced various macros etc in cc.h that were used sparingly. This should resolve tickets 89, 88.
new a53dd51 Apparently I deleted that from svn too soon.
new d627152 Reverted cc.h deletion, added in includes for STL files algorithm and limits. For whatever reason, attempting to include those in common.h results in errors.
new ef5c1a5 Printing out true parameter values.
new 08d9d1d Segfault fix.
new d334c3e Print out.
new d5651d7 Outer iteration added.
new 77aeb05 Getting there with bug fixes.
new 5a1781c Getting there.
new 08be733 Fixes to bugs in the code
new b62901e
new 1e5728b
new 16f1688 added resampling code
new 0a1f12d Remove cross-validation mode from SVM.
new b9f4c29 Remove cross-validation code. Solves #86.
new 44f183c Fixed DRange Contains so that it no longer returns true for any point.
new cfe1fe5 Revert count_ to being private and update test.
new 5abd883 Bug fix in core::math::DRange.
new 4abb8ca wrapping up resampling code
new 633b6dd
new 8f1660c
new ed5ee9e
new 163bb0f
new ced73ec
new a9b38f5
new dc8b587 Fixing.
new 0bcddb8
new 9b3a223
new 026588a
new 42f121f Getting there.
new 7763835 Trying to fix load balancing, almost there.
new 4acc474 vim
new 076c4e3
new 27f200f Fixed some backwards compatability issues.
new 97c7618
new 32e8106 Fix to the fix that broke a few tests.
new b17c846 Fixed some warning that were popping up.
new d43d068 Should actually work and no longer just fool the compiler to get it to build.
new 2fdd655 Getting there.
new 78438dc more bug fixes.
new aaca71d
new c055d16
new 0b7a594 Compile fix subtable test.
new fe77a45
new 7577538 Changed MapVector class so that it does not use operator[] for find operations.
new 196d924
new fa4a0f5
new 0c41976 Adding MapMatrix class.
new 8a2f326
new 83249d0 Getting there.
new 5a49d86
new b84cab7
new d230a90
new fd3fe9c Hopefully fixes the compile error on no
new 51d1b6e Resolved ticket 93, deleted debug.c & debug.h
new 532deb2 Getting there.
new 77c51d4 Compile warning.
new 63f8c2c Compile warning fix.
new f1fc0c6 Fixed a test case that was failing in matrix.h
new 6bffd49 Removed dependencies on base.h, replaced with common.h
new 799d963 Actually deleted cc.h
new 22b5127
new 283e129
new b485ce7 Due to the way constructors work in C++, it is not possible for this check to have any effect. In addition, at that point in the constructor, the dimension will always be uninitialized (and therefore not equal to 0).
new 6964f33 Refactor QueryStat to not use Init(). And remove an ugly space...
new f5d8d1e Remove kdtree.h and other files. All functionality is in spacetree.h now.
new fb04684 Remove tree/kdtree.h from includes.
new 88e3bda
new 6de5cfd If we choose to implement a Kalman filter later, we will do it from scratch.
new fe5579b Neither of these things is useful to us.
new b5f14c8
new e736df7 QuicSVD goes away. Who the hell knows if it ever even worked?
new c628426 Put EMST into mlpack::emst namespace. Use LMetric instead of la:: distance measurement. Don't use a 'using' directive inside a header file.
new 9f2b351 Remove KDE. If we reimplement it we will restart from Dongryeol's version.
new de54d9e This tool is stupid. Bye!
new 9c79864 This doesn't depend on QuicSVD. The documentation for the program is full of lies, saying that it does, but it doesn't. The lies have been left intact, for now. Also, remove dependency on arma_compat.h since it is no longer necessary.
new 7bbf6d8 Stop using la:: and arma_compat.
new be604cc Stop using la:: and arma_compat. No comment on utterly bizarre function which generates an artificial dataset and saves it to a file.
new 17002dc Stop using arma_compat and la::.
new fb5ace7 Stop using la:: and arma_compat.
new 9c8b856 Convert from GenVector and GenMatrix to arma::vec and arma::mat, respectively. This is not tested.
new 1e5e75d Stop using arma_compat.
new 9c32cbe arma_compat is no longer needed because it is no longer used.
new 8117457 Stop using la/ and stop using arma_compat.
new 2a74335 Remove GenMatrix and GenVector. I have waited so long for this day, and it came with such little notice and no fanfare.
new 0a332bc Don't use newer call to inv().
new 1c53c8b Remove sparse matrix support. It is not used.
new 5504a1d Stop allowing SPARSE option and do not look for Trilinos anymore.
new 0f02024 [auto-packager] updating packaging to reflect new upstream release
new 5cb416d cleared out npt, moving current stuff over for major refactoring
new a3e5d64
new e94b080 Reshape to one column, not one row. This fixes a runtime error.
new 94b22c7 Comment out n_point directory until CMakeLists.txt is added
new ff59ec7 added CMakeLists.txt, apparently not having one breaks the build?
new b358bc7 Remove two unused methods.
new f67d033 Change some documentation to be more clear.
new ea89e48 the refactoring continues
new a6aab12 We force TDataset to be arma::mat always, so remove it as a template parameter. Remove EmptyStatistic's dependence on Dataset also.
new 16d1780 Adapt tree usage to not require parameter for TDataset.
new f697fed Add destructor to clean up memory... why didn't this exist before?
new ec6a9d4 Agh space
new bc2f901 This example is horribly out of date and we would be better off rewriting from scratch.
new 443b19b The little utilities contained herein are no longer deemed useful. We can rewrite them from scratch if we need.
new 3919538 Nothing in these directories... they do not need to exist.
new cc90516 Missed this directory which does not need to exist.
new 180d25d Remove all of the script files. We will need to write a new tool to make running experiments over many different parameters, but this can come later.
new 57fdac2 Don't take leaf_size_ as a parameter but instead abstract it out to IO.
new 6b86c04 Remove leaf_size_ parameter so that we can use the tree's one instead.
new 00eb3dd Document the "tree" module.
new f31d569 changed ThetaObjective() so that it takes into account theta_bar. Also, added ThetaBarObjective so we can update theta_bar
new 8c83227 created EtaObjective, need to fix the parameters taken by EtaObjective and BetaObjective
new d03e64b Fixed everything in PeriodicBound so that it works properly, and all memory problems have been fixed. However there are 3 Min and Max Distance function which seem to have logical problems still.
new 877e95a Solve #103 and add a test to verify. Maybe it would be nice if the Armadillo objects got their own line no matter what, but I actually think that is not the best behavior.
new 8ebfe52 Maximum inner product search added
new e47b46a CMakes added
new 93430dd invalid declarator error
new 3bba6f4 max_ip_main compiling
new 5112821 Removed most everything from common.h, deleted common.c;
new 10b5493 Getting there.
new c276f81 Removed success_t, replaced with boolean logic. Also removed index_t in favor of size_t as we shouldn't be worrying about what C standard our C++ program is on.
new 6418cce Getting there.
new e7e5dac more refactoring
new 8fa7b9d Actually deleted base, minor modifications elsewhere.
new 361ca01 Removed the special Armadillo PrefixedOutStream operators since it is not needed and they were not used.
new dfafc2e Armadillo versions newer than 1.2.0 don't need u64 typedef'ed.
new 060c90e The name of the 'promote_type' structure changed to 'is_promotable' in Armadillo 2.1.91 and on.
new 51596e5 Well, there's your problem. </mechanicvoice>
new e25cb2b I must be missing something, it seems like u64 is not actually defined on older Armadillo versions like I thought it was.
new 03b44df Post bound fix and correct answer, then svn update and all-fail
new 80b4764 Actually, the issue is that the header file exists but Armadillo does not include it by default. So we'll include it manually to typedef u64 right.
new 44683b3 angle-prune added - not tested yet
new 4251446 My comparisons were wrong. Also, no need to put u64 in the arma namespace; it already is.
new e1ef009 Remove last unlikely
new 5811cd0 Force BOOST_REQUIRE_*() arguments to be doubles for older versions of Boost.
new a56bb3f Took out core::table::DenseMatrix and core::table::DensesPoint classes and completely replaced with Armadillo.
new d362c69
new d38e930
new 41e86be
new 91aaa83 More meaningful and complete tests for PrefixedOutStream.
new 81e9468 Clean up and refactor the PrefixedOutStream class, and fix a few bugs Pari brought to my attention.
new f0b3df1
new be19436
new eddb95f Make sure the Armadillo header is included correctly.
new eabee51 Move inline function into implementation
new 762c2d1 Remove basic_types.h since nothing in it is used anymore.
new 54fe1e7 Max-inner-product single tree code working fine with and without angle-pruning
new 32544e9 Oops, not supposed to comment out everyone else's directories.
new 7b28b23 Spaces after if statements
new 2d5a56c Parameter names changed; update for that.
new 44dfccf Set a default value for boolean options (false).
new afbbce3 Memory leak fix in loading of armadillo vector.
new 67bec9d By default, verbosity is off, and is only set on if we parse --verbose (the better way to do it).
new 503ddd6 Removing MapMatrix.
new 0a6d964 Also test Boolean options.
new 7058017 Make --help a flag, and initialize tmp correctly to clean up a warning.
new aafe5f4 Oops, forgot to add that third parameter.
new eb6f36a Add Armadillo output support to NullOutStream, and format the file a little more nicely.
new 9ddb914 Segfault fix. Now load-balancing is close to being finished.
new 127dbd7 Adding the lock toe taskqueue PushNewQueue method.
new 5eff0d2 Bug fixes in TaskList exporting.
new ec9fc8f Adding OMP locks to distributed task queue methods.
new 1689691
new ad32c6f Getting there with load balancing.
new 36b7431 Patch for load balance.
new 98db05e Another patch for load balance.
new 04fce15 More patches, getting there.
new 128db11 Taking out print.
new 1568379 Print statement.
new b7dc3b1 More prints.
new d2b916f Bug fix.
new 2b0b224 Another bug fix in MapVector.
new 48d2d99 Going.
new e07ca69 Getting there.
new 07024fc Adding the flag for whether the subtable is being used for query subtable or not.
new f1f3ec7 Getting there, now putting QueryResult inside SubTable class.
new 8599f79 Deep changes to allow associating query result with tables.
new b4ea4d8 More patches before finishing load balancing.
new b972349 Compile fix.
new 51175d3 Final compile fix before load balancing.
new 3880cf3 Another fix.
new 6cfc77a Compile fix, now load balancing finalizing.
new 431650f Remove some unused options, and add some code which could do PGO if we were using it. But we are not using it yet; we will wait until everything is moved to mlpack/.
new 12590d0
new 9e8786c
new 398ce88 Remove several files in base/ because they are not necessary any longer. Updated CMakeLists.txt accordingly.
new 77a8095 Remove common.h (which had nothing useful in it) and put that in fastlib.h. base/ now only contains Armadillo extensions.
new e7b4000 Remove Opt++ support as it was not being used.
new 6be8e16 Remove contrib/ as it was not being used. The items within will be re-implemented.
new bec402e Remove some cruft
new e4b9477 Remove some space (I am doing some testing of svn hooks, so don't mind the trivial commits...)
new 793eed8 Query result inside query subtable now.
new a1341cb Fixing so that local expansion is initialized for non-empty multipole momenets.
new b7dcd32 Still debugging.
new 7450d61
new dffcdbd Bug fixed. Still finishing load balancing.
new 4812b6b More optimization.
new 125ef47 [auto-packager] updating packaging to reflect new upstream release
new 19337db Implemented windows based IO timers, will need to actually compile/run on a windows machine though.
new c9fa02d refactoring continues
new 34102c0 Converting to intrusive pointers.
new 1b8c683
new f10bc82
new 2cac597 Patches to avoid searching through locked query subtables.
new 8506ec2 Ticket #54 and a bit of refactoring.
new c3f0425 Update lin_alg_test for #85.
new 82968f9 Reverting because I broke the code.
new 3ccdc29 Clean up NBC test
new c8d9ec9 Move to more simply named 'nbc_test.cc'.
new b1b2f5d Remove unused test_infomax_ica.h, and move test_main.cc to infomax_ica_test.cc.
new 5f2c981 Convert series_expansion_test to Boost UTF, and fix a bug which caused a segfault in the series expansion code. (#85)
new 2be2d2c Fix some formatting, give the test a better name, and strip trailing whitespace.
new bda5c81 Deletin' the whitespace for future generations. And, fix a bug I managed to introduce where I should have been using GetParam() instead of HasParam().
new ba2371e Comment out unused variable.
new 6b23d0e Use GetParam<> for bools, not HasParam().
new 5ff75da Make sure we terminate when our stream is fatal.
new c866795 There was a case where we did not start the program timer.
new ac1a2bf physpack/ was not used and we will not be maintaining it. It may be reimplemented someday, but for now, it goes away.
new 59ef6b5 Remove stray spaces
new 837af38 Switching to boost::scoped_array
new 0ec54b0
new 11c6643
new f176b78
new cb2a5fd Hopefully I can proceed to load balancing.
new b745e72 Took out print.
new 0ad23aa Taking out shared_ptrs.
new 8318865 Going.
new 29426a0 getting there.
new 82df623 Going here and there, getting to the finish line.
new e1ac48e Additional header file.
new 42bbbd3 Fix.
new 6e94516 This file is not used and not necessary...
new 838f9fd Going again.
new 3235cd3 Repatch.
new 2a9b430 Going there.
new 526276e Going.
new 6fc7b53 More patches.
new f80f3a9 Almost done with load balancing.
new b13a941 Cosine tree essentials implemented -- not compiled yet
new 2d0c069
new 8e983ee
new 0e9ad2b
new e398bfe
new dc0abcf
new 2f38907
new 8f5a3fd
new 414dad9 cosine cone bounds cleaned up and completed -- pre-compiled
new d8227d2 wrapping up refactoring
new fe1b9c1 Getting there.
new d2e3273 Getting there, now ready to test load balancing.
new 21c3414 cosine tree example + compiled and lightly tested cosine tree bounds and distances
new 80746b8 If a reference subtable comes before the query subtable with the same ID, the task export will forget to save the associated query sub list. Now have to fix so that the reference set and the query set are different.
new b6b605c Still fixing.
new 897a48f Bug fix.
new c782471 Getting closer.
new 1dc684d
new ed69a66
new 61b9525 Almost done with load balancing, still debugging.
new 22c9d07
new 2f4ff5f Getting there.
new 7d207e7
new 1083537 Getting there.
new 408c4b3 first version ready for testing
new 2962ebe fixed small bug in BetaObjective.m
new f550603 Fixed some bugs. It runs now, but EtaObjective runs for way too many iterations (perhaps due to higher regularization of 0.1 as compared to 0.01 for BetaObjective)
new 9c4a2c7
new 7232686 Continuing tomorrow.
new d62366a
new 26ec3b2 LockCache method should be called for reference tables stolen from other processes.
new eeee156 branches/fastlib-stl/mlpack: remove the Dataset dependency from svm; modify some formatting in nnsvm
new 33f26cd branches/fastlib-stl: shamelessly hide the broken tests for now
new 6a2ffac DefaultMessages() was commented out for some reason, leaving --help inaccessible.
new b2a427b Reformat offensive code. Delete some unused code. This code needs help...
new a20bfe1 Split definition and implementation into separate files.
new 4874e2e Place SVM components inside mlpack::svm namespace.
new 90a2e53 Use IO output and remove mlpack:: where it is not needed. A few more code formatting issues...
new 1c552fb adding single computation main for verification
new 2980d04 Numerous bug fixes in load balancing, getting extremely close to finishing load balancing and start writing.
new 8a3444f More edits.
new d812bb3 Dual-tree max-ip implemented but not yet compiled because of weird CMake error -- will wait till later to figure out
new d1c411e added single matcher test infrastructure
new 97cb2b7 wrote simple, serial two_point_correlation code; currently only does DD and DR counts (and not at the same time)
new 3562b48 started on exponential family sparse coding implementation from Lee et al.s paper
new d0e0646 branches/fastlib-stl: remove a few warnings
new e3a3431 Fixing.
new 19bd455 Commit.
new 373ba23 Compile fix.
new 189bdab Dictionary Updates seem to work; now to handle the sparse coding step
new 0f3a135 fixed bug in DictionaryProjectedGradient and ComputeDictionaryObjective - I was doing some computations incorrectly due to erroneous notes. I still need to handle the Armijo line search for UpdateSparseCodes (taking into account subgradients, somehow...)
new 4340ef0 [auto-packager] updating packaging to reflect new upstream release
new 5eba71a Fixed a bug where flags received a default value, which resulted in HasParam always returning true.
new f69a3e4 io_test depended on earlier behavior for default values & flags. Fixed.
new 9e9769e Bug fixes, still trying to get load balancing to work.
new dc398dd UpdateSparseCodes seems to work
new 7e1cab0 Still not compiling - some linking error where the .cc file is not getting linked. Can't figure out what I am doing wrong with the CMakeLists.txt
new 54bb2a4 Refactoring math dir : deleting unused functions from discrete.cc
new acce2b2 Refactoring math dir : deleting unused functions from discrete.h
new 8f765ea Refactoring math dir : getting rid of unused kernels
new de3f518 Had removed factorial func by mistake which broke the build. Adding it back.
new 34fc36e Had removed factorial func by mistake which broke the build. Adding it back.
new e678593 Refactoring math dir : getting rid of unused functions
new 8b59e64 added some efficiencies and added function to compute full objective
new 8642d73 New API added to parallel.
new 9628918 distributed two point implementation
new cf1483d
new a3e487d made the code MUCH more efficient in various places
new 20d879c CMakeLists.txt edited to include mlpack_contrib
new b2a9157 fixed a sign bug in ComputeDictionaryObjetive.m
new c37422d added load script for tiny version of rcv1
new 8dd43be isolated gradient computation for Dictionary of Poisson Sparse Coding to its own function, in order to make way for specialized functions for each exponential family (for the gradient and objective only)
new 1b8617d added ComputePoissonDictionaryGradient (should have been added at the last commit!)
new e06091b changed ComputeDictionaryObjective to ComputePoissonDictionaryObjective
new 105f74a fixed function name inside ComputePoissonDictionaryObjective.m
new 788be1c made some changes so that Poisson Sparse Coding has its Sparse Codes objective and Sparse Codes subgradient moved into functions
new 009593c shifted more code over to Poisson specializations. think Im done now. Also, found major bug in UpdateSparseCodes, where we were left-diagonal-scaling the dictionary matrix by Lambda instead of sqrt(Lambda)!
new e2d7958
new dc5451c small fixes, mostly syntaxtual
new 32aee27 renamed ComputeFullObjective to ComputePoissonFullObjective
new c503811 made PoissonSparseCoding call ComputePoissonFullObjective
new 49c5ea9
new b3e9562 added functions for Bernoulli - need to check them for correctness tomorrow
new 8e5a0b5 sep 22, 10.40am
new 921a697 Bug fix in ball tree builder.
new 0f83698 lots of changes, put in Bernoulli sparse coding and added option to choose whether to do Poisson or Bernoulli
new 5efef8a
new ccf09e1
new 42272a6
new dff1144 added functions for Gaussian sparse coding
new 3dca2ba added support in ExpFamSparseCoding, UpdateSparseCodes, and DictionaryProjectedGradient for Gaussian Sparse Coding
new 5534c2b Basic parallel tree test modified.
new 5463788 found major bug, we were mistakenly dividing the l1-regularization parameter lambda by 2 when calling l1ls_featuresign, but all other computations were not concordant with this!
new 9c5de1c Bug fix in the intrusive pointer initialization of reference count.
new a0fd88f Moved the SendReceive test outside for distributed dualtree engine.
new 4c6cc93 Taking out print.
new 7d8824b Patch for optimizing load-balancing turned off case, roll back three times for a stable version.
new 9a3a077 Another patch.
new 1d5f34f Sep 23, 2011 update -- header guards added
new 5bffbce Another bug fix.
new dc931dd Another patch.
new 79324b4 Sep 23, 2011 update -- header guards added
new 16c89b0 Bug fixed, now testing stressfully. Just in case, you can roll back about 5 times to get a stable version.
new de3b598 Change to the way points are compared for equality.
new 23c0ff8 API changes to GNP engine.
new 688ca2a Final fix.
new 77e8338 Another.
new be382c0 Another change.
new 26618ee Fix.
new efdb66b Fixing the monochromatic case.
new c85ea1e Will fix the monochromatic problem.
new 4716b3c Default thread num
new 9f142d8 Changed the way is_monochromatic flag is used in the distributed/non-distributed computation.
new 686b529 Fix to the default argument.
new 0b78331 Another default argument change to kde.
new 415b747 Refactoring math dir : getting rid of spherevolume function
new fcb5990 Refactoring math dir : getting rid of spherevolume function
new c459664
new f33a8e3 Default location for gsl changed.
new 9b926ab Disabled redistribution of cores on the same machine, now will change the policy of initiating load balancing to reduce the overhead.
new 0c67e40 Fix to the root CMakeLists to specify the local installation root.
new ebf8cf9 Going.
new 81c176f Added the code to extract prune counts.
new b729102 Breaking up the file.
new 0131cb8 Transitioning and cleaning up toward a more efficient load balancer.
new d8941a4 Getting there.
new b53835a Getting there to change load balancing.
new 8e09503 Default num thread changed again.
new a62e7da Some bug fixes.
new f84aea3 Getting there.
new 5cd13a3 Transitioning to better load balancing scheme.
new 799e3eb Getting there.
new d7ef03b Commented out task list route for now.
new 63177d7 Getting there.
new 6abf33b Cleaning up code.
new da39913 Some optimizations.
new 292e6b05 Getting there.
new d9f3b59 Getting there.
new 8d2250d Getting there.
new f63fd69 Getting there.
new b9ae392 More cleanup.
new d76bf9b Getting there.
new 7be1d39 Going.
new 779ec36 Plugging back in the load balance.
new 1ee7e9d Getting there.
new 795c9bf Changing the termination condition slightly.
new c43e47a Re-do.
new bd0cc88 Tweak to termination condition.
new 832c1b1 added two point tests
new 67d8d60 single_main change
new f923589 Dual-tree max ip search implemented and compiled, not tested yet
new 47f4dea Dual-tree max ip search implemented and compiled, not tested yet
new c988bb9 Remove series_expansion to clean up some stuff in math/. If we reimplement it we will do it from scratch.
new 09eb655 fixed two_point test, reading a float from file isn't the same as the original float
new 82c26e7 API change.
new f90eec5 API change.
new d2f8a1d More API changes.
new ca18c26 API changes.
new 1eeb20a API change.
new 9b6043f Fix.
new 5bd94f5 More changes.
new 71e595c Fix.
new e7de658 Final change.
new e7e178d Require libxml2-dev for Neil's future work in saving SVM models.
new 3e33227 fixing tests, writing distributed test
new 3032ff0 Dual-tree max-ip-search still not working
new 62fee9b Refactoring math dir : getting rid of unused stuff
new bdcd4c8 [auto-packager] updating packaging to reflect new upstream release
new d0c81ce IO HasParam/GetParam for bool is solved. Both will now reflect the actual value of the bool, which is true if passed on the command line. GetParam will allow you to alter this value.
new 8898ee8 Don't count on a using directive from somewhere else. Use arma::vec.
new 00a61cc Refactor the interface for DHrectBound; change to HRectBound, and simplify a few things. Put it in the mlpack::bound:: namespace.
new 66af7f5 Update DHrectBound to HRectBound.
new 58bb47d Change a few things about how Doxygen works.
new 3683198 Refactoring math dir : removing discrete.cc, discrete.h, geometry.cc, geometry.h
new a750d37 Replacing tree_test, at a good stopping point.
new ff5d1c5 Dual-tree code tested, not correct with angle_prune yet
new df534ff Bug fixes.
new 378a95d working on distributed two point
new 5cbc45c Distributed/non-distributed two-point tests pass now.
new 0983810 Almost done debugging.
new fec34b6 Reverse-merge new tree test which did not account for change in DHrectBound name.
new bca858d Max-IP search: dual-tree angle-prune tested and working on toy dataset
new 3edad63 Refactor DRange out of math_lib.h and then rename it just Range.
new 3d2d624 Implications of DRange -> Range name change.
new 1293111 added full sized tests and different num_threads, everything still passes
new a0630af Clean out a lot of Range code, making the class far simpler. I don't think I'm done quite yet.
new a8248e9 Prune more unused functions of Range. Don't use Init-style functions anymore; use the empty constructor, which now creates an empty range by default.
new 09f6a5d Update tree test to not use Init, and use the default constructor in the bounds when we reset them.
new ae7d8c1
new dd30ab0 Almost there.
new 06305d5 Merged kd tree test with tree test itself. Didn't see the point in adding another binary.
new 04b9947 For some reason, uses more memory.
new d393199 Sep 29 update -- everything works, graphing script added
new c284c12 committing small changes in advance of destruction
new ade357d Add a test for the Range class. It is a proper unit test and tests every function present in Range.
new 07d3326 Numerous bug fixes for load balancing, still debugging.
new 46d984d Clean up kd_tree_test.
new f07cb56 mnist_sc.cc small change to shrink dataset for quick experiments on newtons method in the dual
new 5c436b1 added Init and armijo line search for newtons method in the dual
new 2ec810d
new 419134f
new 9e2516e
new 374c2b2
new 9737d4b
new 05c0ca6
new ac0222f
new 24600bb
new 6480c6a
new 836f5d4 added some plotting tools
new 836cd76
new b9d5c53
new 5e8525b
new 2158a37
new 5f25bf1
new 6b265a4 Move dhrectbound.h -> hrectbound.h to reflect the class name change. Also clean up a little bit of the kd_tree_test (#125) because srand(time(NULL)) is good enough and easier.
new d60a774 The WarmInit() function in class MaxIP fixed to reset the QueryStat in the query-trees, and the tester changed to compute naive only when you have to check for correctness
new a6103e1 data_grapher.pl fixed to align to the correct column
new 7b864d5 data_grapher.pl fixed to align to the correct column
new 92db599 Need to fix the load balancing case, but getting there.
new dc960c2 assert in exact_max_ip.cc fixed to either expect 0.0 with -1
new 4ab5b7a This MVU implementation still has some bugs but before I move everything around I should check it in.
new 2b8c410 Update to use IO instead of fx.
new 43ac2c8 Start writing actual unit tests for HRectBound.
new e47537b Make the new /mlpack directory. The future: it is here.
new 20f4234 This checkin will make coffeetalk-1 happy and heat up the frigid CoC server rooms. The fastlib-stl branch is now (finally) MLPACK trunk.
new 2e7ddf0 Make repository structure standard svn-style.
new 022dd23 Move configuration for fastlib to mlpack. This is for Jenkins and the packaging of MLPACK.
new dd7576c Restructure MLPACK directories to the format suggested in #2.
new 147b7cd Move some things out of fastlib/ and put them in src/core. I will destroy the FASTLIB name forever!
new a87de17 Finish moving out the last of the fastlib/ directories.
new 84d09bc I have waited so long to do this. I really have, I mean it.
new 83d448a I have waited so long to do this. I really have, I mean it.
new 1a8a17d Clean up root CMakeLists configuration a little bit, and remove FASTLIB.
new 524e9dd Move all the MLPACK methods into src/methods.
new 2c6228d Clear up CMake configuration.
new d92d373 sparse_censorship was removed so we should take it out of the CMake configuration too.
new 0cb9307 Update all CMakeLists.txt files to reflect new directory structure. Remove any references to FASTLIB present in those files.
new a32c272 Load balancing works. More stress testing.
new 80ef55f Memory leak fix.
new c65b801 Enabled splitting query subtables.
new 468c740 Some minor bug fixes in updating local computation on load balancing case.
new 0325443 Some more optimizations.
new a43eb96 Now the flushed query subtables are destroyed.
new 4150c88 Distributed kde test now tests load balancing.
new 5a9afaa Added the branch on tree type in distributed kde code.
new d2f4b81 Memory leak in load balancing case fixed.
new 4f2e768 Now dequeues multiple items for slave threads.
new 383ca19 Adding the weak scaling measuring mode.
new 1524fcd Moved the global all-reduction step of two-point into the two_point_result.h, also finished the weak scaling measuring mode.
new 3dc9a44 Added the static cast.
new cc42f98 Another warning fix.
new 027e82a Fix.
new a030a93
new 6fc2457 Fix.
new a6b8bcb Some adjustments.
new 5fd511e Fixing.
new 2c37dcc More tweak.
new 5e0cd16 Now need to maybe tweak the load balancing, but the experiment setup should be good to go for weak scaling.
new be1eedc Move everything to src/mlpack and src/contrib. This makes the setup a little more complex, but it makes the build system work properly (although that has not entirely happened yet).
new fae796e Fix.
new 343aa98 Another tweak.
new 8eeac07 Update all includes so that things work and compile again. A couple MLPACK methods needed to be commented out entirely.
new eb0fea0 Add that core.h file which we were using in place of fastlib/fastlib.h.
new f36d53d Directory structure changed so we need to copy tests from somewhere else now.
new 26d55de Move header files properly to <builddir>/include/mlpack/ and then install them correctly to $prefix/include/mlpack.
new c15cddd Printing out the initial setup time.
new 349587b Dividing by the number of threads in the weak scaling.
new e90fed5 fixed a comment, added paper citation
new 4de0230 Distributed tree test compiles now.
new b0662a6 Re-enabled the multithreaded tree building.
new 2992db0 Refactoring math dir : getting rid of unused functions and constants (#116: Investigate what is present and used in fastlib/math/)
new fa96176 Remove PI; it is included in math.h, although with less precision.
new 618c829 range.h and kernel.h are no longer included in math_lib.h.
new a2ada11 Stop using math::PI; use PI contained in <math.h> instead.
new 6ce13e9 Stop using math::PI
new b4d782a Stop using Sqr(); use pow(x, 2) -- it is faster.
new 872fca5 Don't use Sqr(); use pow(x, 2) -- it is faster.
new b32549f So it's actually M_PI not PI. What am I smoking today?
new dbf52fa It's actually M_PI not PI.
new f503a09 Include the correct files since math_lib.h no longer does that.
new f97be48 Make sure we include M_PI, and if the system does not define it for us, we'll give it our best shot.
new ffa531d wrote very basic two point kernel and tests
new a4368b0 Be a bit smarter about what we glob. We don't want .h.swp and we don't want .h.svn-base or anything like that.
new 455f245 Make MOG compile. I am certain it doesn't work because I know I broke it in a couple places, but it compiles. In the future, we can do a little bit of cleanup work and it will be good to go.
new c97328c Orthogonal range search will be too difficult to preserve and we should start over with it.
new 7a019ef Finish the unit test for HRectBound, completely. Took a couple of methods out and fixed a previously unknown-of error in RangeDistance(arma::vec&). See, this is why unit tests are good!
new 9175c1d Create a simple linear regression class
new c0fff2c error: ‘struct arma::subview_col<double>’ has no member named ‘ones’ fix
new 4a7e6e5 Make sure all of the arff files get into place.
new ce222c3 added task sparse coding directory (matlab version) with basic blocks in place (lpsvm and pegasos)
new d5fc1d1 0.2 to 0.1
new f35cf74 added first version of TaskCoding optimizer
new d272218 Bug-prone disjoint_int_intervals.h eliminated.
new 9d077c1 updated n_point for reorganized mlpack, also removed link against fastlib in contrib/CMakeLists.txt
new e2de4e1 Rename DHrectPeriodicBound to PeriodicHRectBound. Remove the test for now. Also remove a bunch of methods so the API matches HRectBound.
new 4b9a2b1 Fixing the compile error.
new 6afb575 trivial change to TaskCoding.m
new 1a76422
new 8d71934 Going.
new ec8dd5e Change the name of a few methods in PeriodicHRectBound to match. Implement several of the necessary unit tests as a guideline for Vlad, with the most important of those being the MinDistance(point) test.
new 322a5a3 changed minibatch size for pegasos
new fa048ed now passing delta parameter to lpsvm, as it fails miserably otherwise
new 6ea2ef1 fixed way of sparsifying codes in generative model
new ec79091 enabled projection step, although I still do not know if this is necessary
new 4aebb6d added error computation
new 17063ca various changes to TaskCoding.m
new 88eeefd LinearRegression -> mlpack::linear_regression namespace
new 499f925 formatting changes
new cccb489 fastica -> mlpack::fastica, lin regr style
new 064b0bf
new 1111e0c hmm methods -> mlpack::hmm
new a60a6b4
new 34853a6
new cb5b583
new 8214586
new 8dc661b
new 8b23ca4
new 55453af
new 46efd65
new 2d21ab9
new 009216c Fix two warnings relating to unsigned/signed comparisons.
new 4636d12
new c95e187 Added the method to print out global table.
new 1ba14fb Going.
new 59be76b Going.
new a445420 Don't compile the main executable and test executable into the library itself.
new b6fecaf adding (nonworking) single bandwidth test, removed fastlib from contrib's CMakeLists.txt
new 32f257d Update CMake configuration to not comment out everyone's code (only most of it). Remove some artifacts relating to FASTLIB and clean up the file just a bit.
new e202da3
new 68a6653 Different way of measuring weak scaling.
new 4b223e2
new 5af64b1 Bug fix in measuring weak scalability.
new 4ead92f Another tweak.
new 7179983 Fix.
new 9e309ed Disabled redistribution among cores.
new cd6e2e7 infomax_ica -> mlpack::infomax_ica namespace
new e438d2a naive_bayes -> mlpack::naive_bayes namespace
new 4a5a3f9 regression -> mlpack::regression namespace
new 404c0ec added sparse perturbation versions of Gaussian Sparse Coding
new e9c4e87 added some run scripts
new 0899e95
new f8e5670
new 9710097
new 8d280bc
new 96c463c
new b7f7200
new 0027bce
new ed56795
new d112303
new 227570a
new 85b8264 Make main usable, --help explains options now
new 540a257
new dd2211b
new ecb6db4
new 493ab3a
new d065b7b
new 7198a14
new 2a1b506
new 7ca0550 added code (needs to be debugged) for convex MTFL
new 6838a84 added argyrious convex mtfl
new 7fdad7c Oops, we wanted the name of the file, not the vector.
new bd84301
new 407e300 fixed
new 5caca5b
new 8bfda46
new ffd907a
new 80d4b21
new c18bc0f
new 6f18320
new 60372a4
new c040097
new 69bc5b1 Idiot Ryan is idiot idiot idiot idiot
new 459c9e1
new 3882a2e mlpack/trunk: modify the clamp function
new 9291985 mlpack/trunk: modify the clamp function
new 37bb9f6 mlpack/trunk: fix the ClampRange mistake; the previous functions need more intuitive names
new 4913ba7 Resolve #142 by removing the problem entirely.
new 8100457
new fde2028 switched to LP formulation of one-norm SVM, in search of stability
new 22174dd
new 6a85705
new 3e3e3b1 added pegasos minibatch without replacement (bouttou style)
new fc21f05
new a5f2b99 mlpack/trunk: delete an extra space
new d3e8302
new 1d8840d
new 8f4a9f8 Bug fix in multithreaded tree buildling, now there is a speedup under -O3 flag.
new 23d1603 Warning fix.
new 7e03a47 nnsvm -> mlpack::nnsvm namespace SVMLinearKernel, SVMRBFKernel -> kernels/linear_kernel, kernels/gaussian_rbf_kernel
new 134e136 CUDA fix.
new 9a9c160 omp_set_nested(false) apparently resets the number of threads.
new 67f0df2 Need to fix the task division for MPI size = 1, big data case.
new dddb1b3
new be97aaa helps to add the files
new f604df8 mlpack/trunk: per bug 131, add a SaveRestoreModel (and abstract Model) class(es)
new e778ee4 mlpack/trunk: eliminate the newer call to clear breaking the build
new 817d733
new 617fe13
new cae354d
new ac986a1 fixed bug in Learn.m where we accidentally have the same variable name, n_iterations, to represent both n_iterations to run convex multi-task feature learning and pegasos
new ac10b79
new d27a1ed
new 033a4f0
new ee2bcb1
new 3ed22b5
new 00ece1f
new 41340bd
new 6002610
new af6a478
new 7b7b471
new efb4eb0
new 2a9be9a Checking in the reference tree walker.
new cea4320
new e6d4d26 changed GenerateSyntheticData so that all atoms are unit norm
new 5ffde2a temporarily changed TaskCodingWStep to use svm_lower_bounded_margin
new 4515f68 added svm with lower bounded margin
new e8fa7db
new 531595f
new e86816e
new 7725419
new 41cabc9
new 5cb016d
new e9fba44 Dualtree iterator bug fix.
new 3b13264 Reference tree walker finished. This will save memory by conservatively expanding the reference frontier (which has direct impact on the hashed send list.
new 0d634e6
new 77b396d Patches for running on a larger distributed computation per node.
new 25d9f76 Another fix. For a stable version, roll back twice.
new 21ab819 Minor.
new bde4a15 Changed the seed function.
new 2bda581
new 5c727fb added pegasos with lower bounded margin
new 1bccce5 Leaf size increase.
new ec62a70 Another parameter.
new 37cad1c
new a991ef2
new 495eab3
new 699dd4f
new 8818dda
new 3917c65 Going.
new f911f6f Another patch.
new c9f7472 Warning fix.
new cfef325 Warning fix.
new 6086130 Some tweak.
new 7c7d04b More tweak.
new 833465d Final change from 400 to 40.
new 48e3846 More tweaks.
new 50d6462
new 43f27ca Patch to encourage sending the reference set as few times as possible.
new 6ad3aa8 A tweak.
new 2c2b13a Another tweak.
new d397e33 One more.
new 29880a1 Another.
new 755834f Another fix.
new 45cccd6 Compile fix.
new fb5b400 More tweak.
new d53aef6
new f6771a4
new f041a4d
new aec53b7
new 03809a4
new aca1ec2 Added back the timer.
new 7dd1517
new ec26eab changed some display stuff, and now normalize initial W so that each col has unit norm
new d41f7bd faster, via precomputation of X * diag(y)
new 283974b display aesthetics changes
new 0adbcc2
new 1790111
new 8d409ce
new c05a737
new 8e5ac0f Some tweak.
new ac9fecd
new f56d6d6 Fix.
new b9692e9 Another.
new 4a3225c Fix.
new b1ce1c8
new fb8f523
new ee9f8ab
new cde3674
new f5f09d0
new 59bcff5
new 87a01d0 added angle resampling tests, squished some bugs, still a few to go.
new 8d1d746
new 118a8c1
new 8e57478
new 6eb44b4
new ccb4101
new 7e662d7
new c4c1004
new 19656ac
new fb69b8a
new 1515f39
new 6e3a2de
new cc88767
new 018752f
new d2325c9
new e8a63e5
new 16fdf76
new f4d4791
new f47e13c
new d226eab
new 57d87a8
new dba6030
new 5d87202
new 731a41f
new a0b66a1
new 4ef871f
new 71bfe53
new d4de092
new 98a2103
new 6b3978b
new 5669a58
new 030c1ea
new e324bbf Now any thread can walk the reference tree.
new f53c225 Added the heuristic for reference tree walk.
new cf5a7b9 Took out print statement.
new 35ffe81 Performance improvements to kd_tree_test, added peer bounds checking.
new 403e4ba Removed some output's that will break the automated unit tests.
new db06ed1 sorry, broke the build; I'm now completely in favor of Ryan's idea to move contrib out of the mlpack directory.
new b93610e Some changes clean up.
new b340386 Reduced the size of the kd_tree_test again, that way it will *hopefully* finish in less than 5 min.
new 23ff058 Fix.
new 4534086 Took out printf.
new 4f8f7a2 Fix.
new 53612e4 Clean up code; make helper functions more generalized; grammar Nazi. Use L2 distances because I think we have that implemented just a little bit faster.
new 7b639cf More tweak.
new a9de067 Some changes.
new ec0de76 Experimenting now.
new 6c42a13
new 8d2d111
new 932b39a Clean up the code. I think we can make it a little faster by how we do the comparisons. Also there was an invalid memory access issue which is now fixed, in GenerateVectorOfTree().
new 4915657
new 6e27723
new cb72f0c
new 946cd65
new 3f51bf1
new 388354b
new bc08956
new 23d169c
new 7d8f9cb
new cf0eebf
new b4f5899 Make lin_reg adhere to the proposed interface for mlpack methods.
new 8fdb40a
new 3c63327
new f62f68f
new f89afb3
new 3219480
new 100572c
new 117ce43
new b48daef
new ed8d8ec
new bb0113e
new 8f16382
new 78341fc
new 26c3bf9
new 7ee0ea4
new 7f18a29
new 80788ec
new 6bfdb5b
new ed28acd
new 6d0aa48
new 84af238
new f043b0f Simple Doxyfile changes. Let's see if we generate the right API.
new 6e9988a Update Doxygen configuration.
new e025298
new c8f76ec
new 3ef7d78
new da1db35
new 69fbc24
new fe87ead
new a16a8ca Split IO into IO & Log. Fixed everything up, all tests work. Will proceed to rename IO to CLI.
new 83d3e93 For some reason it seems Sed missed gmm and it was already up to date so make didn't touch it.
new 0cf29fa
new 5f9010d
new f403ec4
new ff79cff
new 6117f37
new b1e7a0e Shooping the whoop on our Doxygen configuration.
new 9f62d9f Some optimization.
new 2de759b Testing.
new 452ee99 Dualtree iterator is slower.
new c04b102 Write the main page of Doxygen documentation.
new 2303104 Doxygenate? Doxygenize? Doxitize? Doxify? Doxenation? DOXY NATION!
new 7a8ba94 Fixing load balancing.
new bdc4de5
new bd5d74f Some opt.
new 33f1902 Fixing the load balancer.
new a6d8932 Fix.
new fb2af14 Some changes, now need to optimize load balance.
new 33a1ac8
new 7ec0b66
new 77d4ab8
new 3bf853c
new 7d12af4
new 770a787
new 2b6d8b6
new 486087d
new 7ffaaf2
new ab49af6 Clean up some more Doxygen.
new bbdcc16 Changed the naming scheme of files in MPI read.
new bea7d41 Needs to be fixed by implementing distributed file reader.
new cf8fd53 More comments, now optimizing MPI calls.
new d2e5d9d Merged multiple MPI calls into one.
new 7ad4f43 Problem fixed.
new 4b7a1e2 Warning fix.
new b494b7b Another.
new 86ac7be Another.
new 3be5f20 Another.
new bfb6180 Another.
new 92ebe89 Going.
new 1a4aeb8 Fix.
new 7c50486 Fix.
new 26afa35 Fix.
new 05ef786 Suffix fix.
new 912a485 mlpack/trunk/src/contrib: create my directory
new ddd99be
new d92c85f
new 60e817d
new 682f892
new 03f8fc4
new 4b3598b
new 9359682
new eb4d3e1
new db6d38d
new 553e2af
new 7967016
new b5f6f7a
new 069907f
new 01bdaf1
new a6d7f81
new 8c13a6d
new d2eedf5
new d388fab Some changes so that messages can be buffered more quickly.
new b63a19f Revert.
new 5b4e206 Bug fix.
new d7b9f9a Fix.
new e8625ab Transitioning to compact buffering.
new 6ae2042 Now subtable routes can go faster.
new 69bb71f Fix.
new 9da9b13 Fix.
new f9cfea7 More optimizations.
new 738d71d Merged.
new e7068d5 Reverting.
new ca156c1
new 6c4ee20
new 6ba119e
new 8bd02fc
new 14f8b36
new 5cf5473
new 5e0e4b3
new f37437d
new fab36fa
new e58c9d5
new adc29fb
new 46db369
new f86c599
new dd21c7a
new 22772bb Going.
new c9c4d85
new b8061a1
new ad73a14
new 8f0fb36
new 277365a
new 617da65 Patch for extrinsic prune.
new a174132
new d6469d1
new 078c5d6
new 00b7851
new a390e4a
new 4b8a2c5
new 20e5777
new b1504d6
new 0d58266
new e1683d4
new 97180bc
new e6d4243 mlpack/trunk/src/contrib/nslagle: copy the kde code base from D Lee
new ce8bb27
new e7bbcf7 Patch for more balanced splits in the global tree in distributed tree building.
new 71c49b4 Formatting.
new 49d9c7f Tree test compile fix.
new 6271f53
new 47251b6 added display of sparsity and nnz for Q
new 352cb3f
new d440e59 added preliminary version of censorship experiment
new dbce6be
new 1645c28 mlpack/trunk/src/contrib/nslagle: continue updating kde
new d8ee4ea mlpack/trunk/src/contrib: revert changes to the CMakeLists.txt
new 5b78a93 mlpack/trunk/src/core/tree: revert the statistic.h for now
new 469be6f
new 9bb165a
new 7629ff1 MaxIP search ported to new MLPACK and ComputeBaseCase is modified to use memmove instead of vector and push_back
new 233448f NASA added.
new 8e4334a
new 90d4b33
new 9747593
new fc58da3
new 374d2dd
new 58c0aae
new c3712a3 mlpack/trunk/src/contrib/nslagle: commit fledgling kde kcde
new 7d63b3f
new 03f4380 mlpack/trunk/src/contrib: hide PRam directory until the missing file reappears
new ee26bd6 Make a custom stylesheet for our Doxygen output so it matches Trac.
new 28a25ea
new aa9f1ec Some changes so it works with Trac. I'm sure I didn't get it all right.
new 1dbb3a9 Rank-Approx MaxIP partially completed and not compiled yet
new d2106ea
new ad32fd4
new 2c3c752 A couple changes to make it work right with Trac.
new 7ce56d1
new 2f75ad7 Just a couple CSS changes.
new ba0920f A few more changes because monospace fonts are not being used in the right places.
new e43d98f New argument to specify attribute dimensions for full Gaussian.
new a70e183 Oops, I broke the local documentation style. This should fix it.
new 23420ae
new d11ce35 Add an example kernel for documentation purposes.
new c34caf0 Document GaussianRBFKernel just a little bit better and clean up the code.
new 97cba13 Apparent inability to perform simple math
new 3b338d1 Oct 20 arma error
new 1279412 Check .hpp and .cpp files for documentation also.
new bec76da
new add4586 Refactor and comment GaussianRBFKernel. Rename it GaussianKernel.
new 2f96c5a
new 519ac5b
new 4662525
new 2461241 Comment CosineDistance. Fix a problem I introduced in GaussianKernel. Rename a few files.
new 215fa7d
new ccebecf
new 16a8661
new 99a1873 Fixing the Gaussian distribution.
new 09940e3 Document the linear kernel. Rename some files.
new 23974a1 Add a few contributors I'd forgotten about and don't include kernel.h -- it doesn't exist.
new 1bfe09b Update NNSVM. Don't count on those special functions that were in LinearKernel. I probably broke the save/load functionality, but Neil will solve that for us all with LibXML. The future is coming!
new 0ad0fb1 Oops, that single warning apparently makes the build unstable...
new 73de8f1
new 39b6e5a
new df442f6
new fdcd65f
new 3d63835
new b86727b
new 1d7fef2 Move files to .hpp and .cpp. Comment LMetric and MahalanobisDistance well.
new 997e5eb Fix a couple loose ends I didn't before.
new 060081d Fix includes and const.
new 09b6e2b Update name of lmetric.h to lmetric.hpp.
new 5892934 Update name of lmetric.h to lmetric.hpp.
new ba3cf73 Now debugging.
new 3b2e01d
new 5b92fca
new a932507
new 29e67e2
new a968dc7 lots of changes, including loading of bush half censored dataset
new 60634e4 added lars, mostly due to Karl Skoglund and Jingu Kim
new ea165c8 added Gaussian Sparse Coding using lars (with simpler code that does not generalize to expfam case, as well as perturbed version, and MTL version with perturbations
new e131eed
new 445864e alt traversal implemented and checked, approx-max-ip still to be checked
new 73adfb0
new 1a3b449 added negativity constraint to dictionary perturbation
new 2918380 added active set algorithms for nonnegative least squares with l1 penalty, as well as nonpositive least squares with l1 penalty (both algorithms are nearly identical)
new a32e674 added same as last update but using cvx (probably a lot slower
new 384848f added function for censoring based on some proportion of occurrences of top 10 words in a given topic
new 35ebe4e forgot to add this objective function
new ded361e added another censorship script
new 7442f16 Terminates when --attribute_dimensions_in missing for full Gaussian.
new acc1f70 Fixing the test.
new 9e9848b Change so that SamplingAccumulatePrecompute is called automatically everytime beta is drawn from the distribution.
new 587f0ef Option to simplify outputs.
new 31c7b43
new d8fd170
new 31e5cbe
new e5f8e38 mlpack/trunk/src/contrib/nslagle: add and modify more of the KDE code by DL
new 0e6f22d mlpack/trunk/src/contrib/nslagle: remove my directory from compilation and testing (damn you Jenkins)
new 234a782
new 631c8ca Adding a random generator for DCM Table.
new ace9a38 Random parameter generation.
new e7c9821 Document NeighborSearch class.
new 91ff9d1 Put these things inside the gmm namespace.
new d15f628 Document the SortPolicy classes; we will use the NearestNeighborSort class as the example class. Also change things so they are .hpp and not .h (#152).
new f2b9f16 Remove fastlib repository (fake commit during svn to git transition).
new 2f369e3 Move mlpack/trunk/ to root of repository (fake commit during svn to git transition).
new 0f23d5f Remove mlpack conf; it will live in its own repo (fake commit during svn to git transition).
new 8163576 Hide parameters inside of a namespace to help avoid collisions (#74).
new 048eee4 Hide PARAM declarations inside a namespace to help avoid collisions (#74).
new 8fdaaa6 Approx max ip running, approx tester running as well (but both not thoroughly checked
new 14d273b Approx max ip running, approx tester running as well (but both not thoroughly checked
new 89deb77 Insane commenting of everything. I think the PARAM_* macros should be split into another file because they are big now. Also, rename some files (#152).
new 8e47ded Implications of renaming io.h to cli.hpp.
new ec8fa75 Make sure we include cli.hpp, not io.h.
new 4b4259e Put dballbound into namespace mlpack::bound
new 5f6ef66 Move log.h to log.hpp, log.cc to log.cpp, and comment those files.
new 7efad68 Implications of log.h -> log.hpp change.
new de34498 mlpack::math namespace mess
new 244b427 Hah. That last important file need to change. Yeah, that one...
new d276f5b Move some more files to .hpp or .cpp. Place Option and ProgramDoc classes inside the io namespace. Oh, and document them all, because doing that is a Good Thing.
new 5f7addd Move files and then make sure documentation is created correctly.
new 2c5d398 Uh, I forgot a few things. Stupid Ryan.
new f9c1673 Remove using namespace mlpack::math in favor of math::Range
new c7f987c Comment the rest of the things in the io directory and move the files to .hpp and .cpp.
new 9668d1d Change core/tree, core/math to *.hpp, *.cpp
new f73d8b9 Use BOOST_REQUIRE_SMALL instead.
new a81f321 change optimizers/* to use hpp and cpp file extensions
new 5085e1a Change core/model to use *hpp, *cpp Reformat core/model namespaces Add namespace info to nnsmo*.h.
new f3b763a Change linear_regression file names to hpp, cpp Change #ifndef, #define
new afd4304 Move nnsvm to *hpp, *cpp files. Fix #ifndef, #defines
new acc0556 Move emst to hpp, cpp extensions Change #ifndef, #defines
new a1d3926 Move fastica -> hpp, cpp file extensions Update #ifndef, #defines
new 421674c Removed Dataset. Converted all data::Load and data::Save to armadillo's .load and .save.
new fcfbac3 mlpack/trunk/src/mlpack: rearrange and restructure the save/restore mechanism; clean up some code
new 508b99c mlpack/src/mlpack/core: remove files I accidentally re-added
new ca1863f Move spacetree.hpp to binary_space_tree.hpp (better name) and comment it all.
new 15a8795 Update includes of binary_search_tree.hpp.
new 8702a35 Reformat files in the math directory; comment them, and adhere to some new coding standards (#153).
new 5695e0d mlpack/src/contrib/nslagle: continue modifying the KDE code
new 00b669d Oct 25th, Rank-approximate fixed for very high k-values
new 1611a34 Changed a filename
new 38613b8 Changed filenames
new 1b50ad3 Using math_misc.hpp not math_lib.hpp.
new 0251283 appropriate changes made to work with new mlpack + alt-angle-pruning added
new 2973f3e Update names which were missed due to svn merges and my own failure to check the build.
new a7148a1 Waiting for arma::load() transpose -- quick fix now
new cc0471d Bank error in your favor. Collect $100.
new 4877361 Seriously, I didn't check this in?
new 1bb18f4 Add extra Mat code to load a transposed matrix. The patch has not yet been submitted to Conrad.
new 33e346c Don't include Armadillo directly; just include core.h.
new 194eeb7 Use CSVs not ARFFs. Transpose the dataset upon loading.
new 8d36ca3 Transpose matrices upon load
new dc1ee23 Why was it named .arff when it was a .csv?
new 90dd79d That's odd, I didn't properly convert that one to CSV.
new f1d8ba5 Use overloaded mat.save() and mat.load() functions.
new be15dc4 Different ordering for includes. Include armadillo in arma_extend.h.
new 8965dd2 Corner case: last_coordinates_ may happen to be initialized to what the user passes in as the coordinates; and in that case, the Precalculate() doesn't actually do its job. So, make sure a precalculation is done if one has never been done before.
new 3443a7d Cone-tree code named appropriately
new 5b05ec2 Cosine tree -- co-axial cone tree added and tested
new 0cf46b4 Require Armadillo 2.0.0 minimum, so we have CSV support.
new 9136535 contrib/nslagle: newest, not yet working KDE code; multi-bandwidth, dual-tree
new 791e23c Stupid idiot Ryan should not have checked that in
new 4be1768 Rename files to .hpp, .cpp
new 50e42d2 Add load and save and a constructor that loads model from file
new 863acc8 Fix #ifndef, #define, #endif
new c0086aa Fix braces, #153
new 943f41e mog/* to hpp & cpp filenames, fix #defines, etc
new c894b5d core/file to hpp & cpp
new 1026440 refactored random generation stuff, wrote a simple timing case
new 71aae11 Stop using TextWriter. This breaks already broken code. Waiting on resolution of #131. Also, this introduces forty ten bajillion warnings.
new 84c1bc2 Remove col/ and file/ since they are no longer used.
new 7ccdfd4 Don't include textfile.h because it doesn't exist.
new 4bc4c20 fixed small bug in angle results, made random generation stuff backwards compatible with boost (hopefully)
new 69ff08c Split timer functionality from CLI to Timers.
new 865558d Reformatted #includes according to new specifications.
new 60b17df Fighting with SVN over actually committing changes for timers.
new 96a09cc Formatted according to new brace styles.
new e0b41ba wrote emst_tests, fixed a few problems created by blindly replacing index_t with size_t
new c4ab140 Add data::Load() and data::Save() methods to wrap Armadillo functionality. Sadly we can't seem to get away from that.
new 6cec03f Re-add data directory.
new b3baae9 Add load.hpp and save.hpp to default includes.
new c4d3f33 Use data::Load and data::Save. This should fix our tests being slow.
new f8e0a44 Fixed regression w/ timers.
new f673bbb mlpack/contrib/nslagle: add the multi-tree base function
new c13ef1a mlpack/contrib/nslagle: add the multi-dualtree function
new c62ccd1 No need for duplication
new 286b70f The all encompasing test, it should be just names mlpack_test in the bit directory. All required dataset files are in a folder as well.
new ce9ba14 cleaned up a bit
new b3a95a2 mlpack/contrib/nslagle: commit more changes
new 3517c31 mlpack/contrib/nslagle: commit a possibly working version
new f90bcef mlpack/contrib/nslagle: correct for bounds; track the success level for each bandwidth
new 47394e5 mlpack/contrib/nslagle: commit more tweaks
new e9ca68e mlpack/contrib/nslagle: commit the latest changes; the binary tree apparently is not full
new 6928991 mlpack/contrib/nslagle: I wonder if the algorithm ever really worked...
new f215a8f Use BOOST_REQUIRE_CLOSE instead of just plain assert().
new ec0fc7c Fix compiler warnings so build is stable. This whole output file business still needs to be fixed.
new 5da0ccf mlpack/contrib/nslagle: the algorithm almost works...
new ad2b2d8 Update mog functions, eventually to be renamed GMMs. Work in progress -- not yet complete.
new 2fecd17 Add test for MoGEM.
new 42365ad MaxIP search commit after submission, need to clean up code and add approxMaxIP and fix the dual tree
new 153bef9 New pairwise distance computer
new 45af7ad Cleaned up and moved all stray tests and test data that is included in the general mlpack_test.
new c9d93a9 Someone owes me some food for this... well... if it's the bug.
new 5c52c2c mlpack/contrib/nslagle: KDE almost works, again...
new 1ec9cf8 comments
new 0c20936 vec = double resized the vector to size 1.
new d29408c A better test, but it's not quite working for some reason.
new 6638058 Set intercept to 0 for test debugging.
new 62d2360
new ee23259 Remove the extra load() stuff that was not the right choice in the end.
new 8b42195 No more contrib/.
new 0f0d2ec Fix documentation a little bit. We want the bug list; we don't want .svn.
new 9655ec9 Use new load().
new 7b97b44 Linear regression changes & fixes
new 68609fe Better comments, coding style improvements
new c0acbcf Ticket #126 : PCA code
new 707457c Ticket #126 : added entry for pca
new 6126a3c Update all tests to new formatting standards and make them all .cpp not .cc.
new e9381c9 added comments and made some formatting changes
new 77cdb84 Add HMM test. A bunch of stuff does work.
new d0569ee Modify HMM code. We'll make a new class, HMM<Distribution>, which will serve the purpose of all three of the previous classes.
new 045afdb Change the names of a few methods, and implement supervised training/estimation.
new da66ec5 Add test for supervised transition and emission matrix estimation.
new f6a594c Loosen bounds on test because the variance in the test is a little more than I had thought. I think these bounds are still good enough to know the test works.
new be59f91 Now there's a tricky corner case. If the random value is 1, then that inequality is never satisfied.
new 4d6904d Implement Generate() functionality.
new e0eee0b Widen error tolerance to more reasonable levels (determined empirically).
new 20cdc1c Add function to calculate log-likelihood.
new dbfdf4f It's tired and I'm late, so I make stupid simple errors like this.
new e2baa11 Add one more test for Generate(). The tolerance is a bit higher than I would like, but that's okay.
new e7ac813 Test HMM::LogLikelihood() for the discrete case.
new b0bccbd Comment Estimate() a little better and provide a convenience overload.
new ff72112 Use exact tolerance for probabilities, because it's harder to estimate smaller numbers.
new 9380ac2 Begin construction of Distribution classes so that we can generalize the HMM class.
new 8b6e5e0 Oops, I named a file wrong.
new 0e497fc Update CMakeLists to include new files.
new a20fa81 Flesh out DiscreteDistribution class entirely. Inline functions in class definition.
new 4a93b07 Add tests for DiscreteDistribution. These all work.
new b6f7e93 Fix compiler warning.
new 73ac5aa Make normalization safer; avoid division by 0.
new 805bd1a Add simple constructor and then make sure that every constructor normalizes the distribution.
new 9fa5515 Make sure the distribution is normalized.
new f8c6be5 Test that the distribution is normalized after construction.
new 81838ad Abstract away from the discrete case. Now, everything depends on Distribution (I think).
new fe04eb6 Use new HMM syntax, with DiscreteDistribution instead of int.
new 863989d Document the HMM class more effectively.
new 0f4061f Use a default template parameter for HMMs.
new 6cc6d50 changed the pca api. not using Armadillo's pca anymore. Still making a few changes ..need to check-in the comments to the api.
new 314f6de Code refactoring. Added comments to the methods.
new b0e6ae9 Move mog to gmm and update CMake configuration.
new c79f355 Remove MoGL2E. That can be implemented some other day.
new e25daff Move GMM test to where all the other tests are.
new a5f7627 Add an overload of phi() which can do multiple data points at once; this way, we can avoid recalculating the inverses of the covariances over and over and over again.
new bac6e4e Remove debugging output.
new 0f70d21 Rename MoGEM to GMM. Make cond_prob calculation a lot faster (but there are still some speed issues to work on).
new c4e6d48 Why did this ever pass any tests? I am officially confused.
new ea1daa1 dd
new 6c0203f Checkin mid-progress. Arbitrary data types added, need to clean up NearestNeighbors since it makes a few (too many) assumptions about the matrix it'll be using.
new f19ba7f What is wrong w/ my svn?
new 2faf8d1 Working copy SVN metadata is broken..
new 047be03 Diffed a clean working copy, this should end my svn issues.
new 8234cee Reverted changes, as it is apparent diff did not work. Will work on that, too.
new 8c2c5ee Format things just a little better.
new 0469d38 I am really frustrated by tests that don't always have a deterministic outcome.
new 663e9b4 Update GMM code. It should be a little faster training, but it is still too slow for my preferences. I am not sure what is making it so slow.
new 1e6c923 Compile GMM.
new ef9f876 Flesh out main executable for GMMs.
new 11d2414 Tests for GMM. Multivariate multi-Gaussian training tests included (that was the hardest one to get working right).
new 68bab77 Const-correctness, yo.
new a1730a4 Fix some warnings I inadvertently introduced.
new c717ca2 Add Gaussian distribution class.
new f7012e9 Compile Gaussian distribution class.
new ccb6cd5 Tests for GaussianDistribution class.
new 1c2e1d1 Why is this file here?
new a5db2af #162: use log-likelihoods instead of direct probabilities because direct probabilities get too small.
new 56d5442 Add a first test for a Gaussian HMM.
new d3d360a I accidentally had not generalized to the general observation case.
new 80bdcf0 Add test for Gaussian HMMs where we are training for both the labeled and unlabeled case. Almost done with the Gaussian HMM tests.
new 52264d3 Widen tolerances for unlabeled training.
new 359c8c9 Fixed some formatting.
new 7b3838e Test Generate() with a Gaussian HMM.
new fb08946 Make sure the state probability makes sense.
new 3ab7935 Don't use srand() in tests, so that the results are reproducible.
new bedfe71 Move distance functions and metrics into metrics/, and update the build accordingly.
new 9daa4cd Update kernels to metrics (where applicable).
new 17f2c08 Update kernels to metrics (where applicable).
new 4d548e5 Fix style as per #153 and name local class members as per #118.
new 9f97c88 Update style for #153; it was not completely done.
new da7c6c6 Adapt style per #153.
new 61f1296 Fix formatting as per #153.
new bc3cd33 Remove test file, and fix formatting as per #153.
new a8336dc Update style as per #153. Also, we didn't need the test here anymore.
new d030a59 Fix formatting in tests/ as per #153.
new b750b91 Format EMST as per #153.
new 42da0de Comment FastICA code as per #153. Remove a couple unused functions in lin_alg.hpp.
new b40845b Change filenames as per #152 and fix formatting as per #153.
new 4c3878c infomax_ica.h is now infomax_ica.hpp.
new 46feb25 Remove kernel PCA before Ajinkya's version, since Nick's won't be used.
new 273fee3 No more kernel PCA = no more kernel PCA test.
new ed2a46a Update formatting of linear_regression to reflect decisions made in #153.
new 5ff598a Move filenames to .hpp and .cpp to help finish #152, and fix style in accordance with #153. Removed phi() since it is a copy of the version found in methods/gmm/ (which will also have to be moved).
new f3322ee simple_nbc.h is now simple_nbc.hpp.
new 298e101 Change NCA filenames according to #152 and change style according to #153.
new b4e9ae0 nca.h is now nca.hpp.
new 7248611 Rename files to .cpp and .hpp in accordance with #152, and fix style to be in line with decisions in #153.
new c3afbb9 neighbor_search.h is now neighbor_search.hpp.
new 9a18990 We won't use Nick's implementation of ridge regression; we'll extend linear_regression instead.
new 6f92846 Remove RidgeRegression test since we aren't using that implementation anymore.
new af7ee6c Change to .hpp.
new 1601af3 Change name to .hpp.
new 22baef7 arma_extend.h is now arma_extend.hpp.
new 6edc460 No more regression.
new efaad77 arma_extend.h is now arma_extend.hpp.
new 4ec94a9 Use long doubles for comparison (compatibility with older Boost UTF).
new 1b25360 Style MVU as per #153 and move to .hpp and .cpp as in #152.
new a33eca6 Fix formatting of NNSVM code (#153).
new 4e2096d These methods are unmaintainable and will have to be re-implemented.
new 173d83d Remove SVM test and NNSVM test.
new e1e10f7 This is not used anymore.
new a44f616 Move core.h to core.hpp. Fixes #152.
new 9bbaefe Move K-Means to be its own method.
new 9ec287e Make KMeans into an actual class. It now supports "overclustering".
new f2df00e Add test for KMeans.
new 4d3e57f Add KMeans test and comment out GMM test since its API has not yet been adapted to work with the new KMeans.
new cc93bfc Don't build GMMs because they don't yet work with the new KMeans class.
new 7fdfe1d Add test for MinDistance identical case.
new b772793 Add a test for the identical case for MaxDistance().
new f559de5 Adapt to new KMeans API.
new 50cb61c Start compiling GMMs again.
new 80277ed GMM tests work again.
new 73fe049 <#126: Implement simple PCA> adding pca_test
new 05e36ce <#126: Implement simple PCA> adding pca_test
new fcae3eb <#126: Implement simple PCA> removing pca_test from pca dir (Added it in tests dir)
new f41e5be
new e00bb7b <#126: Implement simple PCA> changed assert to BOOST_REQUIRE_SMALL
new ab0d60d Absolutely minor formatting issue fixes; use BOOST_REQUIRE_CLOSE instead of BOOST_REQUIRE_SMALL.
new 73619fb Abstract some features of KMeans into template policy classes.
new 4b472d4 Adapt KMeans to new policy-based API.
new d0ee678 Test the different policy features of KMeans.
new 9c98053 I thought I was helping, but it turns out I just made things worse. BOOST_REQUIRE_SMALL is necessary because the eigenvalues could be zero. The fabs() isn't, though.
new 17dc704 You have to zero the counts first!
new a24c6f0 A better way of calculating the covariance, more akin to arma::cov.
new 7656478 Executable for K-Means. Celebrate!
new 2c984b1 Main executable for PCA. A couple little tweaks to the PCA code here and there.
new d191b51 <#165: PCA::Apply() fails with Armadillo error> was a minor bug in the indices passed to shed_cols
new f486f18 A couple formatting fixes after Ajinkya's fix for #165.
new ed1fb97 A couple more formatting fixes.
new 6c8c152 Make sure the covariance matrix is positive semidefinite.
new 790a497 Add another test case and simplify the first test case; the second test case currently does not work.
new a61b33e Update timers.hpp and timers.cpp to conform to formatting guidelines (and fix a syntax error!).
new 4842ff3 mlpack/core: apply some changes to HRect, Log, and BinarySpaceTree
new 3184d98 mlpack/core: undo an unnecessary change; remove a pesky warning
new b69af95 mlpack/core: add std::vector as a save/load valid type (so long as the templated type is basic, for now)
new bbb91e5 Change API to newer standards for HRectBound and BinarySpaceTree. Fix some formatting issues introduced in r10459.
new 1f1ed75 Make Range adhere to new formatting and naming conventions.
new d1c6d70 Update uses of BinarySpaceTree to conform to new API.
new fb19816 Update tests to reflect API changes.
new db5f2fa I have truly gone full style Nazi. But hey, now the variable naming conventions are correct here!
new 6569977 Improper use of regex leads to over-confidence about code compilability then sudden erosion of programmer confidence. Moral: your regex is always wrong.
new 55d747b Revamp L-BFGS code to remove CLI from its insides. Naming convention fixes, const fixes, the works.
new df0d25b Fix const-correctness of GetInitialPoint().
new ab53678 Remove FastICA because Nishant will be implementing RADICAL instead.
new c455209 Don't compile lin_alg_test while I think of where to put that code.
new 0ef356c Fix for integer parameter.
new c989357 Move FastICA linear algebra utilities to core/math/ (pending rename).
new a930868 Run the linear algebra test again since it's now in a different place.
new 8ffd46d < #166: PCA fails comparison with MATLAB> centering and scaling was causing the difference. By default other packages do not do zero-centering and scaling with std deviation.
new 97b7538 Remove unused PARAM_*.
new 673ecfb Ripped CLI out of nbc & gmm. Moved over to their respective mains.
new 9a963ec Ripped optionshierarchy out of CLI, deleted files.
new 4cfec54 Overhaul API for NeighborSearch (it probably is not complete) and remove dependence on CLI to help fix #150.
new a52c360 Update tests to conform to new NeighborSearch API.
new 6aa4222 Accidentally committed this minor change.
new e257c8e Remove CLI parameters from LBFGS.
new c85148b Remove infomax_ica since it will not be released.
new 5353365 Update comment to be more accurate.
new f481558 Minor tabbing fix.
new 2c14d36 Remove InfomaxICA test.
new 40db3c5 Remove Print() function in accordance with #164.
new 6f52cd4 Formatting fix, and prune CLI from the internals of DTB.
new 73c2dc2 Prune CLI from the internals of DTB.
new b6dbc34 Put the statistic class into the tree namespace.
new 6e8475f Add (as-of-yet) untested Range::Contains(const Range&).
new 540a988 Add RangeSearch to the list of methods we have.
new be558fb Add tests for RangeSearch; they are comprehensive (pretty much).
new 3743467 Add Dimensionality() function to distributions; use arma::mat and arma::vec instead of std::vector<Observation> and Observation; and don't use size_t in DiscreteDistribution.
new e52432b Adapt test to new distribution API.
new 7fc3e91 Adapt HMM to only use arma::vec as observations.
new 70ad46a Adapt HMM tests to new API.
new 2714216 Compile RangeSearch.
new 398825e Fix sanity check to actually check things correctly.
new c25fb56
new f49508d
new 213e9c2 Add Estimate(const arma::mat&, const arma::vec&) so that this class can work as a distribution for HMMs.
new 27039d4 First simple test for GMM::Estimate(const arma::mat&, const arma::vec&).
new 17a4c20 Move .h to .hpp and .cc to .cpp. We don't need dummy.cc anymore so it's removed.
new 0f1cc75 Compile LARS.
new ebfd37f Big API changes for LARS. Move things into the constructors; rename internal variables. Did a little commenting but I can't comment all that much.
new c85e6e4
new bacc754
new 54d19de changed CMakeLists.txt for radical so that compilation works in .../mlpack
new 580d150 added radical to CMakeLists.txt
new 2ba69b1 Apparently an adversary swapped every occurrence that should be data.n_rows to data.n_cols and vice versa. This has been fixed, and LARS works once again
new 62cb90e added LARS tests, but still need to make small changes before adding to CMake
new 9d7bfce added test cases for lars
new 512e8c3
new 7b7d948 Add GMM test case for training multivariate Gaussians in the setting where probabilities of each observation are given.
new 36fbc9e It helps when you actually implement the stupid function instead of being an idiot and thinking "well I'll just do it later but actually I'll forget that I didn't do it and then not get to go to sleep instead".
new 9eabccf Issue a warning when an empty GMM is created.
new 14c8070 Test GMM::Random().
new e486620 Actually, make that debugging only...
new 9748178 Test HMMs with GMMs; a simple Predict() test. Still need Estimate(), Estimate(...), LogLikelihood(), and maybe some other tests. I am reasonably confident the whole thing works correctly.
new 146c491 changed the test to accomodate pricipal axes in opp direction ie when eigenvectors returned are flipped in sign compared to the eignvec returned by matlab for the same dataset
new 74ee547 changed the api to accomodate centering and scaling of initial dataset. There was a bug as the end result of the transformed data was not centered, the results were not matching those from matlab.
new ab435e5 changed the api to accomodate centering and scaling of initial dataset.
new 3638d01 Don't use srand() in a test case.
new 3898529 Don't use srand() in test cases.
new ee01503 split dtb into _impl.hpp, should finish off ticket 117
new b1dfc0c Add -NDEBUG flag.
new e559885 Transpose before adding rows.
new 24f1689 Misspelling of option.
new d7a7f1a various style fixes to radical
new d6b359b more style fixes
new 9fe64c4 I think I fixed two bugs. need to check tomorrow
new a6d1e13 Reimplemented CLI w/o heirarchy. Eliminated concept of modules from CLI and main functions. So if it was foo/bar before, it will now be just bar.
new a04c458 Did some more formatting of output. Added more shortcuts to methods.
new 4fa4210 we no longer store the data matrix matX as a class member, we changed the call to WhitenX (it is now called WhitenFeatureMajorMatrix), and added comments
new b9dcda2 put Radical in namespace mlpack::radical and moved WhitenFeatureMajorMatrix out of Radical class but into mlpack::radical namespace
new 0504b48 added lots of comments
new 3764f73 small fixes to radical_main since we present radical with a n_dims by n_points matrix
new 1273961 made some speed optimizations via manual profiling
new 7c4c882 some speed optimizations
new e2f81f7 For some reason, this caused a segfault with -O2. This needs to be looked into.
new 9b236c8 added data needed for Radical test cases
new 4e72d55
new 78281d4 updated radical main
new b313874 added test case for radical
new d638092 added radical_test.cpp to CMakeLists.txt for test cases
new 3a8306f updated radical_test.cpp to use data::Load rather than .load
new 9fb3040 fixed small filepath bug
new 5e657c0 you can now set the input and output filenames, as well as the options, as paramters
new 54e84c3 cleaned up lars_main and added command line options
new 3e9c167 stylized lars
new 143b14b removed unnecessary files
new 6ae8614 removed unnecessary file
new c145a37 fixed CMakeLists.txt for lars and switched from _impl.hpp to .cpp
new 1c243d4
new 2c096dd many style fixes, made some functions private, commented out some unused functions
new b8b30da cleaned up lars
new ab715d8 and i present you <Kernel PCA>
new 8b170d5 Yeah, break everyone's build by requiring 2.4.0. It's for a good cause though.
new 803aa1a Add sparse support which can be patched into Armadillo if necessary.
new 8ede0e9 Convert u32 to uword for 2.4.0.
new b2ce582 Templatize the matrix type.
new 0006996 Abstract-ize HRectBound to accept arbitrary types of things.
new bdf2c0a A typedef so other types that depend on the matrix type can use it.
new ab08da5 We can use regular .col() here since we abstracted away arma::vec.
new b557d83 got the implementation into hpp file to include it in the class def. This is need to make the templates work. Good article here which talk about why we need this http://www.comeaucomputing.com/techtalk/templates/#whylinkerror
new 11184bd
new b3e0c0e Stop using unsafe_col().
new ef07d03 Refactor API to be consistent with RangeSearch.
new 685d465 API changes.
new 04f2a9d LARS no longer has X and y as class members. They are passed into the main computation function DoLars
new c7de3f4 updated lars_test to reflect changes to lars
new 0788a85 These aren't necessary with Armadillo >= 2.4.0.
new ded6707 Too much noise means I start doing things wrong.
new acada43 I had been approaching the wrong solution to the issue because they keep bringing me drinks.
new 65eac72 Copy code over from arma-sparse branch.
new 8dbc01d Retry the API change. This time it works...
new be370b2 Simpler swap_cols() and SpValProxy::operator=(SpValProxy&) to make it work.
new ef31455 Why does this fix the test? I don't know, but there's not complete time to fix it right now.
new 785a747 Allow sparse vectors to be passed to metrics (this should get a bit of speedup). Now we leave the computation up to Armadillo.
new b34a12c Abstractize vector type.
new 2039f13 Abstractize k-means so it can use sparse matrices.
new c3b30c6 Explicit conversion to mat.
new 4db8c8d Centroids should be sparse, too, if we want them to be.
new 94df198 Support SpSubview proxies.
new 887e569 Use a const reference internally in SpSubviews.
new d54173b Test sparse K-Means.
new 3e4f4f0 Unused variables.
new 48e3a0f Abstract-ize matrix type used for NCA datasets. The covariance matrix should not be sparse, though.
new 8eaab7a increased tolerance for RADICAL test
new dab5f8f Sparse NCA doesn't actually make sense.
new 9f1b2af removed random seed from radical_test.cpp
new d1a73ed Abstract-ize NBC to allow sparse matrices.
new 55af68f Clean up CLI formatting... for like the fifth time.
new 3463039 Document EMST better.
new d68d9c9 Oops, I need a <>.
new 534cdb8 Make statistics useful again.
new 0696844 New Statistic API.
new 69ce9b8 New Statistic API.
new 2409554 Restructure test.
new e804539 Refactor and clean up EMST code.
new b625bfd Refactoring of EMST/UnionFind API.
new 3b9fdd2 Update for transposition of output.
new 9c343e0 Clean up CLI output again and again. Then change how Timers works because it was being destructed before CLI in some cases. That's the danger of singletons...
new 4d76e86 Make it how it was before.
new 435ef44 Allow compilation with -DARMA_EXTRA_DEBUG.
new e7d39b4 Compile libmlpack.so not libmlpack.a.
new 7152df1 Comment things a little better, and rename one of the timers.
new 8c5880e This was not an input parameter.
new 7346395 Change in HasParam() changes a couple things in this test.
new d01c7f4 Move io/* to utilities/* then utilities to util (shorter, simpler name) and update all references thereto.
new 0f5317f -v == --verbose
new 981ab8f Allow a GMM to be saved and clean up documentation.
new 6b73100 Minor documentation fix for the namespace emst.
new 93441c5 Documentation fixes for GMMs and removal of now-unnecessary README.
new 051813c \bandwidth is not valid LaTeX... thanks regex...
new c4e5785 Two asterisks, not three. What is the meaning of life?
new 7049f6e Last run of modifications for EMST documentation.
new 38c4599 Expand the example for the GMM. This documentation should be done.
new 976b5e2 All these files are unnecessary because I re-implemented HMMs.
new 741a0ff Update documentation for HMMs. Documentation should be done for this class.
new 5826e0d Don't build these targets.
new 034218e Remove these executables because they don't work anymore.
new cd36312 Better documentation for K-Means.
new bc3d068 Did some refactoring on CLI, fixed a potential bug. Also removed some references to PARAM_MODULE.
new 117a912 added some comments to LARS
new 60ed209 more comments for lars
new 817ce6a Fix #174 and another bug in the main executable.
new d58c8af penultimate set of lars comments
new 492cf7f Fix segfault.
new e52d9c8 moved accessor definitions for LARS from lars.cpp to lars.hpp
new b0186f4 Copy test data to the right place after building the test.
new 6419223 Standard header include protection.
new 2de4edb Split math_misc.hpp as per #143.
new a2957bd Change variable names to match code specifications and mark a couple functions const.
new 27b0cfc Add license and copyright to satisfy #175.
new 241d74e That's embarrassing, I forgot the name of the guy who opened the ticket to make me fill this whole thing out...
new 4a88a55 Ignore some other things that we hadn't previously been ignoring.
new b51fd20 Move kpca to kernel_pca; clean up the code to match formatting standards (okay, some of my changes were superfluous), use size_t instead of int where necessary, and change CMake configuration so kernel_pca is compiled.
new ecca2e2 Clarify program name.
new ec3fe5e Redo LinearRegression API and put it into the regression namespace (not linear_regression). Make the main executable more functional and document it.
new 639bfa7 Namespace and API change for LinearRegression.
new 3708a0e Fix a bug which was overwriting memory and may be causing that segfault I am trying to hunt down on the build server...
new ac9b3f5 Refactor and comment NaiveBayes a little better.
new 890fc6a Fix bug and better warnings.
new b86e6dc Document NCA.
new 57be5b0 Not sure why I need to raise the tolerance... maybe something worse is wrong?
new c44c25c Redo API for NeighborSearch for the last time and go over documentation.
new 2d6074a Change formatting of RADICAL code and redo the documentation a little bit to make it more consistent with other programs.
new 6223300 This caused a problem for release-mode, so maybe this is the instability in the test.
new 660e863 Reset the tolerance to normal.
new 1f724b3 Format LARS a little better and give good program documentation.
new 46589be Update LARS test.
new 90b595e No longer need l here.
new bb1e5a5 I can't reproduce this error anywhere! Is something wrong on the build server? Comment out the test for now.
new 7e280df Clean up warnings.
new 702617c Version .so at 0.99.0.
new d412396 Remove unnecessary 'normalizer' variable and add accessor for gamma. No mutator because those two variables are codependent.
new d0d6a8b Use accessors and mutators for math::Range.
new 47f0705 Update tests to use accessors and mutators for math::Range.
new dcb8e2b Add accessors and mutators for AugLagrangian and L-BFGS. Change int to size_t where necessary.
new 39d7c90 Refactor BallBound API and clean it up.
new 726477a Change in BallBound API.
new 610c290 Some SpMat bugfixes.
new f53e32b Document timers and CLI a little better since we changed how it all works.
new 42e9f4f This isn't used anymore...
new 653e64a Add some useful documentation.
new fca8d02 Better documentation. Now we have a quick guide to MLPACK.
new ce76bd8 Remove a few warnings.
new 5946f9d Pretty poor implementations of min() and max() for sparse matrices.
new 18a356c Clean up BallBound code; now, expand things in batch because that's better.
new 58f4a43 Clean up warning, use Info instead of Debug.
new 6d0ab17 Clean up MVU code and add a main executable to it.
new af167bd Make sure that Doxygen actually picks up the guide we wrote.
new 5394afd Inline math::Range.
new e9ab4c8 Use Boost random number generators; account for API changes in 1.47.0.
new b37aebf Require boost::random and link against it.
new 8f1ea6d Stop using rand() and use Boost random numbers.
new 49034c8 Explicitly specify namespaces.
new c8bff33 Give a few specializations for vectors, and remove using directives.
new 190e180 Give direct access to discrete distribution probability vector.
new cb7bacf Update to new direct-access DiscreteDistribution::Probabilities() API.
new a234f7e Clarify error messages, and actually assign the parameter to what is read for a few cases. Use std::string& not std::string for LoadParameter().
new 0e39a07 Formatting for the entire /tests.
new 5c16e0f
new 08ac900 Turning in with some tests for the implemented distances in periodichrectbound.
new 7dd4af9 Properly formatted /gmm
new 4816416 More test cases, as well as formatting of /kernel_pca
new 11583d5 Correction for the range test.
new 073d8a3 Formatting of /kmeans.
new c7db50a The test cases for maximum periodic distance, as well as the code for both versions of the maximum periodic distance.
new 22c572d Removed the extra print statements that I forgot in there.
new 8da7699 Formatting of /linear_regression
new bd7de07 Formatted /mvu
new 6c40b54 Formatting of /radical
new cad0500 Formatted /pca
new de7f8b2 Formatted /nearest_neighbor
new 555c2bb The fix to the previous fix.
new 8573557 Formatted /math
new a162510 Formatted /util
new b13c373 Formatted /tree
new cbdbd27 Normalize vectors because Probabilities() doesn't do it anymore.
new 43ab51c Add main executables for HMMs.
new 1886e3a Explicit namespace usage.
new d5e96bf We have a few more executables now.
new c93e7da Implement operator|= correctly.
new d699ee2 Fix use of uninitialized variables.
new 6df60db Utilities for loading/saving HMMs; to be deprecated later.
new 319a9d7 Move distributions to core/dists/.
new dfdbd24 Add CMake configuration.
new 3c5eb81 Fix formatting for L-BFGS.
new 5df49a7 Fix formatting for AugLagrangian and associated test functions.
new da69803 Fix braces.
new abac812 Fix comment.
new d2493c4 Change name of box().
new d50ad44 Boost <= 1.41 did not have a separate random package.
new 58abed8 Search correctly for Boost.Random. It did not exist separately until 1.46.
new d6df0bb box() -> Box().
new 5ea8a1e Fix >= Boost 1.47 issues.
new f66fc16 box() -> Box()
new ec1bffa Smarter linking of MLPACK against Boost.
new 77450a6 Fixes for old Boost.UnitTestFramework.
new 5f45320 kernel pca works with linear Kernel now.
new 777771f
new d402af4 update version and soname
new 5965238 Don't run test cases that don't work because the code was never finished.
new 9f56844 Fix two warnings and some style.
new 83ab860 kernel pca test file
new 0de8ebd exponential kernel
new ad450a0 laplacian kernel
new dba8a28 polynomial kernel
new 0fcddd7 fixed compilation error for boost 1.47 by adding <> to uniform_01
new a0073d3 formatting changes
new 85d6b32 hyperbolic tangent kernel
new 081184a fixed a few bugs
new 3dec62c tests for the new kernels
new a10e316
new 86b32d5 Fix all the things cppcheck didn't like.
new 9124085 We don't actually need a reference to the new child...
new 94ebf46 non-class type return values are non-modifiable, const qualifier is ignored (-Wignored-qualifiers)
new d74e649 Comment out unused parameter names (suprisingly valid C++), -Wunused-parameter
new edce15b How many unused parameters does one library need...
new 75ef87e Add RandomSeed() function to set the random seed, which is always a good time to be had.
new fadb593 Use uint32_t because that's what the class uses internally.
new 9a79a28 Fix the compilation error from my -Wunused-parameter fix when compiling without debugging and profiling and with -O2.
new 1bb2368 Another -Wunused-parameter fix
new c387bc9 Add -Wextra and -Werror for debug and non-debug builds.
new 42aec38 Apparently jenkins uses an older version of boost and we had a #define that caused an unused variable warning...
new 65cd7d5 Hey, cool! A warning solved a bug.
new 4ce817f WTF SVN? I update, you give a conflict, and when I resolve it, you drop the semicolon? Or was it my fault...?
new 2304532 Add option for random seed (for #182).
new 120dc95 Add support for --seed to HMM executables (where necessary).
new 8fe1b15 Add --seed support for K-Means executable.
new 7c21bdf Minor spelling fix.
new 068540b Set the standard seed (srand()) also, because Armadillo is likely to use that, and in places we use .randn() or .randu().
new c201624 Weird, these aren't necessary.
new 6f52a62 Make documentation more the same-like. You know?
new f61f5fa Add a tutorial for NeighborSearch. That took a little while...
new d7e28d1 Add an actual page for the tutorials.
new b0ca103 Some formatting fixes. We have lines longer than 80 characters but that is unfortunately necessary to make Doxygen work right in some cases...
new b46b8bf So that we get that nice hyperlink.
new 3839ef5 No -Werror for now (the build server gets angry, gcc doesn't have to).
new ce4282c Fix some errors present on older gcc versions.
new fc8c392 fixed some stupid typecasting warnings
new a28291a No need to link against LAPACK or BLAS; Armadillo does that.
new 564ca2f Install binaries in the proper location.
new 64f53df Wait, it's not an ugly hack anymore (it was before, then I changed it and forgot to remove the comment).
new 7a23213 Add 'make test' command. This should make the build fail if the test does not pass. It is not run by default if you type 'make'; you have to type 'make test' to actually run the test.
new 1e3fc2b Add 'make doc' command, but it does not yet install the documentation (that will come next).
new 0bd9289 Rename project to 'mlpack' (so we install documentation to /usr/share/doc/mlpack/ not /usr/share/doc/MLPACK/) and add installation rule for generated HTML documentation (goes into /usr/share/doc/mlpack/html/).
new ad12518 Higher tolerance for Laplacian kernel.
new b262349 Don't use GNUInstallDirs. Assemble /usr/share/doc/mlpack/ by hand (it's not so hard!).
new 4fbf7ee Don't install Doxygen documentation if it was never built.
new 85f3803 The parameter names were... wrong.
new 93b43ea Haha! Other people should be able to make tutorials too!
new f9578ad Fix scoping issues. Stupid Ryan!
new 3c6b097 Refactor AugLagrangian for better use by other classes. AugLagrangianFunction is its own standalone class now to allow for easier specialization. The tests aren't quite done yet (the LRSDP Lovasz-Theta ones still fail and give unnecessary debugging output) but that's the next thing to do.
new 618c712 This will hold an optimizer for low-rank semidefinite programs, formulated by Monteiro and Burer. It was originally using AugLagrangian but I decided to specialize it further to the general LRSDP case.
new 034e687 Basic implementation of LRSDP. Not yet tested.
new 6e4e22a Don't set any RPATH.
new 529c99b Revert RPATH change. We have to build with the RPATH and strip it at install time.
new 2bbcd77 Actually write the "correct" installation commands, so that RPATH gets stripped at install time.
new 9beee49 Add operators for SpSubview.
new f5e4ad6 A script that can turn our output into man pages. This is for packaging, but man pages are good, you know.
new 957c44e No preview in an automated setting...
new 39b4191 Script to make all man pages.
new 2dc1210 Make the directory if it doesn't exist.
new 7180817 Force gzip compression; make sure it is not interactive.
new 3ebbe69 Make rules to generate man page documentation. This is goodliness.
new 08ba6e0 Apparently, when I wrote this, I did not understand how floating point numbers worked.
new 5fe4932 Temporary work check-in so I can work somewhere else.
new 52e925f Temporary work check-in so I can work from elsewhere.
new 6c7d13d Change documentation a little bit to prevent man macro error (hopefully).
new 60a4f3f Fix spelling error.
new 59d14a6 Wow, awk is crazy. This fixes warnings in the troff output given by txt2man.
new e92b8d4 A few changes to the implementation of LRSDP. Still does not quite work yet.
new ab1d06f Limit on number of iterations, and set the first lambda value right for LRSDP (this will need to be changed later).
new eb304a2 It works! I can't believe it works.
new 7484128 Don't do extremely simple LRSDP test; it needs a different first Lagrange multiplier. We'll work that out later. Remove SDP tests from AugLagrangian tests. Compile it all and add it to the usual tests.
new cc1ad99 Allow setting of random seed for RADICAL.
new 010324a Fix a few warnings for unused variables that I introduced.
new 23a33e6 Add the dataset we work with.
new 8302467 Allow two modes of constraint matrices. Not yet documented.
new 599003a Add tests for two other Lovasz-Theta problems. hamming6-4 isn't converging right, and keller4 is working, but takes 5 minutes. Perhaps johnson8-4-4 will be the only test case we use in the long run.
new 77c0a0d Implemented range search, need to implement output functionality. Also need to update the documentation to reflect realities of range search.
new f883858 Default and copy constructors.
new 3a920e7 This fixes the arm test bug.
new 18c93d4 Update for new L-BFGS API.
new e0a1f0b Revamp L-BFGS API, moving around where the maximum number of iterations is set and stored.
new 7f181c4 Revamp the AugLagrangian API to deal with the new L-BFGS API, and take a pre-constructed L-BFGS object at construction time.
new 813a65e A quick hack to make the tests faster. This'll go away when I redo the LRSDP API.
new 258290a Revamp NCA and MVU, which use AugLagrangian and LRSDP, respectively. MVU is not yet done but, bit by bit...
new 2433f54 Don't link range_search_main.cpp into MLPACK; it adds unwanted CLI options. And use spaces, not tabs.
new fe0d1e4 Further refactor AugLagrangian API to make it simpler.
new 5fc87a7 Refactor LRSDP API for ease of usage.
new f83ee8b Clean up LRSDP test and add a dataset which we are not using (but the test is written for it -- it's just commented out).
new 0191349 Just so it compiles for now...
new 17e197b Let's not set sigma to a value which ensures the algorithm will never terminate...
new fb7556e Fix out-of-order initialization warning.
new 6b728c3 Various improvements to LinearRegression and our executable.
new 080c5a4 Incomplete rough draft of the LinearRegression tutorial.
new c91ecdb coding with LinearRegression examples
new 0d0b19c more comments for the comment god
new 2045039 fix ticket #184
new 46a5032 Add RandNormal() and fix some const-correctness semi-issues.
new 442b434 Misplaced space. The horror!
new 23577d5 Initialize StatisticType objects in the root node too.
new 5253621 MRKDStatistic for mrkd-trees. Probably still needs improvements.
new 762a15d A few fixes so that things can compile with older Boost.Test versions.
new 99f656b Some changes; use M_PI instead of math::pi() (for consistency across all MLPACK code), and explicitly specify using namespace mlpack::math so that radical compiles on older versions of gcc.
new 392b696 Make this actually compile when used with BinarySpaceTree
new b93504f Appears to work now.
new e741fae Add a splitDimension variable and getter for determining which dimension a node is split on.
new bd50c5e Tab fix (think I got them all)
new 220e87c fabs(max(,)) -> max(fabs(),fabs())
new 122372e Move to range_search_main.cpp and clean up executable.
new 091cfe6 A couple changes to the kernel PCA test.
new e53aece Clean up some comments and the sanity check on the dimensionality should be the upper limit, not the lower limit -- dimension < 0 is not possible with size_t.
new 19257d8 Put down the crack pipe, Ryan.
new bb740bd This is a copy of the Gaussian kernel... oops...
new a252626 Remove exponential kernel from sources.
new f0438dc Some cleanup for kernels.
new 4874ac4 No more ExponentialKernel.
new 8c488ab An actual main executable and some implementation tweaks for speed.
new 37aeecf corrected elastic net / lasso objective function in the comments. I had forgotten to put the 0.5 scaling factor on the reconstruction error part of the objective
new b989410 Some formatting fixes.
new de950a1 Add --scale and --nocenter options.
new b8e3c60 I had the options backwards; also clarify documentation.
new 0af3c43 Add --scale and --nocenter options. Also center by default for PCA.
new f3f0a1c Helpful note pointing to other documentation, so we don't need to include citations in -h output.
new a98a285 Slight change because CLI outputs differently now.
new df9af92 Remove unnecessary citations and change formatting of citations with respect to opinions expressed in #201.
new 4938588 Remove citations from -h output.
new 47f2f97 Remove citation from -h output.
new 606adbc Remove citation from -h and put @code around it in the RADICAL documentation.
new 9fc882b Fix references in tutorial; rewrite into a little bit and clarify some terminology here and there. Also unnecessary grammar Nazi strikes again...
new 6bfe417 Forgot two references.
new c11244d Fix references.
new 9d7e98b List linear regression tutorial.
new 7d818cf Credit where it's due. I might be missing a name or two...
new 9a00584 Mistype found.
new 0518240 Add a range search tutorial. Should be done...
new 215bea9 Add range search tutorial to list of tutorials.
new 8f62b88 Removed c-strings in favor of std strings.
new 2637a49 That isn't a correct Doxygen comment...
new 6604788 mlpack/core/kernels: add a couple of kernels appropriate for the forthcoming KCDE/KDE combo, per #200
new 59a9d91 Initialize LRSDP A and b vectors to the correct size at construction time, instead of confusingly expecting users to take care of that themselves.
new d994167 The sparse A matrices should be able to have a value.
new 777d2c3 Changes according to the changes in the LRSDP API.
new 6eb0c05 Hey, so, it turns out when you find the package, you've gotta add the include directories too.
new 3990a72 These aren't necessary any more.
new 526adb4 Some changes to mvu. Not 100% sure if it works yet.
new 1275baf added sparse coding
new 7fa1b3c
new 149f09d added small 500-point version of MNIST
new 64db04b fixed CMakeLists.txt to reflect correct demo program name
new 74afd6d fixed small bug in lars: sometimes after kicking a dimension out of the active set, we also need to explicitly set the corresponding coefficient to zero. In that case, we were saving beta to the end of the beta path before the fix. now, we save beta after the fix. This fixes a bug
new 5578e41 fixed a bug in how we were checking the optimality conditions for the LASSO. holy shit, an error in the test case itself!
new 2710d9b added test cases for sparse coding
new 7f743cb updated path to mnist file
new 4a1a00c added modifier (setter) for data X
new 3286b9c added sparse coding to CMakeLists.txt
new 7d2628b added sparse_coding_test to CMakeLists.txt
new 5edaf7d added local coordinate coding to methods
new 7eb35ae
new 015e303 added local_coordinate_coding to CMakeLists.txt
new 6c2ed37 Mostly, hopefully, working implementation of Pelleg and Moore's mrkd tree k-means.
new f812e25 added tests for lcc
new 4c44848 Some changes that had been forgotten.
new b46a057 Unpack tar.bz2 for Nishant's sparse coding tests.
new cd1c039 Maybe it works, but I'm not totally sure.
new fd4e63b Modified string types in cli & related sources.
new 5bf9ff7 Three new methods for trunk.
new 6c86abf Add local_coordinate_coding and sparse_coding to man rule.
new 8dcd69c removed some commented code that no longer is needed
new 94e4e96 Untested Windows code needs to not be untested...
new 2280ff0 Fix #207.
new f9fd099 when useCholesky=true, we now use a once-computed Gram matrix for inner product computations between points. If one is calling LARS repeatedly with the same data X (as in sparse coding), one should use SetGram even when useCholesky=true, and in particular, it is better to use SetGramMem
new 1c6accb Switched to Cholesky-based LARS. this version of LARS now uses Gram matrix in some places. We use SetGramMem rather than SetGram to avoid copying Gram matrix unnecessarily. Also, removed some commented out that was quite old
new d79fbe8 Install range_search executable.
new 6e618d6 Something's wrong with this
new 78181b3 Use in-house random functions, not drand48().
new 1a49096 Make CMake configuration better by linking directly to the library locations, not just the library. This is for Windows compatibility.
new ea39699 Reformat CMake configuration file. Only use -Wall and -Wextra on GCC-like compilers. The special handling of LibXml2 is unnecessary because that's all done by FindLibXml2.cmake anyway.
new 5c588f3 We shouldn't provide these ourselves; CMake 2.8 does that already.
new 0d9c295 Windows #defines min and max; undo these defines so we can use std::min() and std::max().
new af34dad More typenames, required by VS2010 but not by GCC (for some reason).
new 13454d3 Only give stacktraces on Linux boxes; Windows doesn't have execinfo.h or cxxabi.h.
new a747896 Fix apparently untested Windows code.
new fe1a232 No execinfo.h on Windows.
new 377f67a Eliminate ambiguity in a few function calls.
new af38305 Require FORTRAN because FindLAPACK requires FORTRAN.
new d35841c Wait, we don't even need LAPACK. That comes through Armadillo.
new cdfd49b Turns out not every version of CMake ships with this...
new 0f3c989 Special handling of Boost linking properties for Visual Studio. This was necessary for me to make things link correctly.
new ba9c831 Implementation of round() for C99-deficient compilers (MSVC...).
new 4642f45 Use boost tgamma and include that round function we made earlier.
new a22b806 Link to direct location of unit test framework library.
new 3a21503 Various fixes for Windows compilation.
new 1c7749d Be a little pickier with how we build on Windows. Static library because creating a DLL correctly would be a nightmare.
new 47f9f53 Fix #210. Stupid error...
new 1d89ea2 Generate Doxygen documentation with 'make doc' only in out-of-source build directory -- don't clutter source directory. (I'm proud of this)
new 7827baa Make timers multi-run.
new 7f6eef3 Test multi-run timer functionality.
new 9488734 Look for possible dependencies of libxml2.dll, to issue a warning to the user in case they don't exist.
new e0921c5 Link against LAPACK and BLAS on Windows because Armadillo doesn't automatically do it.
new 07155b3 No colors on Windows because command.exe doesn't recognize ANSI color escape sequences...
new 5890ddb Patch by andreasl: no definitions of promote_type<u64, ...> are necessary if ARMA_64BIT_WORD is defined.
new a985ddb Patch by andreasl: change u32 to uword (the generalized Armadillo type, which can handle 64-bit Armadillo).
new f6cd00a Working, mostly finished pelleg and moore mrkd kmeans implementation
new f8fc005 Add more fields to the mrkd statistic
new 98dd09f Oops, I did screw it up.
new e8c22e5 I think that some of the promotions I had written are actually invalid. For now, we simply use what is given in Armadillo when ARMA_64BIT_WORD is defined.
new 02fc05f It makes no difference in reality, but don't define is_supported_elem_type<u64> or is_supported_elem_type<s64> if ARMA_64BIT_WORD is used.
new 4935b47 comment fix
new f29be15 Define timersub() before it's used on Windows boxes. For some reason VS2010 didn't have a problem with that.
new b26f95f Use Sleep() on Win32 systems. This isn't tested yet -- but I'll do that in a moment.
new 918bc97 Greater than or equal to -- because some systems are very precise.
new 1304ea4 Require version of libxml2 to be at least 2.6.0 (which is dated late 2003... so it shouldn't be a problem for people to have it).
new c7bd96b Search for iconv.h on Windows systems.
new 236ff63 Artifact from pthreads which isn't used anymore.
new 554c349 Add GMM::Probability(arma::vec, size_t) as part of #212.
new f35c606 Test GMM::Probability() (both overloads).
new b7afa68 Add a Classify() method.
new b4b1b3c Test the new Classify() method.
new 2303048 Increase tolerance a little bit so the builds don't fail so much.
new dfd9833 I hate test tolerances so much.
new ff2471b Forgot to commit this, fixes forgetting to set minDistance
new 9d3c06c Added enhancements to pca & kernel pca.
new 8c99545 Undo accidental test compilation commit -- we like all the tests.
new dfecdb1 Add to contributors
new d00bf97 Update metrics to support distinct vector types as arguments.
new 26a372d remove useless code
new cd12d5a Modified PCA/Kernel PCA interfaces to remove redundant centering option.
new 7bfcd0d Density Estimation Trees (DET) added to mlpack
new 37cbe7c DET CMakeLists added
new 2966a96 DET CMakeLists
new aa749f9 DET naming schemes
new bfaa90a DET naming schemes
new 1b7752e Handle a case where the step size ends up being 0 but the gradient is not yet the minimum gradient size. Maybe it is a little slow (elementwise comparison is not incredibly fast)...
new 2ace7a9 Clean up some man page warnings.
new b0cc54b DET Tests (almost all done) added
new 5a977eb DET tutorial 1st draft
new ffda3a1 Use Log::Debug instead of cout for debugging output (maybe it should be Info?). Also needlessly replace '\n' with std::endl -- really, there's no reason to do this; I just did it.
new 4cfe873 Declare the function before we use it.
new 9afa5c2 Refactor GMMs so that you can use any clustering method you like. The default is "EMFit", which is the EM algorithm (exactly how it performed before).
new 6aa62fe Use GMM<> not GMM, because it's now a templated class.
new ed58e78 Rewrite GMM tests to use GMM<> not GMM (because it is a template class now).
new c007936 Switch from armadillo's load() to data::Load()
new 9238d35 Fix tabs
new e0be8f0 Fix test compile time errors, missing <> for GMM
new 8640d1c The fabled GMM-HMM training test. The hardest of all tests, only the strongest training implementations survive the double-sucker-punch of GMM followed by GMM. A more rigorous drill sergeant might require tighter tolerances, but unfortunately perfection can't be expected out of the EM algorithm every time.
new 4b25065 Hackery necessary for sparse support using Armadillo 3.0.0 or greater.
new 3924ac7 Include new traits.hpp file.
new 72db5ac Workaround for Armadillo 3.0.0 bug.
new bf4fc85 Fix ambiguity error under Armadillo 3.0.0.
new e724012 Pass one: comment grammar Nazi and fix code style issues.
new 50285db Pass two: const-correctness (mostly) and use size_t instead of arma::uword.
new 120c647 Missed a couple uwords.
new c0c92a9 Rename some variables in the class. Not done yet...
new d01517f Update tests to reflect new method names.
new a5f9a01 Fix longer-than-80-character lines.
new d2cbaef Fix longer-than-80-character line.
new 8835cfb First pass: style. Fix a memory leak or two too.
new 01ba692 Fix namespace ambiguity.
new 6f8fca9 Take care of FittingType when we are passing in means, covariances, and weights to build a GMM.
new 78ff46e Handle Boost 1.33 Random library correctly. I am not sure how far backwards this fix extends.
new fd68700 Fix preprocessor ifs for Boost <= 1.39 Random API changes.
new 0ec80ff Make ourselves compatible with older versions of Boost.Test.
new f1c5386 We need to actually get the version number before we check what it is...
new 99eac8c Zero the memory before we start adding to it.
new 5689221 An implementation of cover trees. It is not yet polished, and the debugging comments are still inside of it (though commented out). I will be polishing it shortly...
new 9657c51 Add two tests for the CoverTree class; a simple test and a big (random) test.
new f725616 Add NumChildren() and Child() to BinarySpaceTree for compatibility.
new 83eb9f8 Fix warnings I introduced. Oops...
new 254ee39 Comment the CoverTree implementation a lot better. Still a few things to do...
new 549c5ad Remove unnecessary debugging output from test.
new 493f911 Regresion is cool, but this method is regression.
new 8174b77 Refactor LARS. Fix comments, remove unnecessary methods, and consolidate constructors.
new 07fcf8c Don't use a pointer for LARS objects; no need to do memory allocation on our own. Adapt to new constructor calls, so there is no more need for SetGramMatrix().
new 7165ada In fact, remove the line entirely.
new ba2405c Refactor in accordance with new LARS API.
new f48e143 Allow arbitrary metrics to be used in the construction of the cover tree.
new 6346334 Test an alternate metric construction of the cover tree.
new 9cc53b5 Fix misleading documentation...
new 58bf1ac s/IO/CLI/g wasn't a good idea.
new 0952226 Allow template parameter class to specify which point should be chosen as the root node. Document template parameters a little bit (but hopefully this will be redone at some point).
new c2a2d65 Add NumPoints() and Point() to BinarySpaceTree. Maybe Count() and Begin() could be deprecated...?
new 37d90c5 Give better debugging output.
new 7d6121f Tabs to spaces, and return a reference, not a pointer.
new 1601323 Add a single-tree depth-first traverser. It is not as fast as it could be.
new c57b0bd Add the NeighborSearchRules class, which defines how the SingleTreeDepthFirstTraverser can perform a NeighborSearch. Adapt the NeighborSearch class to use this. It is not as fast as it could be.
new ced17d7 Ack, how could I violate my own coding style guidelines?
new 2df09d4 Add the very similar SingleTreeBreadthFirstTraverser, meant to be used with the CoverTree.
new 12434a3 Modify the API of BinarySpaceTree to include a few more methods. Starting to settle on a more standard tree API.
new 48a8fe6 Modify CoverTree API towards a more standard API. It can be used with NeighborSearch now... although it probably will fail miserably.
new 115d43c Update our traversers so that they don't consider self-children. I am not too happy with how unclean it is, but I expect it'll get cleaned later.
new 52fde2b Update API to use TreeType::MinDistance() because other tree types may not have a bound object.
new bc78baf Use the tree's preferred traverser type.
new bf25afc Fix some formatting and style issues, and then add a test for nearest-neighbors cover tree.
new 18743fc Remove unnecessary debug output.
new 1985330 Add a dual-tree depth-first traverser.
new 5218ec8 Save just a little time where we can.
new bc32a30 Include statistic.hpp (so we have EmptyStatistic).
new 46f8a38 Add dual_tree_depth_first_traverser.hpp to build list.
new 1957814 Add an option to use cover trees.
new cb3af4b Add implementation of rules for dual-tree search.
new dea573c Use DualTreeDepthFirstTraverser for naive and dual-tree calculations, and remove all of the guts we previously needed but don't anymore (ComputeBaseCase, ComputeDualNeighborsRecursion, ComputeSingleNeighborsRecursion).
new b7a2c6d This bothers me a lot more than it should. (used to say "5mins,4.3secs", now says "5mins, 4.3secs")
new 9910cd1 Make this an iterative implementation.
new 61896da Well, that would break everything...
new ea6b8b0 Add DualTreeBreadthFirstTraverser (at this moment, not rigorously tested).
new 063a62a I didn't do this right; I forgot about the "UpdateAfterRecursion" step and broke everything. So... revert to the recursive implementation for now.
new 1110261 Correctly handle cases where implicit nodes are created.
new 6cdc78c Add a preferred dual tree traverser.
new 067c07e Add preferred traverser and dual cover tree traverser (which doesn't prune at the moment).
new b3ba215 Add rules for cover tree search. This breaks the nice abstractions I was trying for.
new a4aed0d Add a dual-tree test for cover trees.
new 70de44b Add directory for implementation of MaxIP. I think it needs a better name...
new 2f98894 Remove debugging output.
new f3c9fa6 Add the IPMetric, which is the "inner product" metric which calculates the metric induced by a kernel.
new 443e8d8 Add rules for the MaxIP single-tree search.
new 10788af Add MaxIP class.
new 609523c Add CMake configuration so MaxIP gets compiled.
new ee99f80 Add maxip to project build.
new 1833987 Add simple first test for MaxIP.
new e066003 Clarify error message; k can be equal to the number of points.
new 121c87b It helps if the conditional is right, too.
new c4eb63a Give number of prunes.
new 7a9c7cb Add maxip executable.
new 6511fbb Don't get it backwards...
new ee59215 Add template specalization for linear kernel.
new 8583569 Avoid double-evaluation of base case.
new 174fc05 unsafe_col() is faster.
new 171d9dc UL and ULL extensions for older GCC.
new af7500b Reimplement single-tree search. It's faster now.
new 3b3a802 This file doesn't exist. I didn't need it.
new d0c8125 Ensmallen and randomize.
new c1e8043 Initialize products to DBL_MIN.
new 8c9380a Use unsafe_col() 'cause it's faster.
new c652644 Rewrite to only use one queue. Not very happy with this implementation.
new 5e8f67e Add a kernel which I'll remove later. I don't like it...
new a9581ba We can do polynomial kernels too.
new 08e2033 Check in modifications.
new dcc2bf6 Update kernels in ugly ways that need to be removed later.
new 14370b9 Needs to be the square root, not actually K(q, q).
new 4cd5899 Put ugly global variable in so it compiles. This will be cleaned later...
new 07d93db Consider queryProducts kernel evaluations too.
new 628b776 Don't used squared distance in tree construction.
new 6f3cc23 Revamp breadth-first descent to consider tree levels so it is the proper breadth-first descent.
new 26325d3 Count kernel evaluations.
new 94b87e9 This test does not compile with Armadillo 3.2; I have not yet had a chance to figure out why.
new e9a930c Work for older CMake versions (2.8.2) and finding older Armadillo versions.
new 34102cb Halfway transitioned to newer implementation, which does not try so hard to conserve memory.
new 0fb10c8 Rewrite swapping code.
new 28499a5 Some slightly ugly additions -- but which give an order of magnitude speedup during cover tree construction. It turned out that when we were handing the new near and far set to a child, we did not remove points with distance further than the far set bound, meaning that the far sets were way larger than they needed to be. Preliminary results indicate fewer distance calculations during tree-building than Langford's original implementation.
new 60e1694 Relax the separation constraint to include equality (in accordance with the paper).
new 89f2159 Store furthest child distance and furthest descendant distance. This can allow better pruning rules.
new 8dae279 Fix a couple bugs in furthest child and descendant determination.
new 05a7fd5 No far set in root node.
new a5e73dc No far set in root node.
new 6211a2c Parent distance is the interesting one to track, not furthest child distance. Fix a few bugs so that furthest descendant distance is correct.
new 4e7c68c Add two more kernels. They need to be parameterized.
new 4e37402 fixed line that referred to nearest neighbor search
new 573371b wrote EMST tutorial
new f0f6871 Clean up cover tree implementation a little bit. Allow instantiated metrics (good for hyptan or gaussian kernels or any other kernels with parameters).
new 48e3f49 Refactor and clean epanechnikov kernel.
new 0f6727d Remove static Gaussian kernel hack.
new 494ac24 Best not to promise functionality we might never get around to.
new c4e0963 Remove the no-offset kernel; it is not useful and was a hack for a deadline.
new 659f1d6 Include new files.
new af91b32 Fix top-of-file comments.
new 26362ce Rewrite triangular kernel with parameters.
new d381af5 Check in mess of MaxIP code which is being cleaned little by little...
new 77f6497 Test modified for new MaxIP API.
new 5898396 I don't believe this is a valid kernel.
new 0e86a1e Update documentation slightly.
new b8a9116 Finish refactoring for each kernel type.
new 1fcedc4 A couple of files were not included.
new ba8e0b9 Some code cleanup.
new aa83e42 Code cleanup; don't use namespace arma (since that's done nowhere else) and clean and condense things a little bit. Not a big overhaul -- but it's coming.
new 73da623 This was being passed in backwards.
new 92b9129 Modify LARS API to accept non-transposed matrices. This is easier on the user...
new 35072cc Adapt for new LARS DoLARS() API.
new 2b58eb3 More refactoring; remove nActive because it isn't necessary, and include solution in the call to DoLARS().
new 8f1081f Changes to DoLARS() propagating to here.
new 067f8b2 Changes to DoLARS() propagating to here.
new daf29e3 Change DoLARS() to more descriptive and less awkward Regress(). Minor code cleanups, and turn comments into full sentences (grammar Nazi mode activated).
new 3902732 DoLARS() -> Regress().
new f120616 DoLARS() -> Regress().
new fd87cc2 Apparent typo in the test cases meant one combination was not being tested.
new ae14cc3 Changes to main executable in accordance with the modified API.
new 77e3ae2 Add option allowing user to specify if they want the data transposed on input; this is useful for LARS.
new bbee092 Tests for new options to data::Load() and data::Save().
new c9f5c1b Clean up LARS executable.
new 0d0b7f8 This check changes because we're loading X and not transposing.
new d9cbadf CLI::GetParam<bool> seems to crash, and, add a timer.
new f6c77ec Add some timers for loading and saving operations.
new 2d6e0a7 Clean up documentation slightly.
new e78c2f5 Stop timer for early exit.
new cb4e932 Clean up comments for no good reason.
new ef1abf5 Refactor SparseCoding to initialize the dictionary as a template parameter.
new 6f308e1 Change tests to respect new SparseCoding template parameters.
new c3335a0 RandInt() and Random() sped up by just using randomUniformDist
new 8c87df9 A couple of formatting fixes.
new 07a11a7 A couple more tutorials now exist.
new 238f0ce Added a compilable version of NMF code. Test cases need to be written
new 5bdb3cb Basic implementation of NMF
new d070247 Add nmf directory
new dc40778 Move everything into the NMF directory from PCA
new 109643f Move NMF out of PCA
new 0a1d9c6 Revert to PCA CMake configuration
new 159f9bb Clean up comments, and store a reference to the data, instead of copying it.
new 4ee0ebf We don't need to set the reference -- this line is now implicit.
new be7a6c3 Rename DoSparseCoding() to more flowing Encode().
new a74054a Unit test for NMF added successfully. Validation conditions need to be tuned
new 5f4c21f Minor style changes.
new 7e473c2 Fix some syntax errors I introduced, and print the matrices. The test does not appear to be working correctly...?
new 030b1c5 Formatting fix, and handle things a little more carefully.
new 499ec07 Clean up code. Use std::pow(x, 2.0) not x * x. A couple of formatting fixes, and some changes to make some code more efficient.
new f431411 Stop using activeAtoms because it isn't necessary (minor speed boost). Clean up code just a little more.
new e3c6a9a Avoid a matrix copy for matActiveZ and potentially speed up gradient calculation by avoiding instantiation of arma::ones<arma::vec> (Armadillo may have already been smart enough to avoid that anyway).
new 8f5f239 Clean up main executable. Avoid unnecessary copies.
new 4dcca10 Fail on failure to load dictionary.
new d16b92a Avoid unnecessary initialization of dictionary when the user passes a dictionary already.
new 97d04bb Clean up style violations.
new 25ac4e4 Clean style violations in main executable.
new b5a9c30 Template LocalCoordinateCoding to accept different kinds of dictionary initialization. The loading dictionaries from file feature is temporarily broken for the LCC executable, but this will be fixed soon.
new 4c455e9 Update for new LCC API, and fix style violations.
new 96742d0 Make OBJ_TOL and NEWTON_TOL parameters to the methods.
new b2ac85b Change matX to data, matD to dictionary, and matZ to codes.
new 7f0c7a2 Update for new API with better matrix names.
new 569617b Clean up formatting of output, and stop using arma::uword (prefer size_t instead).
new f1cc9d6 Oops, this isn't necessary anymore.
new 2bcaad4 More consistent comparisons
new e6943e3 Change DoLCC() to Encode() and some cleanups and fixes in Encode(). Reduce number of redundant class variables.
new 3d9d617 Fix inaccurate comment.
new dbd59ce Update test cases for different cosine distance.
new 54a983f Comment out testing procedure for now because it doesn't work (yet).
new 647cd0c Clean up and optimize code.
new bf83278 Move RemoveRows() to the linear algebra utility section since it's used in more than one place.
new 630a5ec Include linear algebra utilities.
new 189a7c8 Move RemoveRows() out of class definitions.
new 21f8f3d Remove extraneous spaces
new 15e4adb Minor spacing and formatting changes.
new f84856c Cleaner calls to .rows() as opposed to .submat() with all those arma::span objects.
new f27059a Tests for RemoveRows().
new 1238448 Be pedantic about namespaces.
new 31bdf6c This causes an ambiguity error (mlpack::math or arma::math?) on gcc 4.4.x.
new 20add89 Set limit on maximum iterations so we don't spin forever.
new 9664de3 Better error messages (more descriptive, less awkward).
new eaf9bd0 Severe cleanup of executable, so it actually works again.
new fc81066 Use timers internally, not externally.
new 71ca594 Use timers internally, not externally.
new 8b1db5c Fix unclosed '
new 0e9555f Fix doxygen documentation (forgot a @code).
new 2f286ce Use log negative error to prevent calculation overflows (a first step towards making cT and eT unnecessary). The algorithm has not yet been changed... so LogNegativeError is always used as '-std::exp(LogNegativeError(.))' at the moment.
new c27eeaf Update test API to use LogNegativeError().
new eae024f Simplification of expression
new ac8c9af Yeah, this is simple enough to inline; probably a better choice.
new f0d9087 This function can be const.
new 6f37e40 This function can be const.
new 5ec45f3 Added Aleternating Least Square method to NMF. Require some testing
new 661f5bf First shot at overhauling FindSplit_(). Break deep nesting of if/for by reversing if conditions. Use negative log error instead of actual error to help combat overflow issues. Use double instead of cT (long double). Change default eT to double.
new 0a081c1 Fix lots of formatting issues in DETTest tests. Stop casting to/from float/long double to preserve accuracy of calculations (which are now done on doubles).
new 42b9ce2 Minor style fixes and const-correctness fixes.
new 1a4e466 Uh, I forgot the opening {
new 0604896 Further cleanup of casting issues.
new bbaaed7 Apparently unused file
new 2af3618 Add parameters so user can specify objective and Newton tolerances.
new 7a3aab1 Make objective tolerance parameterizable.
new c9e61b1 Switch to doubles not floats in main executable so it compiles.
new 085d587 added some commented out debug statements
new 9814f9d Clean up casting for old Boost.Test versions which aren't very smart.
new 643ed90 added back in accessor for matUtriCholFactor
new ccf6b08 Rename FindSplit and its variables to names that adhere to the style guidelines. Remove a few unused variables.
new 2e2f744 Update test to modified API.
new 6faadae Fix corner case where found version is equal to the required version.
new db41937 Add PSpectrumStringKernel to be used for maxip/FMKS.
new d28f105 Add tests for PSpectrumStringKernel.
new f0d31b1 Clean up FindSplit() and reduce API to only what is necessary.
new f39d292 Clean up test to adapt to new FindSplit() and SplitData() APIs.
new a0c9d97 Replace tabs with spaces. Remove unused variables. Use separate BOOST_REQUIRE_EQUAL() lines instead of one big BOOST_REQUIRE() with a bunch of &&s in it (this can give better output if one of those is failing, whereas the version with && is not specific as to exactly what failed).
new 6e3cd5a Clean up constructors. Don't hand-allocate memory for minVals and maxVals; remove GetMinMaxVals_() because it was only ever used once; inline it directly into the constructor where it was used.
new df63120 Clean up test. Don't use 'new'/'delete'. Fix wrong index for TestSplitData.
new 46a538c Oops, there was one more 'new'/'delete'.
new 4bbb606 Clean up constructors; use initialization lists more exclusively. Also clean up WithinRange() (inline it among other things; it is short).
new 280c4ee Use BOOST_REQUIRE_EQUAL(), and the function is now called WithinRange().
new eafefeb Further switching from cT to double. Later we will switch to all log error.
new 007b81e Use double instead of long double for Grow() and PruneAndUpdate().
new f9e1d93 Use double for ComputeValue(), and take a reference instead of a pointer; also fix const-correctness of function.
new 37e3498 Update for changed ComputeValue() API.
new d0ccd1f Change API for ComputeVariableImportance().
new 765bd7b Modified API for ComputeVariableImportance().
new 2c3a523 Stop using eT and cT for good. Change all variable names to adhere to naming guidelines.
new d11cdbf Refactor test to stop using eT and cT. Don't typedef MatType anymore, and change variable name to line up with naming guidelines.
new c2defce Clean up main executable file.
new 5694a90 Further cleanup of variable names.
new 63766ad modified OptimizeDictionary to return norm of gradient of Lagrange dual (with respect to dual variables)
new 03fde6c fixed test for sparse coding dictionary step - the dictionary step now runs for more than one iteration, and the check is to see that the norm of the gradient of the lagrange dual (WRT the dual vars) is sufficiently small
new e2bc916 Convert all of DTree (with the exception of ComputeVariableImportance()) to work in the log domain. This was fairly difficult...
new 339c56f Adapt tests to working in the log-space and update APIs accordingly (as they have changed).
new 401fb55 Cleanup of dt_utils.hpp. Get rid of 'using namespace std' in dtree.hpp and update accordingly.
new efdaff1 Remove templatization of density estimation trees (it wasn't necessary). It will be brought back, but not at this time.
new 4d396f8 ...and make sure that the removal of templates is propagated to the test file...
new 3211b91 Clean up CLI parameter names and then rename the executable to 'det' not 'dt_main' so it matches more with other MLPACK executables.
new ade5076 Fix std::pow ambiguity on older compilers
new d31c907 Fix pow ambiguity that I missed last time...
new 449c1bf Actually, I got it backwards, I need pow(double, int).
new aeeb2ca I added in logic to remove duplicate flag parameters in response to Ticket #231. http://trac.research.cc.gatech.edu/fastlab/ticket/231
new e949cf2 This day is off to a great start
new 2e5a829 Remove unnecessary debugging output
new fe7d103 Fix DET so it actually works. A few things here and there needed to be changed.
new 0e3eb60 Disable volume regularization for the main executable for now.
new 8654922 Remove debug output which is unnecessary now.
new d548ddb Rename various parts of NMF to different names which line up more with the style guide; clean up main executable documentation and allow the choice between different update rules.
new b89ec6d The API call for Apply() has changed slightly.
new 2302c3b Allow objective tolerance option.
new c1d22e0 Fix tabs into spaces.
new 297c6cb Wrote all the NMF test case and updated Alternating Least Squares method with pseudo-inverse function'
new 5eed0d2 Restructure trees entirely. Each tree will have its own SingleTreeTraverser and DualTreeTraverser, and each tree type should be kept in its own directory (for organizational purposes). The previous traversers in traversers/ have been adapted to either the BinarySpaceTree or CoverTree and moved there.
new 3f5319a Add a few files we forgot, including the convenience include files which include both trees and traversers.
new 0ea4359 Change include files and APIs to use the new tree traverser setup.
new 355e2ab Modify tests for new include locations.
new 1fbeedf Minor cleanup of NMF code; I think the residue should be displayed in non-debugging mode (optionally with -v) so I switched to Log::Info. Comment on the change to pinv() then rewrite RandomAcolInitialization a little bit to avoid allocating memory unnecessarily. Unfortunately insert_cols() is a little slow because it allocates more memory and memcpy()s.
new c45e06f Add Score() and Rescore(), which will be used for a "new" type of tree traversal which should be faster.
new 5f5ff3f Refactor BinarySpaceTree traversal to use Score() and Rescore() and thereby avoid unnecessary repeated calculations (so I hope).
new be66af4 Remove two now unnecessary files.
new d9cbcfa Oops, those files had to be removed from the CMake configuration too.
new d7baf9b Oops, we need this check in there too.
new f666ab2 Use unsafe_col() instead of col() for speed reasons (this makes a BIG difference).
new d830c60 Ensure we check if we can prune before descending the query tree (this case is possible and it seems, happens quite frequently).
new dff5a84 Fix comment.
new 8db781b Give ourselves a way to force inlining.
new 2ec10e7 Check if we can prune individual points before performing computations.
new 2c60543 Speedups for math::Range().
new 48ced6f Inline these functions for speed.
new b4d877f Force inlining of BaseCase() because that is extremely important to loop unrolling optimizations. I mean like 200-300% speedup important. Huge!
new 8bef87f Respect -s when combined with -c (single-mode cover trees).
new eb26d44 Update single tree cover tree traverser to be smarter about recursion order.
new 8e286a9 Add new methods for finding the maximum or minimum distance to a point or node if the distance between the point and node center (or node center and node center) is already known.
new 88ae818 Add new methods for calculating the best distances when the distance between the center and the point (or center of the other node) is already known.
new 2eae350 Remove a few unused methods (LeftFirst() variants). Add Score() which accepts a pre-calculated base case, which is useful for trees with self-children, like the cover tree.
new c2df649 Rewrite the single tree traverser for the cover tree. It works, now it needs to be sped up.
new 0c2d3ae Fix spaces, and actually traverse to the left instead of just saying it and then doing something else.
new ae24e94 Fixed NMF Test
new aadf2e9 RandomAcolInitialization was modified to take a template parameter so now we must specify the <>.
new 4df5e46 Heh... a template parameter is not an lvalue. So just warn the user and then chug happily away...
new f2db147 Oops, a small typo...
new e4cac54 Tighten bounds on minimum and maximum distances because we already cached the furthest distance.
new d576802 Revamp single tree traverser... again. For now it has debugging output.
new e40a713 Use L2 distance not squared-L2 distance because that breaks cover trees.
new 2fbb365 Get the conditional right. Only map things back like that if there was a query file and we were in single mode. Not just 'singleMode' is good enough.
new 40957e6 Refactor single tree traverser again; don't use priority_queue which is slow. Instead exploit some nice properties which allow us to use a map of vectors. It seems as though this implementation is about twice as fast.
new 0ab819f FindArmadillo.cmake ships with CMake from version 2.8.5-rc1 onwards. So require that.
new ec9e38b #223: I don't think we have ever needed to link Boost.Math anyway. Also use -O3 for shits and giggles. I didn't see much runtime difference but whatever.
new a0590ee I promise, GCC, just this once, I'm smarter than you, really.
new cc5ab75 Split CoverTreeMapEntry into its own file since it will also be used by the dual tree traverser.
new 0922f0b Some warning cleanup.
new 7533f8f Seeming error; we just want the path, not the absolute filename.
new 731c6bf Use correct L2 distance, not squared L2 distance in cover tree test.
new 14206bb Rewrite dual-tree cover tree traverser. The use of UpdateAfterRecursion() is kludgey but it seems to work okay for now. Also, the MapEntryType couldn't be abstracted across both traversers because the DualTreeTraverser needs more information.
new 0bfe7a2 Remove unused CanPrune().
new 1d045dc Be explicit and call std::log(double) because in some compilers (icc) std::log(size_t) doesn't exist. #239
new 73980ad Heh... -h is already in use...
new ed9501d Safer handling of strings which may have spaces in them.
new 91fa2be Missed one handling case
new fb72001 Fix floating point precision error which was causing issues only when compiled with optimizations. I suspect this to be a manifestation of http://gcc.gnu.org/bugzilla/show_bug.cgi?id=323 and making one argument volatile is proposed as a potential simple solution, which appears to work here.
new cbac905 Use base of 1.3.
new f01ba56 Refactor and try to rewrite dual tree traverser so it is faster, but I don't think we're completely there yet.
new 09ad0ec Comment out debug output for now.
new ad52c53 Comment out some debugging output.
new bec217f Update bounds -- the tolerance was being exceeded (just barely).
new 43e8b0b Update documentation for the use of cover trees.
new 0cd6050 Change expansion constant to base (#240).
new d8c7460 #240: Change expansion constant to base.
new 3becf78 Must used square rooted distance to be a valid metric.
new 5a0cc7a Use valid alternate metric in tests.
new 46f6960 Fix a warning which was actually also a bug; Score() takes the base case evaluation as a third argument (optionally), not a previous score.
new f7d2c3a Update copyright file (should this be in a different format?).
new 16a0d83 New contributor
new 1c9b82e noinline wasn't suppoed to be checked in, oops.
new ee6197b Add one more contributor.
new d33a16b A few more modifications to the tree test
new 778649a Propagate r13418 to trunk.
new 3015a1d Trivially minor misspelling.
new f59644f #164: Any objects passed into a prefixedoutstream that contain a std::string ToString() const method will write the results of the ToString method instead of simply being passed directly into the prefixedoutstream.
new 00fbc33 #164: Started documenting sfinae_utilities.hpp.
new 4a256d5 Added more documentation to sfinae_utility.hpp.
new df0e32b #147 Cleaned up code. Added some documentation. Implemented ToString() for GaussianDistribution.
new d29e041 Add inplace_reshape() for reshaping matrices without doing anything to the data.
new 7072af9 Add a test for inplace_reshape().
new fd375dd Document the impending doom which will certainly be caused if you use this function carelessly.
new 2949e52 Complete sentences, yo.
new 1e4ff82 Fix odd spacing and be unnecessarily pedantic with const-correctness.
new d6ed6ae That empty initalizer is implicit anyway.
new 124ed75 Add constructor which automatically creates identity covariance, and don't check if covariance is initialized when calling Evaluate().
new 1615a3b Add tests for new MahalanobisDistance constructor.
new 5b317f7 Documentation fix, and tabs to spaces.
new 029dbeb Documentation fixes.
new e5eddc8 Change template parameter names to be more in accordance with the rest of the codebase.
new 9e6cadc Change template parameter names to be more in accordance with the rest of the codebase.
new 73fcf8d Add TakeRoot parameter for use with LMetric<n, true>.
new ffd7073 Test new HRectBound<n, true> functionality.
new 9b6d713 Make a stronger note that the LMetric without taking a root is not a valid metric.
new 88f3e15 Update documentation for the HRectBound.
new 520fee8 Ack, that's an annoying typo in a bad place.
new 245e708 Another annoying typo.
new 2d1389e Update some documentation for clarity and coding standards.
new 7a6b721 Longer lines than 80 characters? Unthinkable!
new c5bc88f Debugging output, not warning output. Oops.
new bfbbfe1 Fix grammar in comments (utter pedantry) and a few style issues.
new 7097280 Tabs? In my application? It's more likely than you think.
new 71e4f75 First cleanup of code: adhere to formatting standards (mostly).
new cb8ecf1 The mean was not being set to zero in the constructor where the documentation said it was being set to zero. This is now fixed.
new b90decf
new 149ff04 Remove test, because it's just testing internal MLPACK functionality which is already tested.
new a800969 Fix includes.
new ab9667c Updated EMST code to use tree traverser abstractions.
new e21840d Utility to find MATLAB and the mex compiler.
new 5fd588b Build rules for MATLAB bindings.
new 13913be Build rules for the EMST MATLAB mex binding.
new e550876 Makefile no longer necessary.
new 9622b21 Finish CMake configuration changes for MATLAB bindings. This *should* break the build (and will test what FindMatlabMex does when MATLAB isn't installed). I'll have it fixed shortly thereafter. Yes, this is somewhat lazy testing...
new 09ac17a This comment is no longer necessary.
new 49fefa5 This comment isn't necessary.
new ed8adeb Actually issue errors when mex is not found.
new e1bc113 Clean up script a little bit, make it a bit friendlier.
new 86369b0 Clean up configuration so that MLPACK will compile on systems without MATLAB. Also handle CMake policies more gracefully; I can't believe CMake just doesn't ignore policies it doesn't know about. Poor design...
new c160302 Remove all the cmake_minimum_required() bits that weren't actually necessary because there is a cmake_minimum_required() in the root CMakeLists.txt.
new 7e5aee3 Further clean up script and handle things better when MATLAB does exist.
new 3368514 Use MATLABMEX_FOUND not MATLAB_MEX since CMake string comparisons are as stupid as my cat.
new 565c6bf Comments and cmake_minimum_required removed because they are not necessary.
new abf9f7a Script to modify the file which controls the MATLAB default path to add the "MLPACK toolbox", as I am calling it. Also in reference to an earlier commit message, to clarify, my cat is quite seriously weapons-grade stupid.
new c5a7cbc Add MLPACK MATLAB bindings to the default MATLAB path.
new 59b2577 Add new developer (Patrick did the MATLAB bindings).
new d3eb574 Update copyright
new 5087cea Add DETs to the list.
new df4f776 Change name of output and update MATLAB binding accordingly.
new dfa9fdd Tabs? In your codebase? It's more likely than you think.
new d8d421c
new 0af3285 Slight reorganization.
new 4f2af16 Weird misspelling fixed
new a8b4ca2 Stochastic gradient descent will live here.
new ebdd747 Clarify documentation. L_BFGS is a minimizer.
new 9426ff0 Not yet tested -- but implemented in a few minutes. Turns out SGD is pretty straightforward...
new 66ce420 Modify namespace, and create CMakeLists.txt.
new c7734e8 Add SGD, and add functionality to LBFGS test functions (which will probably be removed later).
new fa9385b Fix a few errors in these files.
new 94bb5cc Add a test function and make it work right.
new 64aba8f Add a test for SGD.
new 168d907 Move everything into the mlpack::util namespace from mlpack::io or mlpack::utilities.
new 4f6309e Update to use mlpack::util namespace.
new 685dc3d Fix formatting issues and prepare for new functions.
new 8332c26 Fixes to use mlpack::util not mlpack::utilities.
new df9775c Implement decomposable error function and gradient, then make NCA use SGD and not L-BFGS. That's a lot of acronyms... for now, parameters to SGD are specifiable through the NCA interface, but I think in the long run NCA should be templatized to use an arbitrary optimizer.
new 7554ee1 More parameters for NCA in accordance with the change to SGD.
new ba9a82e Allow normalization of points, to prevent underflows.
new 3bfe4cc added range_search and gmm; CMake updates for kmeans
new 8bba58e Remove the normalization stuff... that is not the right way to do it.
new 58d83fb Slightly smarter normalization strategy for large datasets.
new 1c4cb05 Also support a random seed.
new 589ef4a Stupid, stupid, stupid (#256)
new 61acedb Oops, I missed one utilities -> util change.
new e4bf0f2 Explicit cast
new 3b49c3d Better default tolerance; 1e-5 is too high and may "accidentally" converge too soon.
new b1138e2 We were neglecting a term in the gradient...
new d5cc4c7 Tests for the separable evaluation and gradient of the NCA softmax error function.
new 1906a07 Add parameter to determine whether or not SGD is shuffled.
new 23e6ead For real, I seriously considered anger management classes while hunting this one down.
new 2efe656 Allow passing an initial matrix.
new 81048b4 Change the way things are normalized.
new 7cfce1c No need to print the final matrix.
new f4b6027 A better normalization strategy. And actually document how you make NCA work well.
new 884c73f Output the size when loading. How cool!
new 574b076 Rename in accordance with the submitted paper.
new cbbf310 Update include location.
new e0bf022 Rename all MaxIP files to FastMKS.
new bfc748a Rename MaxIP test to FastMKS test and update everything accordingly.
new 6acc813 Remove sparse support from trunk.
new 1b399df Oops, don't remove inplace_reshape().
new 0a846fc Only do sparse tests if sparse matrix support exists.
new 35e45c5 Add explicit constructors for sparse vectors, which are applied only when Armadillo 3.4 is used (this is a backport of new functionality).
new 1961e7e No need to typedef u64 anymore; set size_t == uword by defining ARMA_64BIT_WORD on systems where size_t is 64 bits; clean up preprocessor #ifs so that Row_ and Col_extra_bones work correctly.
new 7b14772 Update CMake configuration for removed files.
new ddd5d04 Fix links. #249
new de17b21 Workaround for the case of sparse matrices.
new cb4c4d7 Bake in support for HDF5 -- if Armadillo has it.
new c6092bc Test HDF5 load/save functionality.
new e0f8b9d Fix a code error, fix build instructions to include package managers.
new f783571 Actually, we can't just define ARMA_64BIT_WORD willy-nilly because it makes weird weird WEIRD things happen. Yeah, no joke. If you want some fun sometime... try that...
new b0a62a5 Check for a 64-bit system where ARMA_64BIT_WORD is not enabled, and warn the user if that is the case. MLPACK still works fine without ARMA_64BIT_WORD, but it is not a bad idea to ensure size_t == uword (by defining ARMA_64BIT_WORD on 64-bit systems).
new 9bfd889 Issue a warning when a user tries to compile MATLAB bindings and they have a version of gcc which is "not supported" by mex.
new e83b219 Fix to work with older GCC versions in cases where math:: is ambiguous (stop using arma::).
new d57b13c No need to warn if the MATLAB mex compiler is using a newer glibc than the system.
new 3b99a1a Use specific doubles for RHEL5 Boost compatibility.
new 8498d51 Clean up MATLAB bindings for EMST.
new 3f84021 Update AllkFN binding documentation to how it should eventually be.
new 02b6e81 Tabs to spaces
new a273f75 Very minor documentation change.
new 554f789 Add build rules, tabs to spaces, and remove unnecessary header files.
new e0462de Update headers, tabs to spaces.
new 45af02e Remove unnecessary Makefile, change to appropriate headers, and add header comment (and tabs to spaces).
new 18688ca Remove unnecessary Makefile; add header comment, remove unnecessary headers, and change tabs to spaces.
new d1b4e82 Remove unnecessary Makefile, switch tabs to spaces, add header comment block.
new 9d68319 Error in comment
new b19dd0a lars, nca, nmf, pca, kernel_pca
new 2c1288c Clean up warning.
new 031e870 Fix documentation.
new 96a492a Manual tree constructor
new d4e9bca Test for the manual constructor.
new 94da729 Update for cover tree API change.
new 6ed8b72 Add option to compile MATLAB bindings.
new 191704b Make recursion into the bindings optional.
new 974aa83 Add a few new bindings and make the mex compiler required if compiled with -DMATLAB_BINDINGS=ON.
new 7b7e035 Move conditional on matlab bindings to matlab-specific subdirectory.
new 4286f66 Put MATLAB_BINDINGS conditional at a lower level.
new 5e7915f Add CMake configuration for this binding.
new ac555d4 Tabs to spaces and correct includes.
new bcb5d76 Remove unnecessary Makefile.
new b4a029e Remove unnecessary Makefile, tabs to spaces, use correct includes.
new cd15bef Tabs to spaces, fix includes, remove unnecessary Makefile.
new aafa8f5 Fix includes, tabs to spaces, remove unnecessary Makefile.
new b212b5b Fix includes, remove unnecessary Makefile, tabs to spaces.
new 9962f0d Add mutators for ParentDistance() and FurthestDescendantDistance() and fix a comment.
new 2e1bf95 Add a method to get the furthest descendant distance.
new 939dfb4 Add a test for the furthest descendant distance.
new d1fa9e0 Calculate queryNode.Stat().Bound() on the fly instead of just one time at UpdateAfterRecursion(). This slows things down, but can probably be modified to be faster (maybe it is not necessary in Rescore()?).
new a91790c Don't use UpdateAfterRecursion().
new bc1e811 Update comments for correctness to resolve #261.
new ed82b53 Another comment cleanup.
new 3bac59d Refactor NCA to take an optimizer as a template parameter, and default to SGD.
new 813a1a8 Update test for new NCA constructor.
new 698e4ec Add option for optimizer type to parameters.
new eeb306e Add function for cover tree pruning.
new 6d03162 Add Prescore() function which can be used to prune based off of parent distances.
new 29cbd78 Use Prescore() to prune reference children without evaluating the base case.
new 34e47db Try to prune when copying reference maps.
new 414543e Add new (hackish) rule for pruning while descending queries.
new ba8e8f0 Fix NCASimpleDataset test.
new a3f3fc2 Change formatting to fix style.
new 5f18a1b Clean up RADICAL code and add some more output.
new 30274c4 Clean up documentation slightly for the case of slow runs.
new 55e6776 Implemented the ToString SFINAE pattern.
new 77d8074 Implemented ToString methods for the math folder.
new 73b4c28 Working on implementing the ToString functionality for the tree folder - getting a seg fault with the cover tree class.
new d379046
new 6b5843a Update to newest version (I mistakenly branched an old version).
new 92cb01d Minor formatting improvements and warning fix.
new 1ba221d Further implementation cleanup; build rules fix, and move test to test directory.
new 36796b2 Build LSH.
new 188fc3e Add tests for LSH. They may be modified as time goes on.
new 9628229 Implemented tree folder ToString methods. Anything involving a mrkd_statistic, binary_space_tree, and cover_tree are encountering segfaults with when they are being destructed, though.
new 60cebb4 Abbreviated the Range ToString method to return one line.
new 3536e6f Resolved tests to compile with ancient versions of boost.
new bd90d1e Standardized code style for DiscreteDistribution's ToString method.
new 15848cd Initializing MRKDStatistic's leftStat and rightStat fields and standardized cover_tree/cover_tree_impl.hpp
new 70c9120 Fix line widths.
new 46fcf98 Do not make copies of objects when printing to output.
new 13ff6bf Add copy constructor explicitly.
new 38e07de Add test for cover tree copy constructor.
new c9b4ad2 Minor refactoring of BinarySpaceTree and addition of copy constructor.
new 0aaf376 Test for copy constructor of binary space tree.
new 3e9b681 Fix unsafe code in HRectBound; bounds can be NULL.
new 5170148 Refactor MRKDStatistic into three files (maybe a little overkill, I realize now). Add accessors and mutators after making internal variables private.
new 9372430 Update for MRKDStatistic API change.
new 978d1be Flush status message to output before the size of the loaded matrix is determined.
new 6b65c36 Some tricks to get u64/s64 support on more recent versions of Armadillo.
new 1465ee8 Add parent and Parent() so that trees can be traveled both down and up.
new 85ec022 Add test for Parent() method in BinarySpaceTree.
new 7f20a85 Issue a warning (not a fatal error) if Armadillo's configuration file does not exist. The presence of that condition will probably cause errors later on, though.
new f4544ea A few changes to PrefixedOutStream and NullOutStream to deal with references better.
new a29c93a Refactor calculation of bound. It may need a further fix.
new 59ff347 Don't use Prescore(); it doesn't work. Comment out for now (it may be removed later).
new 8c478c8 Add two new files to build.
new c2646ea Better calculation of bound. We could still optimize a little bit. Debug output is for #243; this solves #264.
new 4c1ba2e LSH class updated: Hash width computation moved within the class and removed from the main file. More comments added to the LSH class. Search function made tunable allowing the user to chose the number of hash table he/she choses to search in.
new b078096 RANN moved into trunk from contrib/pram. Test added to the mlpack/tests/ directory along with relevant datasets
new 0237aa5 test data loading fixed
new 3fcc092 Clean up string util files (no functionality change).
new fdc8bf4 Oops; turns out there _was_ a functionality change...
new 7e83288 LSH Test modified
new 9f8e30e Add traits for trees.
new f9e836a Add test for tree traits.
new 95af153 minor update to remove some warning for the pow() function
new 6e616d2 minor update to remove some warning for the pow() function
new 4d0c1fe It turns out we can actually make the bound a little tighter, which I accidentally showed yesterday.
new f14dcfc Make GMM::Estimate() return double.
new 7a346ba Update test for changed GMM API.
new 7648bbf Clean up LSH code and add random seed parameter.
new dace582 Add LSH to listed methods.
new adc521a Remove using directive and extra whitespace.
new 4f260e2 Simple cleanups of RANN code.
new 462f8ca LSHSearch class MetricType template removed and only metric::SquareEuclideanDistance used appropriately throughout the class
new 2434431 cleaned up commented code in allknn allkfn. adding the incomplete hmm binding
new 3490082 Far less hackery is required for Armadillo 3.6.2.
new 761932b Old versions of Armadillo are no longer allowed, so this code for Armadillo < 2.1.91 is unnecessary.
new d7d8375 Fix warning.
new 74fedba Fully qualified name of var() for compatibility.
new 43e72ec Exclude Armadillo 3.4 from K-Means sparse test because sparse var() was not implemented in that particular release.
new fb15aa6 LSH requires resize() which is not present until 2.4.2.
new 377d06e Got the name of the macro wrong...
new ca2202e Armadillo 3.4 has some sparse bugs which cause this test to get stuck in an infinite loop. The bug is not present in Armadillo 3.6. Therefore, don't run this test on Armadillo 3.4. If a user ever reports it, then they should move to a newer version of Armadillo.
new 2717469 'force_inline' added to ra_search_rules_impl.hpp
new 362211a Add history.
new f2844ce Abstract away the unmapping of points. Also fix a few bugs in AllkFN because that executable was really not kept up to date with the AllkNN executable.
new a9fd9c5 Test Unmap().
new 2200186 Forgot to test-build allkfn...
new 9f4e023 Change rowMajor parameter to transposeData parameter, which is set to true by default. This is in line with the LARS executable and fixes a bug; the LARS executable transposed the data when it should not have.
new 295f55e Update for changed LARS API.
new 47d13ff Comment out checks for now; setting the random seed does not guarantee the same results across architectures (and Boost versions) and therefore isn't a good test. We will need to write the test differently (probabilistically).
new 7cd6c5f Clean up tests; split into four (not three) tests, remove random seed setting where appropriate.
new 39ea66b Move default arguments into declaration of function to make clang happy.
new 9d76068 Cleanup for clang warnings.
new 83e09c3 Update style; remove _s.
new b778c1d Add Parent() function.
new a42ffc0 Update test so Parent() is also tested, and also update constructor parameters.
new 81ffbf2 Reset parents correctly in the case of implicit nodes.
new 495d66a A few more examples to reduce the probability of error.
new b469fc2 By default, take the root. Then it is a true metric. (L2-squared distance is not a metric).
new 4ccf4f4 By default, take the root. L2-squared distance is not a metric.
new 522add2 Still use L2-squared distance by default; this needs to be fixed.
new 72aaa4f Don't use L2-squared distance by default.
new 8fab86b Update tests because LMetric<2> is no longer the squared Euclidean distance.
new 2b72c8b Use the bound in the ICML paper.
new 45d6a25 Update to only use L2-squared distances (for now).
new 2e66ae3 Simplify constructors; we don't use any of the odd ones.
new f623683 Simplified statistic construction.
new a635dea Adapt to modified statistic API.
new 7492efe Adapt to new statistic API.
new 8cd8610 Style changes
new 2b1b6ba Oops, I did not realize there was an _impl file...
new 8dca77a Update statistic API.
new 3124dc9 Update statistic API; for cover trees, actually call the initializer.
new 310b3d6 Don't use start anymore.
new f3b9e46 Clean up code a little, and allow returning of the metric associated with the hyperrectangle bound.
new f9cd90f Remove empty constructor; store dataset; allow return of metric with Metric(). We don't seem to pay an extra price for this because sizeof(BinarySpaceTree) > 64 bytes but < 128 bytes (two cache lines). Also, reducing the size to one cache line doesn't seem to provide much benefit (at least on amd64).
new 8e3bbba Add Metric() function, and refactor a little bit. The metric may be stored locally if none is given.
new 3f47b07 Add test for Dataset() and update because the empty BinarySpaceTree constructor no longer exists.
new 8f67fa2 The name of the executable changed. Update documentation accordingly.
new 1d39994 Minor documentation change.
new 4ba7ea0 Add a readme. Readmes are good.
new cc591b8 Fix bug in bound function for neighbor search. It is necessary to keep two separate bounds for each node.
new f290afe Add a new trait.
new 9a851d2 Allow returning of instantiated metric and centroid.
new e400700 Add Diameter() function, which is useful for obtaining the furthest descendant distance.
new 07e5cbb Test Diameter().
new 980979c Cache furthest descendant distance.
new dae762d All definitions should come before mlpack includes.
new dd1e7f5 Make FastMKS work in the dual-tree setting. Hooray!
new 31affc2 Clarify documentation significantly on Train(). Only allow setting of dimensionality in constructor and by hand, to prevent unexpected behavior in Train(). Check dimensionality of observation sequences in Train().
new a051563 Better debugging output for DiscreteDistribution.
new 9d2724d Explicit namespace inclusion.
new 7ed13a9 Clean up warnings.
new f4d6111 Use custom FindArmadillo script, which will find (and link against) HDF5 if necessary.
new bb36977 Clean up output a little bit.
new 9077efa Update name of inclusion guard to fit with the rest of them.
new cbd5cfb Uh, this is a major problem.
new f57515f Superfluous c_str().
new 6726243 Make Save() actually return a useful value.
new 66c53e1 Add Load() and Save() functionality for GMMs.
new f59bdee Test Save() and Load() functionality for GMMs.
new ab082b9 Use GMM::Save() instead of a handwritten function.
new 32d0122 Update coding standards.
new bad0480 Add perturbation to ensure that the covariance matrix does not end up empty (and therefore singular).
new 77a8e34 Add option for number of trials.
new b79d833 Add perturbation to covariances when necessary to prevent zero-valued covariance matrices.
new 1f8f8d1 Zeroes in any element of a diagonal of a covariance matrix can cause problems.
new 1097826 This should be informational output which is present even when debugging symbols aren't.
new 4ac83d4 Do not divide by zero. This is important when there are outliers whose conditional probabilities for all clusters may be zero. The results are unaffected.
new 8990c61 Too many spaces.
new cd67b53 Put in checks for non-invertible covariances after training; add perturbation to avoid them where necessary. Also avoid dividing by zero.
new e8ed160 This is necessary (apparently) until the FindArmadillo changes either get committed or wrap_libs fixes the problem entirely.
new a78c7bd Parameterize perturbation, tolerance, and maximum number of iterations.
new e13b011 Add parameters for EM algorithm, and also add parameter which adds random Gaussian noise.
new 335dac4 Don't use a specified perturbation but instead a simple (but rather slow) algorithm to detect positive definiteness of covariance matrices and force them to be positive definite if necessary. All of this is "singularity avoidance", to keep covariance matrices from becoming extremely small and then introducing NaNs and infs everywhere.
new 6b735e5 Remove perturbation parameter and allow specification of whether or not matrices should be forced to be positive definite.
new aafe501 I think this warning can be somewhat misleading, so it should be removed.
new c831589 Eek, I broke the build!
new 6601ff6 Use the same fix from GMMs to ensure that covariance matrices are positive definite.
new c7b52f4 Allow parameterization of the tolerance of the Baum-Welch algorithm.
new 7f26ee2 Add option for tolerance of Baum-Welch algorithm.
new 094c553 Slight documentation fix.
new ede8078 Minor formatting change.
new ed4477e Oops, this is not the accessor/mutator design methodology we are using.
new 3ed8874 Avoid issuing two warnings for one problem.
new 420d951 Add option to get the clusters back when the process completes.
new b456adf Wrong index, pointed out by se7en7 in IRC
new dafbdf4 Fix bug in error checking, and make given errors a little more descriptive.
new f626c10 Better error checking, and, actually *use* the initial guesses if they were given to us. Logic is hard...
new ff9cb1c Test the new functionality of k-means: initial assignments and initial centroids. Also test that k-means fails on corner case datasets -- it should.
new 00c3b82 Add a new initialization method, which is an implementation of Bradley and Fayyad's scheme for better k-means initialization points. It seems to work well.
new fd93a81 Add test for Bradley-Fayyad initialization (RefinedStart).
new dd54e7f Add accessors and mutators, and mark function const (as it should be).
new ab9ae32 Minor formatting change.
new 2777641 Remove Pelleg-Moore support (as per #251). Allow the user to specify a file to save centroids to, and also allow the user to ask for Bradley-Fayyad initialization, and give options for the parameters to that initialization.
new 3ce277c Allow Bradley-Fayyad initialization for k-means as initialization for EM algorithm.
new b82036a Oh yeah -- actually allow the user-specified parameters to *do* something...
new 0f7ed38 I don't like how Doxygen does @see; this should look a little better.
new 7351a70 Fix documentation for prettier @see results.
new 8ee32f5 Remove ambiguous option
new df5cf85 Name of argument changed
new 95b04bd If loading fails, don't try to continue.
new ee336d3 Patch for #272, pointed out by Marcus -- incorrect example.
new 0811cae Add directory for k-means tutorial.
new edcaa37 Clean up DET tutorial significantly. It could still use some work -- but then, so could the actual DTree API.
new 511fa11 Remove reference to alternate volume regularization example.
new 65da594 The last section shouldn't be a subsection.
new 62bf1cb The last section shouldn't be a subsection.
new 445c0ef The last section shouldn't be a subsection.
new f64134f The last section shouldn't be a subsection.
new 67dc113 output_file is the option, not outputFile...
new 13626c0 Stop timers if saving or loading fails.
new 9ac14e6 Fix parameter names (asleep at the wheel?).
new 4d0eab4 Change DistanceMetric to MetricType to be more in line with the rest of the mlpack codebase.
new 023ee38 Wow, I spent a lot of time writing that. It's mostly checked for errors.
new 0cbc8a6 implementation of the \c EmptyCluster() function makes Link to k-means tutorial.
new 42caced Add directory for FastMKS tutorial.
new d716df6 It all has to be one big comment to be a page...
new eb13247 Refactor cover tree constructors into one CreateChildren() function, which saves a lot of space. A little bit of changing needed to be done to set the scale right in the root node, and as a result the assert that checks that the furthest descendant distance is within the scale has been removed (since that has never been a problem). This is for #274, but the other constructor will not be changed until mlpack 1.1.0.
new 99dd696 Widen tolerances on tests that seem to be failing often.
new f8bbe0a Widen tolerance even more.
new 228ec30 Update IPMetric API and document it.
new 38cf6f4 Update FastMKS API and do some documentation. Add some new constructors for flexibility.
new 16f537f Remove base option -- just for now -- and update calls to FastMKS constructor for new API.
new aec01c0 Clean up rules file a little bit; make BaseCase forced inline.
new 2547860 Remove parameters that don't exist.
new bab14c2 Stop counting kernel evaluations and distance evaluations. This may be brought back but before, it was done in a very ugly way...
new 22056b3 Modify main executable to support --base option again, and give better documentation.
new c58b0fa Don't use global distanceEvaluations anymore. Remove debugging output.
new 5721fee So Doxygen picks up that comment too...
new 003721d Clean up polynomial kernel and reverse input arguments so they are now in line with what FastMKS actually implements.
new 599b66b Update for PolynomialKernel constructor API change.
new 06315ae I don't have a reliable connection, so check this in so I can work on it from my local system.
new 1304f23 Fix reference.
new 23f7e37 Fix reference.
new adee64b Finished FastMKS tutorial.
new a0fe2ee Add new tutorial to list.
new 1955696 Fix @file lines.
new 2ade5c7 Fix @file lines.
new 7833006 Add links to new tutorials.
new 22ba312 A notice that FastCluster() doesn't work.
new cac0c47 Update documentation (#275).
new 09bf007 Patch for #278, contributed by Marcus Edel (thanks!).
new 3f55d67 Avoid inverting empty matrices. Also fix a possible uninitialized memory issue.
new 63a795e Merge in history for 1.0.5.
new cfdd1d1 Two functions which are useful for RangeSearch.
new aadce00 Add RangeDistance() hooks to HRectBound.
new 2b086b6 Incompetence is a surprisingly accurate predictor of build-breaking checkins.
new 8a58952 Incremental checkin so I can work from another system. Begins outline of the RangeSearchRules class.
new 25a6b1c Add NumDescendants() and Descendant() functions which will make things much easier for range search and RANN.
new 528a3c3 Test NumDescendants() and Descendant() instead of Begin() and Count() (since those will eventually be removed).
new 8a58c9f Add Descendant() and NumDescendants() functions.
new 867f13e Test the Descendant() and NumDescendants() functions. These tests were surprisingly difficult to write but should be rather comprehensive.
new 0dc2d76 Fix warning.
new 7ad1a07 Add HasSelfChildren trait.
new 645d761 Tests for HasSelfChildren trait.
new f98a8cf Revamp RangeSearch as per #244. Now this works with cover trees too!
new 007f6d7 Comprehensive test for range search with cover trees.
new 7636333 Grevious spelling mistake.
new e5d287f A commit from a long time ago shows I committed the Contains() function without testing it, and, well, sure enough, it's a failure. This (hopefully) fixes it.
new 60f7810 Finally add test for Range::Contains(Range).
new 123a266 I'm not sure what the older test was, but it was undocumented, so I removed it, and then added my own. I also updated the authors file for accuracy, because none of Ajinkya's tests are here anymore.
new 6c3fcab Fix #280 and revamp KernelPCA implementation. It should now be much faster.
new e44ddbd Add new contributor.
new d301b21 Update copyright.
new eff2d49 Minor formatting fixes and better documentation.
new 9e640ed Stupid const error. Did I not test it?
new 3ce3653 Move IPMetric to general metrics directory since it will be useful for other things.
new 4b314ca Use Log::Assert.
new 060839b Move IPMetric to mlpack::metric not mlpack::fastmks.
new 66e21a5 Document what the namespace contains.
new b78444b Fix for #289 (thanks Marcus)
new 46c3da5 Remove unused file extensions from Doxyfile.
new 2f54da2 test commit
new a0e1b33 Removing "test.txt"
new fd86c33 Do not compile DET code on Windows because it causes the compiler to segfault. Sigh...
new 76818c3 Yeah, well, it's not like anything was going to fix the Windows build anyway. Now it crashes in some other way.
new 600d264 Sometimes the map is empty, and dereferencing an empty iterator results in unhappy behavior.
new a510bf4 Make the NMF decomposition more accurate in a bid to fix the failing test.
new b07a552 Fix ambiguous math reference error, to pass the test on OS X with clang.
new 62db976 Fix unused variable warnings.
new a3e34ce Widen tolerances on GMM tests.
new c3d69a9 Add target_link_libraries for librt to support clock_gettime() for Linux.
new 8c359aa Update the timer class, to get stable time values with more accuracy for the common operating systems.
new e98f8dd Extra cleanup of Windows' ridiculous #define min and #define max. Seriously guys?
new 4ce6f9b Remove unnecessary include.
new fa853a1 Remove unnecessary include.
new 4fa3f35 How did that happen?
new dab4c23 Reorder includes.
new 51f7377 Windows does not like the #define private public hack, so do not use it there. Also remove it from a few tests where it wasn't actually needed.
new c03d3a5 logNegError is private, so don't test that on Windows.
new a2b5331 Copy HISTORY from branches for mlpack 1.0.6 update.
new df87943 Remove unnecessary include.
new e5c02d4 Fix #291, which is a corner case in situations where the dataset consists entirely of the same point.
new 60269f7 Some formatting fixes, and create a new test that tests the scaling to unit variance option.
new dc11083 Fix the scaling parameter; what was being done before did not make sense.
new 925a95f Fix ambiguous math reference error, to pass the test on OS X with clang.
new d1f85c2 Oops, I forgot to remove the random seed from the test...
new e01f8fa Fix ambiguous match: option -s matches --seed and --single_mode.
new 34ffa8b Fix index out of bounds error when using det with a labels file.
new 918227c Make CLI::GetParam<bool> return the same value as CLI::HasParam().
new e48203a Test that HasParam() returns the same as CLI::GetParam<bool>().
new 58a2b63 Clarify comments and fix bug that occurs when no query set is specified.
new 99a4e91 Fix dangling spaces and use Log::Assert() not assert().
new a8a3438 Test single-dataset mode. In writing this test, bug #293 was created.
new 55a0a86 Fix ambiguous match: option -s matches --single and --scale.
new 40c6fb6 Testing diff in commit emails.
new 8e479c1 Test diffs in commit emails again.
new 1a38de8 Fix ambiguous matches for -N and -L and set default optimzer sgd.
new e3e7773 Move constructor to top of file, and check the size of the s and y cubes before optimizing (not just at construction time) because they can be changed (see nca_main.cpp).
new 9ea3850 Rename a few tests so they compile correctly.
new 3d642ed So, actually compiling the L-BFGS test might be a good thing...
new 1c77008 Fix ambiguous call to pow, to pass the test with clang.
new 6788751 Comment out --fast_kmeans option so it does not work at all, for now.
new a951848 I have been looking for this memory leak for months. Apparently I forgot that this file exists, and once I found it, the leak was obvious.
new 1141488 Does this fix the cover tree two datasets test? It seems to on this box.
new 6791413 Don't recurse into the map pruning section if the map is already empty.
new 8dd248c Add utility functions to normalize labels.
new e52e91d Modify core.hpp to include label normalization methods and update build configuration.
new e51d444 Test label normalization.
new 662d779 Remove debugging output.
new 56fe16b This may fix the segfaulting in the cover tree tests.
new ebebac8 Change label type to arma::Col<size_t> not arma::uvec.
new d95cd26 Change label type to arma::Col<size_t> not arma::uvec (this is more in line with the rest of mlpack's labels).
new 87653f5 Update NaiveBayesClassifier API to take labels as a separate vector. Also, normalize the labels in the main executable.
new 881fe49 Uncomment checks that weren't failing in the NBC test and update for newer NaiveBayesClassifier API. Also, normalize labels before running NBC.
new bf80d43 Use arma::Col<size_t> instead of arma::uvec for labels.
new cae14c7 Normalize the labels before performing computation, and use arma::Col<size_t> instead of arma::uvec.
new fbaff8c Update test to use arma::Col<size_t> for labels instead of arma::uvec.
new 03000a1 Ticket #293 initial fix -- review waiting.
new 2581da9 Chebyshev distance (L-infinity distance) added to lmetric.hpp
new 75c7b1f LBFGS test compilation failure fixed
new b6be47c metric_test.cpp -- arma::sum changed to arma::accu; LINFMetricTest corrected.
new 6cf8c5e This should fix the failing build on old Armadillo versions.
new d937335 Oh holy crap, I am the worst, and I have broken everything.
new c714612 I always say "build before you check in!" and then the simple fix I try to commit breaks everything because I didn't have time to build it or thought "oh man, this will definitely work". I bet if I searched for commit messages like this I'd find dozens...
new d6f76dc Older versions of Armadillo require as_scalar() because gcc isn't able to figure out that the result will be a double.
new b369829 Fix ambiguous match: option -d matches --degree and --new_dimensionality.
new 73c866f Simplify centering code. Maybe it's faster?
new 024aaa0 Clean up PCA test.
new 1a366c0 Refactor PCA to use SVD because it is faster.
new 0be4ff9 Add opportunity to set initial centroids.
new 503ad19 Add command line option to set initial centroids.
new ea2eab9 Minor formatting fixes, make things const 'cause that's what's cool to do, issue a warning if -r and -I are both passed (because in that case -I is ignored).
new 4b6886c Spelling fix.
new f76d51b Remove c_str() where possible.
new 6a28aa1 Remove c_str() where possible.
new 6516abb Widen tolerance on HMM test.
new f57fc0e Fix misleading comment.
new 30e1e73 Marcus, finder of errors, has found yet another one.
new 07e6a22 Adjust tolerances.
new 9bcf374 Adjust tolerances.
new aaed1a0 Minor version update. This is not a very maintainable solution...
new 6361eda added download link to build page on mlpack.org
new 3d558ba CF framework and ALS added
new d02cc76 For now, don't build the CF package. It uses sp_mat and that isn't included in all Armadillo versions. The solution will either be to force Armadillo >= 3.4 or #ifdef around the sparse support.
new f38db27 Clean up trailing whitespace, reformat a few lines.
new 4c16a3f Code cleanup, and refactor DTBRules so it does not depend on UpdateAfterRecursion(). Now, EMST actually provides speedup when run in dual-tree mode (hooray!).
new 61a53c5 Fix typo that breaks kmeans.
new 73b9d3b Add a parenthesis to fix some grammer. A big deal!
new 776950b Clean up RANN code, document tau parameter more thoroughly, and refactor RASearchRules so the file has fewer lines and less to maintain. Clarify output when --naive is passed. Remove redundant tau validity check.
new 7f4ceae Add --cover_tree option to range_search.
new 4c06b6f Ignore the cover_tree option if the naive option is present.
new 44be1b6 When removing implicit nodes, ParentDistance() was not being correctly preserved.
new 40e8d38 Add some changes from Sumedh (#298). This improves the Predict() function and adds an error check in the executable (I moved the error check from the Predict() function).
new 392e77e Add new contributor.
new ee3f7f8 Fix compatibility with older Armadillo versions and fix warning in linear_regression_main.cpp.
new 3b1e492 Improve centering of the kernel matrix.
new 26d146f Handle corner case where ||a|| or ||b|| is equal to 0 (and prevent division by zero).
new 1aa177c Fix a comment.
new 218fe8f Fix output, because it does not output the squared distance any more.
new 8d3e29b Update documentation for new output; squared length is not given.
new c7a6e64 Use the correct option to output the desity estimates.
new 9af1f1d Fix ambiguous match: option -p matches --in_place and --percentage.
new 4bf834c Add some new functions from Sumedh.
new eb77773 Add test functions for new stuff from Sumedh.
new c0653bf Add -V option to specify how much variance to retain.
new f0963c2 Add lastKernel and lastKernelNode for pre-emptive child pruning.
new 028f11a Add KernelTraits, a useful template class that can tell you about things, like whether or not your kernel is normalized. This is useful for FastMKS, and will probably be useful for other things later too.
new 6df9e2e Just include all the kernels, because I mean, why not?
new b22f8e7 Add a test for the KernelTraits class, and a long rant which explains why this checkin didn't happen two hours ago.
new 2f8d825 No need to transpose matrices.
new 952b6ea This was the version of code used for the FastMKS benchmarks in the recently submitted paper, "Dual-tree Fast Exact Max-Kernel Search".
new ea7da4e Print base cases and scores as output even when not debugging.
new fef13bb Often number of prunes can be useful information, to make sure that anything at all is being pruned.
new 80d1c59 Uh, this should fix the broken build. I will clean this up in the forthcoming days. The traversers are re-implemented to make the overloads of Score() and Rescore() that take base case values unnecessary, and actually the dual-tree traverser now satisfies the definition given in the ICML paper correctly.
new 88bd68b Add functions to get number of base cases, number of node combinations visited.
new 071463a Overhaul NeighborSearch so that it only needs one overload of Score() and does not pass around the base case. This fixes the failing tests with cover trees. Also, QueryStat is split into neighbor_search_stat.hpp and renamed NeighborSearchStat.
new e742bcd Update test for new NeighborSearchStat class.
new 5565e72 Two things: actually do some pruning, and, get parent base case evaluations correctly. I cannot believe how long it took me to track that down. Ugh...
new 2ea5125 Add RangeSearchStat class.
new 7bec0dd Move to right namespace.
new 9599e55 Use RangeSearchStat (although nothing is being done with it yet).
new 799a0a9 Use RangeSearchStat in cover tree objects.
new f05e152 So, to test this file, you have to type 'make range_search'...
new 8b2b7ba Adding Cosine Trees
new 77a85b4 Refactor test to clean tree statistics before running new range searches.
new 317c89b Refactor RangeSearch to work properly for both cover trees and kd-trees with the new cover tree traversal.
new 90998df Fix comment.
new a26388d Use RangeSearchStat with cover trees.
new ea2a9e9 Added tests for CosineTree and CosineTreeBuilder
new d23e305 Added tests for CF Module
new 54d5b5b r15817 overwrote the current tree tests with ones from mlpack 1.0.4. This reverts that change, and reformats the cosine tree testing code.
new 28a0563 For now, don't build the CF test. This is because CF depends on sp_mat, which is not available in Armadillo <= 3.4.
new 94b787f Remove EuclideanDistance() and CosineSimilarity() functions; instead, use CosineDistance from kernels/. Also remove trailing spaces (thanks, vim!).
new 9f71f94 Converting row-major to column major
new 17e1eb3 Removed an older version of tree test and added a new one
new 7cd9a53 Fix compilation errors and merge actual changes from r15826.
new 742e1d4 The parent-child pruning bounds were too tight. They did not consider one of the bound terms and the cross-term, and thus failed, especially when considering a leaf node where the furthest descendant distance was 0. Also update documentation a bit so that big chunk of code makes a bit more sense.
new 460c350 Update tutorial.
new dabb5c5 A few fixes.
new af5659c A few more fixes.
new 03b84a8 Hey look, I removed three lines of code while not changing the functionality of anything. Convenient!
new b78fabf Use the option to set the leaf class table file and unify method call.
new 965857e Integrate ComputeCost() as ComputeError() for #298, written by Sumedh.
new d149922 Add test for ComputeError() for #298.
new 1fa4649 Use Sumedh's dataset for the perfect fit test.
new 975e2a0 Interesting that this compiles even though the sum of a dot product is a meaningless expression.
new fe58d60 Fix warning, add const.
new 06d9aee Make Predict() function const-correct.
new 69184ad Widen tolerances.
new 84294f9 Very minor syntax fixes.
new 48f40b4 Add lambda parameter, so this now supports ridge regression.
new ea5976e Use an empty dataset, like Sumedh suggested, to test ridge regression.
new 2089796 Avoid an additional matrix copy (insert_rows() and shed_rows() are a copy each time). Also make the input matrix const.
new e6c6a02 Fix other constructors so they play okay with lambda.
new ff8363c Update the timer example call and output.
new 631aa01 Minor typo.
new 2c60542 Fix in implementation to avoid copies.
new 98b11db Add --lambda option to linear_regression.
new 83c8311 Update documentation.
new c9648f3 Add section on ridge regression.
new 898e598 Add a note about running a timer multiple times.
new 55d3123 Update NMF to work with sparse matrices also.
new 18c81b5 More fixes for correct sparse NMF.
new 2ea1e9f Test sparse NMF.
new 28e6a1e Armadillo 3.6.0 will be required for 1.0.7 because that is the first version where sparse matrix support was actually available.
new 1b7f2cc Update documentation to reflect Armadillo 3.6.0 requirement.
new b257707 Update documentation to reflect 3.6.0 requirement.
new 8ab7b98 Because we now require Armadillo 3.6.0, we can use each_row() and each_col() (thanks Marcus for the reminder).
new 73a89ff Fix comment headers for doxygen, remove trailing spaces, and use NMF instead of ALS because it now supports sparse matrices.
new c94e7fe Instead of using ALS, use NMF with a sparse matrix.
new 84d003e Remove als directory.
new 9cbb4a3 Reformat GetRecommendations() function and rearrange cf.cpp to reflect ordering in cf.hpp a little better.
new 2d51131 Why not call CleanData() in the constructor instead of repeatedly in other parts of the implementation?
new 017c206 Clean up CleanData() function. Don't use temporary matrices; there's no point to doing that.
new ffa9d5b Fix ambiguous call to RandomSeed, to pass the test with clang.
new e927f6a Minor comment fix.
new 57d95be Use sparse matrix batch constructor.
new 6781573 Clean up Decompose().
new 0ab9b51 Decompose() is only called once, so just inline it because it's simple.
new 5b9e6f1 Remove GenerateRating() function because it's only one line and only used in one place.
new 534ac4c Remove CalculateApproximateRatings() since it is only ever called once.
new 1cff011 Clean up Query(). It makes me feel a little gross to be so pedantic as to change 'neighbourhood' to 'neighborhood', and maybe I'm taking "code consistency" a bit too seriously, but it's too late and I've already done it.
new 2649c42 Inline CreateQuery() function since it is only used once, and use better Armadillo functions to make the generation cleaner-looking (probably no speedup).
new 9165d1f Remove GetNeighbourhood() because it is only called once. The check that numUsersForSimilarity < numUsers is redundant because AllkNN will make that check.
new 1d5d011 Remove CalculateAverages() since it is only called once, and inline it into Query(). The code has been cleaned up a bit and should run faster now because it does not use a temporary column vector.
new ca2e9b6 Refactor CalculateTopRecommendations(), including a complete overhaul of how recommendations are actually calculated. std::pair<> and std::map<> are often quite slow, especially in that implementation. This is faster.
new 6a4dc8b Issue a warning if the correct number of recommendations could not be provided.
new 9ba72d3 Remove CalculateTopRecommendations() function, because it was only called once. The 'recos' variable, as best I could tell, was not used for anything.
new 68a8d65 The very large and dense 'mask' matrix is now unnecessary.
new 4be8690 No! The spaces were WRONG!
new c709624 Remove Query() function as it is only used once; inline it into GetRecommendations().
new 409163f Remove method that allows modifying the data matrix, because references can't be re-pointed, and also because the sparse data matrix is only built in the constructor.
new b2c9148 Clean up CFTest, and fix some comments that were wrong.
new 7cbc98c Add convenient function to get sparse matrix.
new 8baefe7 Add a ridge regression test case (huh, I wonder how I forgot to check this in earlier).
new 3708a02 Add a test to make sure the output of the CF object is reasonable. I think this is a good test...
new 4efa293 Clean up main executable; a bit of const-correctness pedantry, and don't use c_str() if it isn't needed.
new 5382e2d Fix comment (thanks Marcus).
new 3a27bed Build the CF test.
new f0df7a0 Build CF module.
new 2133591 When --query_file is specified, only give recommendations for those users.
new d8f50cc Remove options for output files that weren't being used, and comment out options that aren't implemented yet.
new db5d6f9 Better comments for unimplemented functionality.
new 790c4ec Actually use number of recommendations and size of neighborhood in calculations.
new abbf4ae More comprehensive documentation on options and input/output formats.
new 8116fff Refactor EMFit<> so that the covariance constraint is a template parameter, and update other components accordingly.
new 23ae203 Make function static.
new 7cf9c3b Add tests for NoConstraint and PositiveDefiniteCovariance.
new 19b95a3 Rename PositiveDefiniteCovariance to PositiveDefiniteConstraint, because I think that's a better name and nobody's going to stop me (...I think?).
new d80ede4 Update name of constraint class.
new 77f4310 Oh hey, I have to check this in too.
new c79ddf4 Add DiagonalConstraint.
new 7382ca5 Add test for DiagonalConstraint.
new b9673bb Add EigenvalueRatioConstraint class for EMFit.
new eb659f8 Add test for EigenvalueRatioConstraint.
new bc3c0f3 What, how did I miss this? I definitely built the test and checked it...
new cc4e988 Remove fake functions that should only be specific to the kd-tree.
new 69d2a71 This is premature; wait for this until later.
new b21e357 If the root node ends up having an implicit child (not an illicit child!), remove the implicit node.
new 8cc6153 Remove unnecessary functions that were originally for kd-tree compatibility.
new a4b0955 Handle cases where the reference map is empty a little better.
new 836332d Overhaul RASearchRules so that they will work correctly with cover trees.
new a9b2914 Test RANN with cover trees.
new fbbc133 Add a note that this does not work.
new a9f39da Do not compile MVU.
new 58c3eab Fix some comments. No functionality change, and also this was probably pointless.
new 7611211 Yeah, it makes a difference to inline the BaseCase function (#281).
new b731251 Force inlining (#281).
new d85ee78 Backport batch insertion constructor to Armadillo < 3.810.0.
new 45508c0 Remove backporting for versions earlier than 3.6.0 because that's just not necessary anymore (3.6.0 is the minimum Armadillo version).
new 8474712 Oh, right, update the least maintainable part of the entire build system that I haven't figured out a solution to yet. Argh...
new 4d37fb7 Update copyright file to include new contributors.
new 27c8439 Update citation.
new 17b3353 Update changelogs.
new 1ca6651 Minor updates for normalized kernels.
new 3a9c697 One more thing...
new 6d2fd45 Update to latest version number.
new 7c79c1a Widen tolerances slightly.
new b1326d1 Move DTBStat into a separate file.
new 94714ed Check the matrix dimension before dropping unnecessary rows.
new 187d49a Add Epanechnikov kernel for kernel PCA.
new c4cace4 Allow GMMs to be trained using the existing model as a starting point. This could probably all use some serious refactoring now.
new e3e80d9 Add tests for estimation with the existing model as the initial point.
new f9045e6 Add logistic regression directory.
new 76fa71b Initial commit of logistic regression by Sumedh Ghaisas (#305).
new b8d2841 Add some comments and fix a little bit of formatting.
new 05bc80f Rename LogisticRegressionFunction to LogisticFunction.
new 91ce8b0 LogisticFunction is incorrect; it's actually the objective function for logistic regression, which is not the logistic function. Also remove unnecessary overloads in LogisticRegressionFunction.
new c40a059 Refactor Evaluate() function so that it works alright, and eliminate unnecessary parameters to the function. Move LogisticRegressionFunction implementation into a .cpp file because it is not templatized (for now).
new 5aece4e Add test for LogisticRegressionFunction::Evaluate().
new 6c90b28 Oh yeah, this is necessary...
new 65c6cea Add a randomized test for the logistic regression likelihood function that is not just comprised of simple examples.
new 03a801a Add test for regularization of objective function.
new 555fb65 Add test for Gradient().
new 3686feb Add correct implementation of Gradient() function.
new bbecac1 Make Gradient() const and add comments.
new 0a9b798 Add some comments.
new 8c33f24 Remove getSigmoid() and add class documentation.
new 432dc71 Break Predict() instead of the whole build.
new c2be6f0 Revamp Evaluate(parameters, i) for SGD and related optimizers. NumFunctions() also needed to be fixed.
new 1793f72 Add test for Evaluate(parameters, i) for SGD and related optimizers.
new 0c17bc6 Test regularization for separable Evaluate().
new 496c18a Update Gradient() for the separable case.
new 7451edc Test Gradient() in the separable case.
new 7267140 No need to multiply by responses[i] or (1 - responses[i]) because those quantities will always be 1.
new 18beafc Add test for regularization in Gradient().
new 766a29b Add a test for the separable Gradient() function.
new 62108e0 And this is why I hate maintaining documentation for things that I don't control; it goes out of date really quickly and people get confused...
new 7aa2f49 Remove memory leak (#310). Thanks to bianjiang for pointing this out.
new cfdfb2f Don't print "Iteration X of 0."; just "Iteration X".
new ae19ace Refactor functions so that they do not expect the extra column of ones for the intercept term.
new 78933d6 Refactor tests so that they do not give the extra column of ones for the intercept term.
new 2701b42 Make predictors and responses const.
new fbbee5a Make predictors and responses const.
new 2965c9f Don't hold lambda in LogisticRegression because it isn't necessary. Also make predictors and responses const because we don't need to modify them.
new 871cd98 Refactor LogisticRegression class. LearnModel() can be private, and we can const-ize a lot of the parameters and functions. Also restore functionality to Predict(), ComputeError(), and ComputeAccuracy(). This does not ever make a copy of the predictors matrix and doesn't add a column for the intercept, which is faster.
new 1293e2f Add tests for actual LogisticRegression object.
new 0278509 Goodbye, slightly misleading documentation.
new f72372a Add function to get the function that is being optimized.
new ac9630f Add function to get predictors and responses.
new 5b85eb5 Add a constructor that allows passing an instantiated optimizer.
new 8b4363b Test constructor that takes an instantiated optimizer.
new c19d989 Update history file incrementally, because doing this all at once at release time is difficult.
new be55f84 Add FurthestPointDistance() function.
new 61e3aa2 Test BinarySpaceTree::FurthestPointDistance().
new 6818f76 Implement FurthestPointDistance() for cover trees.
new 51e0a9c Regularization gets subtracted, not added. Thanks to Sumedh for pointing this out.
new af4718e Update test for positive regularization... oops...
new 17d0460 Clarify comment.
new b3d77bb Remove predictors and responses because they don't need to be stored by the LogisticRegression class, and then add a constructor so you can pass a given set of parameters.
new 02535ac Don't hold the optimizer and error function since they are only needed at construction time.
new dbc690f Add main executable for logistic regression.
new 3ff2ed2 I don't remember doing this, and I have no idea when it was, but hey, using namespace std in cpp files is a cool idea.
new 78a747d Add information so a version can be obtained easily during runtime and also at compile time.
new 215a590 Some documentation on versioning information.
new 0487767 Oops, a typo.
new 3928ccc Link to tutorial on versioning information in core.hpp.
new cb3225f Fix typo: furthest <-> nearest.
new bc4bd66 Update so that it gets compiled into libmlpack.so.
new 169204e CMake script to create svnversion.hpp, if needed.
new 4e50875 CMake scripts to find and update svnversion.hpp, if necessary.
new 64dd830 Fix dependency on stringstream.
new 1b3acf2 Safe check for if we are in an svn repo.
new f2f1146 Remove redundant check for working copy.
new 33e64ac Add svnversion.hpp to list of sources to track, if necessary.
new 4a0dc43 Fix error so that core.hpp is properly included.
new e52724d Ignore svnversion.hpp.
new 0bc57af Update copyright for the new year.
new bc5f91e Add Mudit's name to the list of contributors.
new 2307a99 Increase precision of saves.
new 1ebce66 When using the constructors that don't specify a model, make sure we create an actual valid GMM and not just random memory.
new 3bb8380 svn:ignore --> 'build*' in case you have multiple build directories.
new 4c63690 This wasn't actually calculating the variance correctly.
new c4d0ef4 Handle cases where scales are 0 correctly.
new 80a9c09 Pull in updated history from version 1.0.8.
new bbab33c Ticket #314 resulted in a bunch of useful changes.
new 6139137 Fix from Michael Fox for #242.
new 2c4eecc Add tests when the data matrix has linearly dependent features.
new 9cf0b0c Add new contributor.
new c3e90b7 Fix spacing.
new 6a000a7 Added ToString() to core/dists, core/kernels, and core/metrics Added a test for the ToString() methods
new 55a113e Updated Test for working optimizers
new cef741a Added Tostring to SGD.
new 395f361 Addes Tostring here early, mostly because SGD required it.
new 71fbc0e Changed so that "dimension" is not declared, to avoid compiler warning.
new d0a971b Changed so that "numPrunes" is not declared, to avoid compiler warning.
new 03494b4 Added L_BFGS
new 7adb295 Added ToString to LBFGS
new 9a279bd Fixed AugLagFunction Test; working on AugLag proper.
new 6125af9 Added ToString method
new 1d871b8 Added ToString for AugLag Itself.
new 8c81e2a Fixed AugLag Test
new e902538 Fixed my own error in ToString of AugLagrangian
new 7795f48 Fixed Test Error
new 286e90f Add CMake configuration for LRSDP, and split it properly into cpp/hpp/_impl.hpp files.
new 739f873 The Problem was the Test; Added ToString to AugLag's Test.
new 201d6cb Added BallBound ToString test.
new 3857516 Don't make an extra line when indenting things.
new 8104e72 convert << util::Indent(probabilities); Minor modifications to ToString()s in distributions.
new ba63f19 Add new contributor.
new c84d5cc Update ToString() for all kernels except the PSpectrumStringKernel.
new 770b4a9 Update so filename is like other filenames.
new df1f46e fixed ticket #316 (hmm::Predict() in hmm_impl.hpp)
new 106672d Remove license, that doesn't get applied until a release (until then it's implicit, yo).
new 064428d Inline non-templated constructor.
new d89ee04 Update documentation (thanks Yubao).
new a6dc629 Fix documentation (#321); from Siddharth.
new 72de45a Fixed Positive Def Constaint under gmm; previous error was "/gmm/positive_definite_constraint.hpp:28: error: expected primary-expression before ‘(’ token" at lines 27 and 33.
new 7807955 Added ToString to GMM
new c4e5809 Some ToString added, some updated (typos and indent). Test updated.
new bd2479f Fixed my subversion error, hopefully.
new a3eca33 Fixed a Mistake in HMM's ToString
new d2bc75a Added and Modified more ToString methods.
new a209510 Fix collaborative filtering test (#323).
new 65bec15 Add a boolean specifying whether or not the dataset is rearranged when the tree is built.
new 551bde4 Cache the distance from the center of the node to the center of the parent node.
new 32695f4 Test BinarySpaceTree<...>::ParentDistance().
new 9f9b4fe Also test ParentDistance() in the case where the tree is built and mappings are used.
new ffe7636 TraversalInfo, a new idea for doing things. This will need to be further documented...
new e80bd00 TraversalInfo class used by nearest-neighbor-like problems. Maybe it could be the same as the one in src/mlpack/core/tree/.
new 255218b Change build to include ns_traversal_info.hpp.
new 9619678 Add traversal_info.hpp to build system although I don't think it's used anywhere.
new 99140c6 Make rules classes for various dual-tree algorithms support (but not use) the idea of TraversalInfo classes.
new 8607287 Minor changes to SortDistance().
new e57ad28 Overhaul NeighborSearchRules to work correctly with TraversalInfo objects. This is related to #243.
new c767493 Modify SortDistance() usage because SortDistance() API has changed slightly.
new 014b4f4 Modify BinarySpaceTree::DualTreeTraverser to properly handle TraversalInfo objects.
new 41a730e Modify CoverTree::DualTreeTraverser to properly handle TraversalInfo objects.
new d544deb Adapt SortPolicyTest for new API.
new 07a4094 Remove unused score variable; this fixes a lot of warnings.
new 909e76e Modified StringUtil to take a number on Indent, implemented LSHSearch ToString, updated Test.
new 0341b5a Added more ToString, updated test, took advantage of new tab function.
new c8de967 Patch from Siddharth for #324.
new 7666cb4 Finished toString of the methods folder ( sparse coding and rann ); updated test.
new dd58e5a fix forHMMTest/SimpleDiscreteHMMTestViterbi
new 304e476 Remove license text.
new 99eba9e Slight code formatting modifications.
new 0ac2184 Don't initialize empty distributions.
new 7b9ff48 Remove unnecessary newlines from after mean and covariance output.
new 2d9abe7 Actually print the kernel.
new 9fa36cf Minor fixes to ToString().
new 81c3b81 Minor fixes to ToString().
new 2478634 Minor changes to ToString().
new 52f2b20 Minor changes to ToString().
new e5d9577 Minor fixes to AugLagrangian ToString() methods.
new 5d63c78 Move things around so LRSDP can actually be included in stuff.
new ebc8ae1 Some updates to what has been going on (lots of things!).
new 323ed99 Ah, right, one more thing.
new fdc2679 Minor changes to ToString() output.
new 6fe2dde Minor changes to tests; in some cases matrices/vectors are now initialized so they provide more output.
new 172a350 Remove PeriodicHRectBound (#30).
new 96094b0 Remove this file too...
new b21d868 Remove PeriodicHRectBound from tree tests.
new 0643767 Denote that we removed PeriodicHRectBound.
new 8a2b428 PeriodicHRectBound is removed (#30).
new 9c5ddc0 Updated Test and pspectrum_string_kernel
new 2a96324 Updated Test and some info for ToString.
new a7febb0
new f6d4008 Revert commit by unknown contributor.
new cee9f5a Test commit
new 557d08c Revert test commit.
new a07b4eb Update citation format.
new 800bee5 Fix from Siddharth, fixes #324.
new 6a2195b Add new contributor.
new 2afaf2f Fix formatting and fix contributor information.
new 0480218 Didn't mean to check in arma_traits.hpp...
new a6501d4 Oops, forgot to check in this change from Siddharth.
new 8ca8c38 Example tree. Not really to be used, but for documentation.
new 1e92e90 Refactoring from Saheb: don't do naive search with trees.
new 7ddf945 Add new contributor.
new 945fac6 Clean up RangeSearch implementation so it works with TraversalInfo struct.
new adfc68c Use TraversalInfo for FastMKS. Right now, the parent-child prune is not implementd, so this is significantly slower than the released version (but it at least works, unlike the last svn revision).
new 32fdc74 When the parent-child rule can't be applied, the correct bound wasn't being used before. This fixes that.
new 1851d50 Do child-parent and parent-parent prunes correctly for FastMKS. This actually accelerates the dual-tree implementation, which is cool. By how much? Not really sure, maybe 10%-20%?
new c5965b5 Update the line about dual-tree algorithms being faster. 'cause they are.
new 8ded964 The Prescore() and PrescoreQ() functions aren't used anymore because I figured out how to do child-parent and parent-parent prunes without them using the TraversalInfo object.
new 1f8b573 Patch from Saheb: do actual naive search for RangeSearch and NeighborSearch instead of using the hack for BinarySpaceTree with leafSize = n_cols.
new 6322216 Add some Armadillo traits for template metaprogramming. This abstraction may change as time goes on.
new 2498505 By default, include arma_traits.hpp.
new eb44a20 Refactor MinDistance(), MaxDistance(), and RangeDistance() to accept any Armadillo vector type.
new 965d9e2 Refactor MinDistance(), MaxDistance(), and RangeDistance() to accept arbitrary types of Armadillo vectors using IsVector<>.
new 9084dd6 Having an implementation for the example tree is kind of a dumb idea. Also make sure CMake knows about example_tree.hpp so it keeps it up to date.
new 3e5a9f6 Clean up some namespacing, and add a test for sparse AllkNN using kd-trees. Also add one for cover trees, although it does not work yet.
new 3437ce4 Templatize arguments for BestPointToNodeDistance().
new b4bc237 Refactor NeighborSearch so it works with arbitrary TreeType::Mat types. That abstraction should probably be cleaned up a bit.
new 47859c2 No more implementation.
new 2955359 Stop timers correctly when Log::Fatal is called (or when Load() or Save() return early).
new 8c5140b Rank is not yet a parameter, but this heuristic from Siddharth improves upon the previous "rank = 2".
new 9b44fc4 Fix mixup of rows and columns.
new ced91b1 Widen tolerances ... again.
new ce48c53 Patch from Siddharth: make the rank parameterizable, and merge the constructors into one.
new 906b91f Update for changed CF API (patch from Siddharth).
new 3784abf Some changes to LaTeX options in the Doxyfile.
new fd7a162 Explicitly use namespace mlpack::neighbor.
new 1d8bfc6 Remove using directive that has been there for six years. Sigh...
new 48116d2 Remove numPrunes -- it isn't used.
new 4421441 The maxLeafSize parameter is unused (other than an assert) so remove it entirely.
new a330d5f Initialize uninitialized variable (#336).
new bf2ad9c Remove numberOfPrunes variable, and initialize baseCase (#336).
new efda5e0 Patch from Siddharth: templatize CF to accept arbitrary types of factorizers.
new bb171e3 Fix regression in r16308, which slowed down cover tree traversals by potentially up to 50% (at least, that's the slowdown I saw...).
new 83ea01d Actually use the right parameter name.
new b49848a Ok, handle NaNs correctly, and also check this in in trunk, not in the tags...
new cd286ca Remove incorrect comments.
new aa321b0 Better rule, which forces the score to 0 for AllkNN. Not sure if it'll work for AllkFN. Also, I think there may be a bug in the traversal info handling for the BinarySpaceTree DualTreeTraverser.
new 1c88d1e What was I thinking? This is a _far_ better solution than r16359.
new b8747ec Modified patch from Saheb for #301; this unifies the constructors for NeighborSearch so they work with all tree types. The modifications I've made make it so that the referenceCopy and queryCopy matrices aren't full copies of the referenceSet and querySet matrices when the tree doesn't modify them (in the case where they aren't modified, it's not necessary to copy them, that's just a waste of memory).
new d095f52 Fix to go with patch from Saheb... forgot to check this in earlier.
new a3cb786 Make the ExhaustiveSyntheticTest use kd-trees with a leafSize of 1. This changeset brought to you by the magic of regular expressions, which mostly worked...
new 4539ee9 Oops, use single-tree for the second iteration.
new bc49c7f Through the magic of regular expressions, I've refactored this test to use kd-trees with one-point leaves.
new dba130c Fixed arma_traits by removing duplicate template instantiation, so that visual studio would be able to use it too.
new 7973e83 Update documentation to reflect changes in RangeSearch.
new a2feea8 Incorporate patch from yashdv to move splitting procedure to a different class.
new ad4ae0a Add new contributor.
new 23fc3ac Make parameter const because const-correctness is a good thing.
new b272f36 Don't use the SquaredEuclideanDistance.
new bd1ff33 Don't use the squared Euclidean distance.
new 0618cdd Fix minor error that I didn't correct last time.
new cc8bfb9 Refactor LRSDP into the main class and a separate function (LRSDPFunction). This is a patch from Abhishek Laddha for #318.
new 57b9be5 Better ToString() output.
new 4e1d178 Annotate changes to LRSDP.
new e1fdb81 Add new contributor.
new 93beaa8 Whatever bug used to be here before isn't here now.
new dde19f3 Use const reference parameter so it works with temporaries too.
new 0d106c9 Doxygen fix so that local paths aren't included in the built documentation.
new 58f92ce Actually catch all of the instances where single quotes start lines.
new 4e84e9f Patch from Siddharth for #342.
new 297fcc3 Document API change in an attempt to piss people off less when their programs are broken.
new ac7502e Clean up implementation of GetRecommendations().
new f200cd5 Update documentation due to API change.
new 262ebe2 Spelling fix; thanks Barak!
new 0081a00 Patch from Saheb for #301; refactor RangeSearch constructors so that leafSize is not a parameter.
new c5561c6 Modify test for new RangeSearch API.
new 6013414 Add rank parameter. This might not be applicable to when we have other decompositions, though.
new 4817caf Minor documentation fix, and sometimes the labels need to be transposed.
new 206648b Don't transpose the labels upon loading; expect that they are going to be one line per label.
new 47bb810 Get the number of classes correctly.
new 9143332 Don't transpose on save; one point per line.
new 154cb57 Overhaul implementation; do not use gmm::phi(). This gives serious speedup, as high-dimensional matrix inverses are not being calculated. The previous calls to gmm::phi() would invert a diagonal matrix without being able to assume that the matrix was diagonal. This explains the very very poor benchmarking results for nbc in mlpack.
new cf6bff8 Adapted patch from Vahab for #344: incremental algorithm for variance calculation in Naive Bayes classifier. This is optional and can be specified in the NaiveBayesClassifier constructor.
new 5bf6ae3 Test incremental variance functionality.
new eae14ef Change to two-pass algorithm suggested by Vahab in #344.
new bc3d650 Add new contributor.
new bdd4f83 Add sparse autoencoder contribution by Siddharth. This is the version given in ticket #345 as Changes3.tar.gz.
new ed1e4ad Add test for sparse autoencoder, contributed by Siddharth.
new f8c663a First pass: add file headers, include guards, and then my vimrc auto-stripped all trailing spaces.
new b0af555 Minor (and ultimately trivial) documentation changes; add documentation for SparseAutoencoderFunction constructor.
new 13bbeed Syntax cleanup; just some spacing. No functionality change.
new 9ea390d Adapt test to work in the larger framework of mlpack tests.
new ce9936e Simple style changes; no functionality change.
new 357860d CMake configuration to compile sparse autoencoders.
new 3d92c56 Build sparse autoencoder as part of mlpack.
new 654865f Test sparse autoencoder.
new b3c5f9b Remove unused variables to fix warnings.
new 848fdcf Change Sigmoid() function to avoid matrix copies via the return value.
new adc6dfb sparse_autoencoder_function lines 55 through 58 modified so it would build. It doesn't pass the test, but it builds now. Please fix.
new f7d4559 A better fix for the failing build.
new fa9101b Revert accidental commit.
new d941b4a Rewrite NMFALSTest so that random failures should be less likely.
new a9e677a Const parameters will cause this to be two billion times faster.
new 4ee34f4 Save the correct labels; thanks Anand!
new 2cbe7ef Add files and some preliminary code for R tree
new 482e443 Fix comment and clarify that it's pertaining to the runtime constructor, not the template parameters.
new 0449ba4 It turns out the implementation of FurthestPointDistance() was just wrong. Thanks Andrew for pointing it out.
new e30506e The test for FurthestPointDistance() was wrong also.
new e5b360d readability changes to BinarySpaceTree::FurthestPointDistance()
new 7d49f86 Add new contributor.
new 1e5af1f Remove the Pelleg-Moore k-means implementation; it is being replaced.
new a3be165 added more code for the rectangle type trees
new 25bd564 added module 'lmf'(Latent Matrix Factorization) to accommodate SVD based update rules alongside NMF based update rule. CF module is updated to use LMF module.
new 55b2a15 remove the silly folders I added when I meant to add txt files.
new 463aeb5 now add the actual files the way they are supposed to exist. No real code yet.
new 390e7d6 Remove HasParentDistance trait, becase it wasn't used anywhere.
new ea72f0c added comment to base case. Some more preliminaries for rectangle trees.
new 442a952 add a short and hopefully useful explanation of what different files are for, focusing on BSP trees.
new 09198d1 add a description of statistic
new 5bea54e Don't select points from clusters of size 1.
new 461b6bd more code for the RectangleTree. Still not built yet.
new baba8bd more R tree stuff. Still no build
new 15c72dd more R tree stuff. Still no build
new acfa22e Ensure that BaseCase() is called right after a node is scored.
new 9dff6de It's no longer reasonable to say the FASTLab developed mlpack, because first, the FASTLab no longer exists, and second, there's a lot of code from other places. I should have removed this years ago, but I never noticed it until today...
new 9ce7a74 What was this macro even for?
new a9153ab Refactor core.hpp into two files; one for non-mlpack includes, and one for everything else.
new 78d42b3 Use prereqs.hpp to avoid weird include order dependency issues.
new 9291a7e Use prereqs.hpp instead of core.hpp; core.hpp is required for the implementation, though.
new dcf0289 Include stdint, for uint32_t support.
new 47eec8c Use prereqs.hpp instead of core.hpp; however, the implementation requires core.hpp.
new 93adc78 Fix header guard names. This is an incredibly pedantic fix.
new 7a6437e Remove unnecessary includes.
new 7df5091 more R tree stuff.
new 588370e more stuff for R Trees
new 669f8f8 Changing LMF(Latent Matrix Factorization) to AMF(Alternating Matrix Factorization). NMF and CF modules are updted.
new 245182b more R Tree stuff
new fa627db R tree stuff
new cc3671b added code for accessing immediate child nodes (need to think of a way to rename this to be less confusing). Some more quasi-code to split nodes and insert points.
new 3f9d23d Trivial spelling fix.
new 27e4131 Fix/update some comments, almost finish the splitting algorithm. Several miscellaneous changes.
new 69556a0 change name of leafSize to maxLeafSize. more stuff for the R-tree. Some name changes, some more node splitting, a start on traversal.
new f2e17ed Typo which causes a segfault.
new 6925692 Oops, this actually happens in two places.
new 3c6ee3d a few miscellanious small changes. Added to CMake.
new b6f9e01 add the missed files.
new 8766861 require kd-trees to have leafSize of at least 1. Add an assert to ensure that the SingleTreeTraverser isn't called on a tree with only one node.
new c7e7684 Rectangle Tree Traversal implementation.
new deb9fc7 change a comment to be more accurate. Add on --r_tree option to the knn_all program. Doesn't do anything yet.
new 0a3a1b3 comment out compilation. Some small changes to support R tree in all_knn
new 457c523 fixed some mistakes. Still commented out to allow build.
new 52e5582 * Modified AMF module so that now it uses tolerance checking rather than minResidue checking * Added SVD batch learning
new 7eaf48e * fixed include error
new 7660602 * Added momentum to SVD batch learning * AMF now calls Initialize on update rule before starting the optimization * Every update rule should now implement Initialize accepting data matrix and rank
new c88879a more fixes. Compilation still commented out.
new c380e58 more of the same.
new 304e256 Inline the simple R tree descent heuristic.
new 65f76de Remove leafSize parameter from DTB constructor.
new 4e62dfc Decision Stump added
new bd7aef7 Fix #334 by ensuring vector accesses don't go out of bounds.
new 44bf754 More bug fixes.
new 5405420 Fixed armadillo issues, along with removing uninitialized and unused variables
new 661958b more bug fixes
new ea8ff93 keep the root node at the same address.
new 46d0d01 bug fixes
new 452d68a Link against libstd++ when using Clang, and also use -Wall.
new d559ce3 Fix for convergence, because sometimes the residue may increase (especially with ALS update rules).
new 6e9ef0e Make a note that this set of update rules often creates lots of NaNs when sparse matrices are used.
new dbe8ccb Significant refactoring of NMF tests. The sparse tests were generally invalid because NMF is not guaranteed to produce a unique decomposition. Instead, now we test the Frobenius norm. Also, the tolerances needed to be significantly adjusted because of the new convergence criteria in the AMF class. Lastly, the SparseNMFRandomDiv test and SparseNMFDefaultTest have been removed because those update rules seem to often result in NaNs when sparse matrices are used as input.
new c6baea9 Remove backup file from emacs or some other inferior editor that isn't vim.
new 92ad00f First pass: comment standardization, fix header guard names, move .cpp to .hpp because it's all templated functions.
new b3b1d55 Use bool instead of int.
new 501ef6b Perceptron Added
new d881abd bug fixes for memory leaks
new 94f8308 bug fix. had n_rows when I needed n_cols
new 4ecf788 Minor changes to test. const-correctness and comment normalization for Doxygen.
new 796acc7 Decision Stump test fixed
new 0b56b07 Use const double where possible instead of having a variable used throughout the function. This is only for clarity and consistency and is not likely to make any runtime difference.
new 8e76f8f For clarity, use separate split and binLabels objects instead of storing the label in the split matrix. No casting is necessary anymore.
new c2cfc11 Remove unused variables.
new 3b82032 Oops, missed one unused variable.
new 48ef3f9 Remove classLabels; it isn't necessary for the DecisionStump class to hold it.
new 835cb66 * Templatized termination of AMF matrix factorization * added 3 termination policies 1) SimpleResidueTermination 2) SimpleToleranceTermination 3) ValidationRMSETermination
new 6624a42 Assume the response to be the last column of the input file, as pointed out in the description.
new ab27666 Fix ambiguous math reference error, to pass the test clang.
new fa80c3f Easy fix for #355.
new 92b60b3 Document minor fix.
new 5800c8a Remove oneClass and defaultClass variables. There is a shortcut that can be taken when all the labels are the same, but the Entropy() function does not appear to be working correctly.
new c0d7b85 * Changes in AMF abstraction, Termination policy is made first template parameter * fixed minor formatting issues
new 23a1099 Removing old cosine_tree code.
new c866e89 Adding new cosine_tree code.
new 432fdc0 Rectangle tree and tests. Construction seems to work.
new bf0e023 memory leak fix
new 79fd529 Combined CosineNode and CosineTree classes.
new 4699840 Rewinding the code review
new a0b3a94 Fixed subvec calls.
new e40fc56 change the tree to store size_t in the nodes and keep the dataset together. Other misc changes.
new 5621000 Very simple change to fix build on i386.
new b617669 Initial commit of simulated annealing optimizer from Zhihao Lou.
new 87748e7 Minor refactoring for brevity.
new e496a4c rectangle tree traverser
new 81c4584 fix build
new dc22914 commit to ease debugging
new fdd7d39 Move LaplaceDistribution to mlpack::distribution and expand upon it, but then remove MoveDistributionType template parameter from SA class because really, the MoveControl() function is written specifically to work with the Laplace distribution. I was incorrect to think it could be templatized so easily. The implementation of the Laplace distribution has been inlined, too, which may help it be a little faster.
new 554f12c Create separate target for moving mlpack headers. This should fix #322.
new bd34b3a Remove now-unnecessary include.
new e50716d work arround for CMake bug.
new b439137 Remove documentation for MoveDistributionType.
new 11d78cd Rearrange parameters -- maxIterations is probably the most likely to be changed, and also maxIterations tends to be the first parameter for other algorithms.
new b2a0826 Rename parameters, clean up documentation; very minor tweaks. No functionality changes.
new 339486f * faster implementation of SVDBatchWithMomentum * tolerance termination policy is modified according to new policy * test point selection in validation RMSE termination is shifted to constructor
new a826c9b Refactor to avoid holding variables in the class itself (reduces the size of SA a bit). Remove an unnecessary variable too. Minor changes, no public API changes.
new 5a3630c Add comments to private functions in header file.
new dbf8fdf Explicitly use arma::sign().
new 726837d Adding QUIC-SVD.
new d35bd6c arma::sign() doesn't exist in Armadillo pre-3.920.
new adc64e4 Why was svn:ignore set for cf.cpp? Removed.
new b82327c svn:ignore build directories.
new ae88e2a Minor cleanups; no functionality changes. Make some things const where possible.
new 15f6dab Removing files added by mistake.
new 65e001d Set default CoolingSchedule.
new b924916 Add some more tests for simulated annealing, including a highly nonconvex function (the Rastrigin function).
new 1c27cea New test added. Improved entropy calculation.
new faa9381 Refactor tree construction so that arbitrary tree types can be constructed.
new 7fe247e Refactor tests, use BOOST_REQUIRE_EQUAL(), and add a test for EMST using cover trees.
new dbaa214 Oops, I did not mean to comment out the sparse k-means test.
new 1dbbd03 Removed a few tabs.
new a128b7f * modified termination policies * fast SVDBatch implementation
new 6539b46 * error in SVDBatchTest resolved
new 1a25a36 Bump minimum required Boost version to 1.49 for boost.heap.
new 8ffc85a Split RAQueryStat into its own class.
new 2b01310 Refactor RASearch so that it does not accept a leafSize parameter and can build arbitrary tree types.
new bde2477 Fix constructor calls, and automatically construct a cover tree with the default RASearch constructor.
new 519e791 First pass -- move files to match naming policy, change initialize() to Initialize(), standardize comment formatting, fix some Doxygen commands. No serious functionality changes.
new 29fc8c4 Minor formatting changes according to the style guide (mostly, I think?).
new ea0fb14 tree traversal
new 963c74d Added check to solve ticket 347. Note that this does not changeany functionality, just adds a warning.
new 4fc56e7 R tree traversal test code.
new 88e9f90 * added SVD Incomplete incremental learning * added Termination Policy wrapper for SVD Incomplete Learning
new d7fa153 Minor refactoring of AMF class; mostly renaming for consistency and clarification of comments.
new fb7d980 Trivial spacing fixes.
new d026d81 Rename for slightly changed API.
new 4a4a524 Move warning to prereqs.hpp, because sometimes prereqs.hpp is included and core.hpp is not.
new fc6cc9d Don't include <armadillo> explicitly, because <mlpack/core.hpp> does that already.
new cc2f00c Add new contributor.
new 6fcd9bf Note that we now have simulated annealing.
new 43dbca8 Don't include <armadillo> before <mlpack/core.hpp>.
new b595048 Disambiguate: math::RandomSeed() -> mlpack::math::RandomSeed(). Issue noted by Zhihao.
new 9222526 Patch from Zhihao: sa_update.diff.
new 7a98ed0 Return the correct type of the matrix, because it isn't necessarily dense.
new 21f2bb9 clang complains when default parameters aren't part of the original declaration. Also vim removes trailing whitespaces, so this diff looks way longer and more complex than it actually is...
new 6e825dd Add support for HMM initial states. Slight modification of API for creating HMMs by hand -- the initial parameter is now required. This change may affect some existing results, and the new results may not perfectly agree with MATLAB, but MATLAB does not have the flexibility to seriously support initial probabilities. It is possible to set the initial parameters such that it will emulate MATLAB behavior right, probably by setting the initial probabilities to the fi [...]
new 1b1c87c Test HMM initial probabilities.
new e002fc1 Document that #315 is fixed.
new 76ae36d Fix some formatting, fix backwards entropy splitting, add getters/setters, and comment a little bit about the internal structure of the class.
new 30216b2 Another test to make sure the correct splitting attribute is used.
new 3dde93d Include mlpack/core.hpp.
new 3643362 R tree now has dataset and indices
new c440af0 Entropy calculation improved.
new f05fd18 Const-correctness and 80-character lines... very trivial fix, no functionality change.
new d961238 Fix some formatting issues; no functionality change.
new 0d91b12 Use bool instead of int for tracking convergence.
new a69331b Don't use arma::unique() because it's slow.
new 94be125 IsDistinct() improved.
new 4812b37 Very minor changes.
new 40f65e4 Lengthen comments that weren't 80 columns long. This may be the most trivial fix ever in my long, decorated history of trivial commits.
new 5607d5b * added local minima storing functionality to termination policies
new 57cf11c Changes are part of perceptron code review, as discussed with Ryan
new aafe06c Minor improvement. No major functionality changes
new 98dcfd6 Add MinimumBoundDistance(). This represents the minimum distance between the center of a node and any edge of the bound. Note that for ball bounds, this is equivalent to the furthest descendant distance.
new cae0701 Fix elusive bug that only occurred in particularly rare situations.
new 9ba5fae Add MinWidth(), which is a better solution than having the tree calculate it by hand.
new 50e755b Test MinWidth().
new 7a3a69f Use the bound's cached MinWidth() for MinimumBoundDistance().
new 88da7fd Use slightly safer Width().
new f74af58 Oops, this needed to be divided by 2.
new bcecbb3 Adding Regularized SVD Code
new 1b916f2 Simple style changes for consistency.
new c13aa93 Don't save a rowvector into a colvector. Use the build in option of the save function to transpose the vector.
new 1db6997 Point deletion. Massive refactoring of Children()[i] to Child(i). Really minor point deletion test.
new 39666eb Rename executable.
new f56a3e8 Refactor main executable. Some further refactorization will need to be done when everything transitions to arma::Row<size_t> for labels.
new 194844e Rename executable.
new 481aeda more tests. Really silly bug fix.
new 27164e0 * Added convergence test for SVDBatch and SVDIncremental learning
new 3c83b02 Minor updates
new 4f7d98c Adaboost design issues, to be discussed, then changed later on
new c247ee6 * added svd incomplete incremental learning tests * combined functions IsConverged and Step of termination policies into IsConverged
new daac702 The size parameter is unused outside the constructor; also, commit this change to trunk this time...
new 1d04af7 Minor changes
new fdbcc58 Minor changes to the macros in the *main.cpp files.
new 95ca3b6 Adaboost and Perceptron modified (improved constructor), going for tests on one Weak L
new 4b6eb72 point deletion. bug fix. more detailed test.
new a121aab Actually calculate score and base case for first node combination.
new dfd280a * remaned SVDIncrementalLearning to SVDIncompleteIncrementalLearning * added SVDCompleteIncremenal learning * added CompleteIncrementalTermination wrapper
new 5b0a368 R* tree split and descent heuristic.
new 50d5789 Add nystroem method for kernel approximation.
new eddebf3 Add test for the nystroem method.
new 44b26ee Embedding nystroem method into kernel pca method.
new 0c83d09 Outsource the matrix multipilcation.
new e117a71 Avoid direct multiplication with a diagmat.
new 15196c2 Changes to implementation of adaboost. Implemented adaboost.m1
new d1bbdf4 Adaboost.mh implemented
new b65e4ff Comment normalization.
new 4c921ed R* tree split. Default to using the R* tree in allknn
new c49d4ee Refactor to be stricter with types (arma::Col<size_t> instead of arma::vec).
new f90e57e BiBTex added to adaboost_impl.hpp
new 273d61c Adding tests for Reg SVD.
new 6296040 Integrate nystroem method into the kernel_pca_main.cpp file.
new 158567c Improved nystroem localisation ('oe')
new 50e7445 Bug fix. Node splitting tests.
new 85a1439 Adaboost improved. Tests for the UCI iris dataset added.
new 8aaa148 Adaboost test improved and now works. Improved adaboost.
new 97c849e Contribution from Yash to solve #250 and make BallBound usable.
new 3563834 Tests for ball trees and BallBound<> by Yash, to solve #250.
new d6c31c2 Point out that there is a known bug.
new e56b5bf Fix normalization bug (transpose); Some more comments.
new fe9c233 Some notes on some things I've done.
new d53ae6b Additional things that have changed. I incorrectly wrote in the last commit about stuff "I had done" but I'm not sure why, given that each of these contributions are from people who are other people.
new d6f7ef5 Ball tree tests for EMST.
new b06ec72 Initialize reverseStepCount to 0 to avoid memory issues.
new 1201471 Fix an uninitialized value.
new 9f56dad Increase tolerances a little bit, because they were failing in some cases.
new 8579106 For each random dataset, ensure that the size of the implied user/item matrix is numUsers by numItems by manually setting the last element. Some formatting and const-correctness fixes. Also, increase the number of iterations for the optimization test since it didn't seem to be converging (hopefully the specific number of 10 passes over the data was not chosen for a particular reason).
new 52d8125 Patch from Sumedh: fix some uninitialized values.
new 3c4b4d8 Patch from sumedh: Mat::row_col_iterator
new f5baba1 Patch from Sumedh: more tests for SVD
new de45cf4 Patch from Sumedh: tests for row_col_iterator
new 234378b R* tree bug fixes.
new 09e5feb Propagate HISTORY.txt change to trunk.
new 10a950d New tests added for adaboost.
new 3bc61b5 code cleanup for R tree
new 699a2b3 Update documentation.
new 8b6b398 Propagate documentation fixes to trunk.
new 5207892 Merge in changes from release branch. I guess I should have done all this before I branched.
new 473dd46 Fix warnings.
new 1dfcbac This warning only appears on i386.
new fae17d8 Fix botched LaTeX formula.
new 2b3fa12 Set date of release.
new a58837e More comprehensive tests.
new 3f8b59f Fix typo.
new d740ec5 R tree clean up. Change Child() to match BSP tree. Copy constructor takes a second argument to specify whether it is a deep copy.
new d0ad39f Don't do base cases before recursing. This is slightly cleaner code and will properly handle the case where the tree is only one node deep.
new 6620cfd Extremely minor changes.
new fa79435 More tests for Adaboost added, with tolerance for change in rt also provided.
new ae2ddb1 Refactor KMeans so that the actual Lloyd iteration step is separate, since there are many ways to do a Lloyd iteration.
new 8bfd3fb Add some comments.
new f5e4221 Refactor test for changed API.
new ca8cbba Further refactoring of KMeans. Fix MaxVarianceNewCluster, and also change it so that assignments are not passed in (since the inner KMeans loop doesn't really keep track of these now).
new 31d0a65 Fix changed API.
new 298ef02 Explicit cast for older versions of Armadillo.
new b217294 Explicit cast to arma::vec for old versions of Armadillo.
new af2da3c Yet another reverse-compatibility fix for Armadillo.
new 4d4ce86 Return statements for operator++() and operator--().
new 56a3504 Fix out-of-order initialization warnings.
new bba6f35 Fix error in random sample generation.
new 8328ac4 Add LaplaceDistribution to the list of default-ly included distributions.
new bc3b890 Adaboost now works with Decision Stumps; added tests for the same and extended tests for Perceptron too.
new 2886b9f Minor code cleanups.
new 27a79dd * added plain SVD factorization - wrapper of arma::svd for CF module
new 9518d4c * added tests for PlainSVD
new 828f555 Removed phi, added gmm_convert_main.cpp
new aa2f885 Removed phi, added gmm_convert_main.cpp
new 7b3d863 Changes to work with new, hierarchical GMMs
new 36d0dad Changes to work with new, hierarchical GMMs
new e335d48 utility for converting legacy GMM XML files to new format
new 42e57d0 Hierarchical GMMs store params in GaussianDistributions. Makes code clearer and simplifies Save/Load.
new e5845f0 Changes to work with new, hierarchical GMMsHierarchical GMMs store params in GaussianDistributions. Makes code clearer and simplifies Save/Load.
new 09a203f Hierarchical model support
new 0f95ab8 Hierarchical model support
new 167021f Hierarchical model support
new 1f64b4e Hierarchical model support
new b6943e6 Hierarchical model support
new a7686bf Implemented Save, Load
new 090f9ba Implemented Save, Load
new 8f4b871 Implemented Save, Load
new efc43b0 Implemented Save, Load
new b03a1fc Added hmm_convert (legacy file converter util)
new 8739905 Hierchical model support
new 2bbe127 Implemented Save, Load for hierarchical model support
new 20c6a5b Implemented Save, Load for hierarchical model support
new 3c8b5d3 Added legacy file conversion
new 8fce55a Legacy file conversion, deprecated old SaveHMM, LoadHMM functions
new 66ed2e4 Legacy file converter util
new 45bde38 Added Save, Load tests
new d68858e Updated Save, Load tests and updated tests for hierarchical format
new 730767a Remove duplicate declaration of ReadFile() to fix the failing build.
new 45d83df Remove const identifier since it gets ignored and throws a warning.
new becd757 Minor formatting changes for row_col_iterators, mostly to adhere to the Whitesmiths style.
new 10d40be Test sparse iterators, when we can.
new 93aaabc Point deletion bug fix.
new f6f56b2 Fix incorrect check (how did this happen?).
new 84edc09 Oops, I fixed this backwards. The actual error is the output.
new 34cf8ff * changed row_col_iterator::operator-- implementation * added documentation to termination policies * minor fix of PlainSVD module
new 2ed0c9f * modified PlainSVD module to return normalized frobenius norm * modified PlainSVD tests * added row_col_iterator operator-- tests
new 9657fd5 * minor changes
new 4b7294f GMM::Save() now adds type information to XML files
new 8b9294b phi.hpp no longer used, see GaussianDistribution::Probability()
new 926492e removed #include <mlpack/methods/gmm/phi.hpp> which included only unused functions
new 18cf37a Add header comments and clean up BiBTeX citation a bit.
new 1810717 Add header comments, fix header guard naming to be in line with the rest of the files.
new b366a19 Add some const and fix some formatting.
new 6dc2730 Change names of functions.
new 0245ecd Some formatting fixes.
new 887dc99 Simplify a matrix calculation.
new 57db87d Set ARMA_USE_U64S64 in hopes that the types of problems Gilles is having on the mailing list will be solved.
new d5e4c9c Refactoring and optimizations on Adaboost.
new 797503d added Save(), Load(), Type() to LaplaceDistribution
new ed80898 * changed PlainSVD to SVDwrapper * SVDwrapper is templatized to support other SVD factorizers * Added simple typedefs for simple API
new 48e5271 Return *this for operator--().
new 8928ba3 Fix odd tabbing issue.
new 64e29ef * added documentation to all update rules
new 88428ba X tree commit
new 0dd1ee0 First pass: make lines 80 characters long, tabs to spaces, and bracket surgery (or something).
new e576866 Typing failure.
new 438d0b7 Don't add row_col_iterator support after 4.349 (currently svn trunk) since Conrad accepted our patches.
new 10d89ab When Conrad took the patch, he stripped out a lot of compatibility between iterators, so... take the tests depending on that functionality out.
new 541f21d First pass: make things 80 characters, minor style fixes.
new 69fea5f How did I accidentally remove two lines? I'm not actually sure.
new 757886b Center the reconstructed approximation and the kernel matrix.
new 7a0fad6 Scale the transformed data matrix.
new c438f4e Use the maxIterartion as template parameter.
new 3317c56 X tree
new 067da88 Decision Stumps modified, along with adding Classify() function to AdaBoost. Other minor changes (renaming).
new dce0d32 Minor formatting change, and use zeros() instead of fill().
new 21c415a Made Reg SVD work with CF.
new 90af07d First pass: try to make things 80 characters (I didn't touch the big long type lines...).
new 6f60dad Typedef to the rescue! Much easier to read now.
new 0496768 Simplify some loops.
new b387f11 Significant test refactoring for style. Also, use BOOST_REQUIRE_CLOSE and BOOST_REQUIRE_SMALL for floating point comparisons.
new 3bde69b Use templates to significantly simplify code and remove multiple versions of the same function.
new ee0d6e2 First pass: make it 80 characters, fix a few coding conventions. No real changes.
new c413bcc First pass: line length, bracket surgery (similar to rocket surgery).
new 3f43656 First pass on R* tree split code; make things 80 columns, use convenience typedef, minor style changes.
new 6602fa8 Changes to Decision stump and AdaBoost.
new b8cdc72 Minor documentation changes in CF.
new c934741 * added AverageInitialization to AMF
new d8b5bec Some brackets and stuff like that.
new ff1c084 * added NMF, SVDBatch, SVDIncompleteIncremental and SVDCompleteIncremental to CF executable
new fea90d0 Only depend on automatic linking when MSVC is used, and prep for OpenMP support.
new 5135f04 Added code example for Reg SVD.
new f557c18 Add HRectBound<>::Volume() and a test for it.
new 34f1ef3 Clarify some difficult ternary operator operations (the compiler should give something that is resultantly the same code anyway). Also, use the new HRectBound::Volume() function to simplify some later calculations. Testing seems to indicate no noticeable slowdown or speedup.
new edf6687 Added QUIC-SVD code example.
new a40f2cf Revert most of r17065, since my testing was actually on the R* tree and not on the R tree, so my results were useless. In reality those changes I made more than doubled the tree construction time.
new 43b6364 Inline HRectBound functions. Minor to negligible speedup, but certainly no slowdown. (at least on gcc)
new 64324ff arma::prod is faster, in this case.
new bbb271c Avoid math::Range copy, although realistically gcc should be avoiding that anyway when it recognizes that the variable is effectively const.
new be993c6 Simplify methods a little, and use int& instead of int*.
new e0ef801 Don't use auxiliary structures; find the best node with O(1) storage. Minor speed improvement.
new c53f8a7 Added Reg SVD to CF executable.
new 9d4db15 Added help information in CF executable.
new f83ac7d Dual tree traverser.
new 5126dcf Formatting fixes for GMM conversion utility.
new b88ae3b dual tree traverser bug fixes.
new f4ac9ef Remove trailing spaces thanks to vimrc, and fix comment correctness.
new 37a09cc Spacing issues and remove apparent debug output.
new ce6f4de Standardization of comments for doxygen.
new 35af6e7 Dual tree traverser bug fix.
new 2881fb8 Comment normalization for doxygen, and remove no-longer-relevant comment.
new 1533288 Convert tabs to spaces.
new abef8f1 Convert tabs to spaces.
new 2e3c04b Resurrect Phi tests from gmm_test.cpp.
new 0dd74be * added AMF tutorial
new 3b2888b * added AMF tutorial to index page * minor changes to doc files
new 35afa58 New tests added for the AdaBoost classification function.
new fc9038a Style changes. No code changes
new 408222b I forgot to add Udit to the list of contributors!
new d08dc79 A first draft of a smarter FindArmadillo script, which takes into account whether or not ARMA_USE_WRAPPER is being used.
new cdfb98c Be quiet when finding things so as to not duplicate output.
new d0e6102 Use FATAL_ERROR instead of FATAL. Also find ARPACK quietly.
new fa34b5d Adding Softmax Regression module.
new b807398 intercept no longer penalized and can be turned off, observation weights now supported
new 296f930 intercept no longer penalized and can be turned off, observation weighs supported
new e2a6b31 typo in comments
new 5c11710 Display base cases and scores for single-tree mode.
new 4dddc0e Refactor CalculateBound() and improve to fix regressions noted in #365. This bound seems to actually perform better than the bound used for 1.0.8; however, it is slightly slower. This is likely due to the more complex TraversalInfo structure; so, that bug should be solved by the traverser and not in the rules, it seems.
new 561ba6d Correctly handle SortPolicy abstraction.
new 813441a Workaround for the fact that BallBounds may have larger furthest descendant distances in their children.
new dfd0953 Minor formatting changes.
new 57cfaf1 Forward-port fix for usage of log2().
new 1753059 Note that the Armadillo code is MPL-licensed.
new d049835 Backport another sparse matrix constructor for softmax regression.
new 886a2c1 Update HISTORY.txt.
new 91d3bf2 Handle variance calculation with zero eigenvalues.
new 16859b0 Remove unnecessary include directives.
new 0dfe447 Switch int to size_t in order to fix a very large number of warnings.
new 81e6589 Fix some more signed/unsigned comparison warnings that I introduced with the previous revision.
new aa7bcf2 New distribution (a combination of LinearRegression and GaussianDistribution) for implementing HMM Regression.
new e9fddfc Implementation of HMM Regression
new 7b27f1f Added HMM Regression files
new eb787c1 Comparision-type warning sorted out.
new 51c7496 Fix even more warnings that I've introduced.
new 9648243 I fixed a little bit, but I know this doesn't fix everything.
new 3c291f2 Comment out XTreeTraverser test for now as per #368.
new bead209 Add comment pointing out that there is a bug.
new 5d653f1 Right now, we can't load a vector, so we load a matrix and extract the last column.
new d305c20 Move MAX_OVERLAP to be a member in the mlpack::tree namespace to fix errors on Visual Studio. Thanks to SinisterMJ for pointing this out. #369.
new 0766e4b Add explicit declarations of template function specializations for linker fixes on Visual Studio.
new b8dbd21 Tabs to spaces.
new 7b8ecf5 Spacing and line length fixes.
new 2dd0589 Fix a couple bugs pointed out by Francois Berrier: SGD isn't actually shuffling, and also the final returned objective may not be correct.
new 695da4c Refactor k-means significantly. Remove overclustering since I think nobody is using it (I don't think it's a very interesting technique) and it may be buggy. Speedups for the situation where only cluster centroids are desired.
new 2f0aadb Implement Elkan's algorithm for k-means (it's pretty fast).
new 09eef7f Remove comment about overclustering.
new 2c5b482 Remove references to overclustering from tutorial.
new a3c210e Refactor test to remove overclustering parameter.
new 5d06621 Update and clarify build tutorial, since DEBUG and PROFILE are OFF by default in releases.
new 1290d89 Refactor for different KMeans API.
new bd67d4c Refactor for API change... forgot to check this one in.
new 18a22c1 Add a warning if the user wants 0 clusters, because the thing is probably going to crash (but maybe for some LloydIterationType that might be what's desired?).
new 6fcce81 Explicit std::sqrt() call.
new 4f3c0b9 Add implementation of Hamerly's algorithm.
new 0034275 Refactor input arguments so --algorithm is an accepted parameter, which provides more flexibility as I add more LloydItreationTypes.
new c965068 Refactor ElkanTest and add a test for Hamerly's algorithm.
new 508df11 Fix distance calculations, and fix residual calculation.
new 1283992 Fix a bug; now this algorithm is much faster.
new 1701b9a Add Pelleg-Moore k-means. This implementation is faster and prunes more tightly than my previous attempts (which I didn't check in). (That, of course, simply means that my previous implementations were wrong, but this one isn't.)
new 6ecd7c6 Add test for Pelleg-Moore k-means clustering.
new 7123314 Refactor: only track distanceCalculations, not scores and baseCases. Also remove traversalInfo because it's not used, and count distance calculations during cluster domination calculation.
new ecb190f Clean up an unnecessary sort, and remove spareBlacklist.
new 524315d Comment the Rules class a little better.
new 9d83cce Better comments for the PellegMooreKMeans class.
new 8d209f6 I suppose we should exercise at least some caution in the destructor.
new 0f89009 Don't ignore distance calculations during cluster-moving calculations.
new 4621272 Force C++11 support for future versions of mlpack. I wouldn't be surprised if this breaks the build in some places.
new 319d50b Allow std::cout << mlpackObject, as per #319.
new 85af734 Test std::ostream << mlpackObject.
new 22a31e2 Now we have C++11, but there's no constructor copypasta problem anymore.
new 4275e82 Oops, include ostream_extra.hpp.
new 7fd57f1 A prototype algorithm for k-means clustering, which probably works best when k is very large and so is N.
new 521bc9e A test for the DTNN k-means algorithm.
new 9c5e977 Safer includes, for the situation where the user does something not smart.
new eea0a24 Yet another instance of me failing to commit all my changes. Add a BaseCases() and Scores() function to NeighborSearch, so that a user (or DTNNKMeans) can obtain how much work was done after the search.
new 82a9085 Fix a bug that meant that centroidsOther was copied only when it shouldn't have been, and was never copied when it should have been (note the iteration++ at the end of the loop).
new f30e461 Properly handle the case where the tree doesn't rearrange points -- like the cover tree. Then create a CoverTreeDTNNKMeans template typedef so that a user can easily use cover tree DTNNKMeans with KMeans<>.
new 2c4b63b Add test for CoverTreeDTNNKMeans.
new 8a87c23 Make the Mahalanobis distance a true metric by default.
new 16e1dee Added Smooth and Filter functions
new 4d10e7f Added Smooth and Filter functions
new b9307f7 Added regression_distribution.hpp/cpp, removed hmm_regression
new e9cb643 Rename hmm_regression.hpp
new 2cde152 rename hmm_regression.cpp
new 0617a55 now regression_distribuiton.hpp
new 2672583 Now regression_distribution.cpp
new 3c72e59 Fix -Wreorder warnings after reordering of data members in class declaration.
new 2d5f916 Minor formatting changes and streamlining of Armadillo expressions.
new 9a7bf69 Minor formatting fixes: tabs->spaces, etc.
new cc4468b Minor spacing fix.
new 882cf19 The const gets ignored (-Wignored-qualifiers).
new c95b87a Fix use of uninitialized value; this should help segfaulting SVDBatch tests.
new a2e3a64 Increase number of samples and give debugging output, in order to try and track down the bug I am seeing in all the Jenkins tests.
new 82188da Fix logistic regression tests by enforcing a tighter tolerance for SGD convergence. The changes introduced to SGD in r17196 to cause SGD to shuffle also caused situations where SGD can converge way too early, causing the two tests to fail. Tightening the tolerance to 1e-10 appears to be the solution to this issue.
new b35e8c2 This is an experimental method that I am working on. Right now it is not very useful as I have not implemented all of the pruning strategies that I intend to.
new 573cfd5 Add DualTreeKMeans files to CMakeLists.txt.
new bdc8824 Add DualTreeKMeans as an option to the kmeans program (and also DTNN with cover trees).
new 786998e Add a simple test for DualTreeKMeans.
new af949b5 Be explicit with calls to arma:: functions. Although gcc accepts this as-is, we don't have a guarantee that all compilers will.
new 019ecbc Add a semi-hackish breadth-first traverser. The tree abstractions will need to change to support arbitrary traverser types (probably by adding a template parameter) but for now this works to make DualTreeKMeans work.
new ac7d703 Add breadth first traverser.
new cc10701 Here's the file I forgot -- include the BreadthFirstDualTreeTraverser class definition.
new 6c4e8ff Use FATAL_ERROR instead of FATAL, so that CMake will actually crash when C++11 isn't available.
new 2470078 Refactor code for better comments and better adherence to coding conventions. No functionality change.
new 2065b79 Fix incorrect class name.
new 02950dc Refactor Elkan-type prune into its own method, for simplicity.
new 81a6e93 Add Pelleg-Moore type prune. This improves performance -- at least a bit.
new 4a67301 Loosen tolerance until a better solution is devised (currently I am waiting on an email from Nishant).
new 783f28b Remove debugging random seed.
new 8da5cc0 strlen() returns the length of the string but you must account for the null terminator yourself. Hence, this code sometimes caused random invalid writes and crashes.
new 4ff522b If gradient2 or gradient1 are zero, then BOOST_REQUIRE_CLOSE will fail, so use BOOST_REQUIRE_SMALL in those situations.
new 631955e Not sure how I missed this spelling error...
new e45ce79 Smarter handling of HDF5 dependency search, especially for Debian systems where things are Weird(TM).
new 695e591 The calculation here was actually incorrect.
new e4a0ff4 Refactor CountMostFreq() so it is faster, simpler, and doesn't sometimes return uninitialized values.
new 230bd4f Better handling of the weird case when includes are needed but the library isn't.
new d840852 transition now protected, not private
new 52a4305 HMM regression method
new 5011d66 Implementation of HMMRegression class
new 7020105 hmm_regression.hpp and hmm_regression_impl.hpp added
new b944478 Dimensionality() now returns proper values
new 5159126 Re-ordered initializer lists to fix warnings
new b7cbda9 Slightly loosen tolerances for NMF tests.
new 6d60e7c Fix -Wunintialized, reported by govg.
new 0f2aa34 Pedanticism: return a value at the end of main().
new b0ba1b4 Nope, turns out I am wrong. C++03, C++11, and C++14 all assume a program reaching the end of main() without returning anything will return 0.
new a63e408 Fix uninitialized memory issue (dsPredictions was never set).
new 04d4d3d Don't test on Armadillo 4.300.0 through 4.400.x because there is a bug in Mat::load(istream&) which prevents loading from type hdf5_binary. (The bug is simply the omission of the hdf5_binary case from the switch() statement actually.)
new fed7bf2 Issue a runtime error if the user is using Armadillo 4.300.x through 4.400.x and tries to load or save HDF5 files, since that is a bug in Armadillo.
new 0ccb8e3 Refactor GeneralizedRosenbrockTest to deal with intermittent failures better. Also use 4 trials for RastigrinFunctionTest.
new 8872fb7 Refactor for cleaner code and avoid storing WH explicitly if possible.
new 4b5d4ff Minor code cleanups.
new eb6333f Somehow this never got added to the CMakeLists.txt.
new 68ee9ba Remove debugging output.
new f039262 Refactor test with negative elements to decompose the random matrix into its proper low-rank decomposition, then test the reconstructed matrix.
new ce6d580 Disable C4519 errors entirely.
new 77ebf51 Include prereqs.hpp for compiler definitions and adjustments.
new 00808b7 Disable C4519 in prereqs.hpp not core.hpp.
new 529a281 Handle setting seed properly for Armadillo RNGs past 3.930.
new dde478a Significantly shrink size of test dataset because this test was taking 10 minutes.
new 2b381f4 Fix memory leak.
new 9bde6b4 Widen tolerance slightly.
new 5a1e5e7 Widen tolerance slightly.
new 7fdf213 Widen tolerances slightly. Maybe this test scheme isn't the best?
new 4471cac Check frobenius norm overall instead of just for one element.
new 3e131eb Comment out NoCholeskySingularityTest in accordance with #373.
new 4d014e8 Reduce noise slightly and increase dataset size, which will slow down the test but make the results more accurate.
new 5504bb0 Tighten convergence tolerance for RastrigrinFunctionTest, since it doesn't seem to be coming close enough to the desired minimum.
new db174b1 Slightly loosen tolerance.
new 6483b18 Better handling of small gradient values.
new ce04a24 Minor tolerance widening.
new 92508aa Accidentally checked in unstable code.
new d8cbcde Slightly widen tolerance.
new f17f8b0 Handle negative gradient values correctly.
new 0fa1b46 Fix convergence criterion according to Nishant's suggestion.
new 67b64d8 Loosen tolerance a bit, since it seems to fail once in a while. It's definitely not broken though.
new 4c25854 Tweak SGD parameters a little bit.
new 808b52d Remove random seed to make test reproducible.
new 6d46f1d Widen tolerance for norm difference, and tweak parameters a little bit.
new 3ccd1bd Minor style fixes.
new c8316e9 Add maxIterations parameter to limit the number of iterations used in the Newton method.
new 0546303 Fix ambiguous math reference error, to pass the test clang.
new c0da3d0 Use maxIterations for Newton method loop instead of nested Armijo line search.
new 8983d40 Fix memory leak, although I'm not sure it's responsible for the i386 failures.
new 3e6cccf Adjust tolerances.
new 5484cf7 The failure probability is already small, but not small enough it seems.
new 7250d23 Better handling of Armadillo configuration files, since ARMA_USE_HDF5 may appear twice incorrectly (reported by Giampaolo).
new d07e761 Update with 1.0.11 release notes.
new a3859f0 Update notes; more has since been added to the k-means code.
new 9884d5f Merge changes to mlpack-1.0.11 tag.
new e5e7ec3 Why did I merge that change in? It broke everything. Revert...
new ce91de5 Slight readme update to point to main website.
new 2a71618 Make size_t known before including cxxabi.h to fix the build on FreeBSD.
new ef87d13 Tabs to spaces (trivial commit; testing gitdub email notifier).
new eb9fb58 Minor tabbing fix; still testing gitdub.
new dd7e7fc converting README to markdown format
new f024b62 adding index links
new a909014 fixing mlpack homepage link
new 77af3ac Add build status badge.
new d1fd84e adding readme
new 224ac90 fixing formatting
new 1d5abfc Update README.md
new 1cb2407 Update README.md
new 371bd31 A (potential failure of an) attempt to use alternate headings to make things easier to read as flat text, and also to use relative anchor links, and also to convert 'MLPACK' to 'mlpack' for consistency.
new 3070e41 Conjugatin' da verbs.
new 1032645 Add download link, for people who come across mlpack via Github but might be better served by a stable version.
new 15338d6 I meant for this to be bold, and vim even told me it wasn't going to be, but typical me, I did not listen.
new 3918593 moving HISTORY.txt to markdown format
new 6041afc fixing headings
new d8675e6 Merge pull request #5 from ajkl/master
new 4420173 Minor change to test gitdub.
new 34363ee Add implementation of identity activation function.
new a12ddcc Add implementation of logisitc activation function.
new 3a602af Add implementation of the rectifier activation function.
new 869894f Add implementation of the softsign activation function.
new 3040403 Add implementation of the tanh activation function.
new a3ab2ee Add connection traits class.
new f362f79 Add implementation of the full connection class.
new 75453ee Add implementation of the self connection class.
new 31e30b0 WIP: first cut at sparse LR-SDP solver
new d2512fa remove superfluous inline
new de2665b Rename variables to be consistent with rest of codebase
new af7bb6f fix compile errors
new a3b0e0f fix bug in test initialization
new db9f929 temporary hack: remove the last edge constraint
new c71bad0 Merge pull request #362 from stephentu/sparselrsdp
new aaafd99 Clarify the warning.
new 550e754 Add implementation of the random weight initialization method.
new 72c96ba Add implementation of the Nguyen-Widrow weight initialization method.
new 16a12e4 Add implementation of the optimal initial value setting initialization method.
new 13da3da Add implementation of the weight initialization method by T. Kathirvalavakumar and S. Subavathi.
new cf4ac33 Merge branch 'master' of https://github.com/mlpack/mlpack
new c553f9c Add implementation of a feedforward network container class.
new 42d9d25 Slight style changes, and comment utility functions and put them inside the relevant namespace.
new ac3261f Add implementation of the iRPROP- method to update the weights.
new e0c7057 Add implementation of the iRPROP+ method to update the weights.
new 3dfc05c Add implementation of the RPROP- method to update the weights.
new a5ec7bb Add implementation of the RPROP+ method to update the weights.
new 5193f33 Add implementation of the steepest descent method to update the weights.
new c98abd5 Simple change to test Jenkins webhook.
new 417d148 Change build status URL.
new 626183a Minor syntax change for Jenkins repo testing.
new 19597a8 Add implementation of the LayerTraits class.
new 9ce1ce1 Add implementation of the BiasLayer class.
new e6dd3d6 Simple spacing fix.
new 41dbbda Add .gitignore file for build directories.
new 5454079 Add implementation of the orthogonal initialization method.
new da0ae50 Add implementation of the NeuronLayer class which can be used as basic network layer.
new 2806bcd Add implementation of the MulticlassClassificationLayer class.
new 0d8c85c Add implementation of a recurrent network container class.
new e9276c4 Minor comment fix.
new 48b6278 Add implementation of the LSTMLayer class.
new 768ec81 don't hardcore Evaluate for the lovasz theta objective function
new 1b91cfd Merge pull request #371 from stephentu/master
new 97fdd15 Add implementation of the SoftmaxLayer class.
new 3e5387d Add implementation of the cross-entropy error performance function.
new eb9ff1b Add implementation of the mean squared error performance function.
new fffc5c7 Add implementation of the sum squared error performance function.
new 5ba9482 Add new contributor.
new 89c5b8a Add activation functions test.
new 4f272eb Add connection and layer traits test.
new 4fbb949 add small max-cut test case
new 7943b10 use a better starting point than all ones
new 310cdd2 Merge remote-tracking branch 'mlpack/master' into testcase
new 7731c69 Use a deterministic starting point for max-cut test
new 07a8922 Merge pull request #372 from stephentu/testcase
new 8af80dd Trivial capitalization fixes for style guidelines.
new 1a36310 Add test for the init rules.
new 2def5b0 Modify tolerances for NMF tests.
new 3ffdd14 Loosen default tolerance: accelerate convergence.
new 9e170a2 Always get the boolean value and store it in a temporary, because the Boost unit test macros do weird things and will cause bizarre problems.
new ed24d0e Add performance function test.
new 1323e67 Remove some RandomSeed calls for reproducibility.
new ab1c9f1 Add matrix sensing SDP test case
new a9f4eca cleanup sensing test
new 0243bd5 add comments for sensing SDP test + remove redundant data
new 98afef2 Merge remote-tracking branch 'mlpack/master' into testsensing
new 018d920 don't let the compiler infer matrix result types
new 9d65c78 Merge pull request #373 from stephentu/testsensing
new a7ec740 Minor capitalization fix for consistency.
new 05658b4 Minor style fixes.
new f097195 Add network traits class.
new 4c7d5ec Change to BSD license from LGPL.
new 8fbe489 Switch to BSD from LGPL, and update a few things.
new 7de9908 Remove extraneous licensing information. It must have been added originally by mistake.
new 0bd39a9 MLPACK -> mlpack.
new 43b6cfb Update version number as a bit of a workaround. The change to git means svnversion.hpp is broken.
new ebe073a Fix failed build.
new 1341a7d Store the gradients to allow batch learning.
new 060559d Remove Covariances() and Means(); fixes #346. ~R: fixed
new 069d995 Initialize the gradient storage with zero.
new e71bd00 Remove the input parameter since we can't provide an input for batch learning and it wasn't used anyway.
new 4b6f492 Updated link to download the latest version.
new 02fb5d4 Add Trainer class which serves as container to train the networks.
new 4a676a0 Return a number in the interval [0, 1] instead of [0, std::numeric_limits<eT>::max()].
new 53fabe2 Minor style change.
new c045132 Add -lm for failing clang build on some systems. http://clang.debian.net/status.php?version=3.5.0&key=UNDEF_REF
new 0b1234f Comment out parameter name instead of (void)ing it. Just a little style fix.
new 78f1cfe Comment out parameter name instead of (void)ing it. Just a little style fix.
new 1a5321b Style fixes (trivial).
new 78f4ec6 Add header guards.
new eb593ed Fix all -Wunused-parameter.
new ed30386 Don't initialize random seed in test.
new df9ff11 Fix -Wunused-private-field.
new 681ffc1 Remove MRKDStatistic; its functionality is gone. It's been replaced by some of the other KMeans code.
new 7c2c295 Warn if ratings of 0 are found
new f01be71 Merge pull request #376 from stephentu/master
new cd828ed Minor style changes.
new 602a2a9 First cut at matrix completion method implementation
new 3141936 Add matrix completion test case
new ed346ef Comments
new 66e6220 Address some stylistic issues
new e453bff Merge pull request #374 from stephentu/matrixcompletion
new e9c2dd5 Minor style issues.
new 5a53b84 Some changes for the sake of Doxygen.
new 10687fa Style fixes: capitalize method names.
new 3e719f7 Probably needless const-correctness.
new a48de05 Add some backtracing output to CheckValues().
new 2d23dbe Asleep at the wheel?
new b5313fc only use PGO when compiling with GCC
new 17cce15 Merge pull request #383 from stephentu/pgo
new 94076cc move matrix_completion_impl.hpp to matrix_completion.cpp
new 56cd1f3 Merge pull request #382 from stephentu/master
new 3cd4f6e Use accu(a % b) not trace(a * b).
new f85b12d Change trace(a * b) to accu(a % b). Apply this to test functions, too; speedup seems negligible but it's surely not a bad idea.
new 343df29 Merge pull request #384 from rcurtin/tracedot
new 69a3af5 Update history with recent changes.
new 75dd581 distributions now offer LogProbability() in addition to Probability()
new 1bf3770 Add test cases for the feed forward network.
new 9be67ed Remove unused test case.
new 5e2b58d Add binary classification layer.
new 59ad65d No need to change the sign afterwards.
new bf3dbe7 Take a mean gradient step over the batchsize.
new fee1e1c Tests updated and new datasets uploaded.
new 9df5c74 Merge pull request #389 from uditsaxena/master
new e2a8093 Basically you don't need to shuffel the input in batch mode; However at least there is the option now.
new 62d8f6d Add the ability to define the training parameters.
new b1fb09a Slightly adjust the number of neurons to decrease the runtime.
new 1677a5f Fix spacing for include warning.
new 6e9e773 Minor syntax fixes.
new 8305b36 Minor syntax fixes.
new 061c1cb Update bug tracker to Github.
new 5971887 WIP: gaussian distribution caches covariance factorizations
new 70cec2a WIP: fix one test case
new 7f0493c fix some distribution test cases
new e5e95e6 some more distribution test fixes
new 71107d9 ensure random covariance is positive definite
new f95b6b8 fix HMM load/save tests by ensuring covariance is positive definite
new 45fb3e9 remove stray commit
new 8dc661c invert the lower triangular matrix the right way
new cd0eae7 Merge pull request #390 from stephentu/master
new eeae6f5 Properly handle old Armadillo versions. Pre-4.500 doesn't have arguments to chol().
new 460fe44 Add a relative objective value termination criteria
new 0801db6 Set the default starting penalty to 10
new 88758c7 add back missing edge constraint
new e0ef104 Add matrix sensing SDP test case
new 9a185ef add comments for sensing SDP test + remove redundant data
new 9fca520 Update naive_method.hpp
new 6cbf1c2 Update naive_method.hpp
new c321d54 Use the correct input to accumulate the elements. Thanks to Shangtong for pointing this out.
new ec63d92 WIP: a compiling, but non-functioning primal-dual IP SDP solver
new 9b9618c WIP: a compiling test case
new a1f7aae WIP: hammer out a few bugs, still doesn't work
new c2df6c3 WIP: fix a few more bugs
new abf4a6b add a check for dual feasibility
new 347fe8a WIP: commit missing data file
new eecf8e1 restructure the primal-dual tests a bit
new 4163316 error checking of initial matrices
new 24dd0a8 lovasz theta SDP test
new 3b82ee0 Add log chebyshev approx testcase
new 11243b5 add a comment on why the MVU test fails
new cf90bb3 comment out MVU test case
new 6ad2c10 add correlation coeff sdp test from wiki
new d412841 minor cleanup of comments
new b8d7384 Add some comments/TODOs to the primal-dual implementation
new e4f4c0a implement the mehrotra's predictor-corrector rule
new 46cbde3 refactor KKT solver
new fe56151 more refactoring
new 8262005 sparse svec
new 1e77fdc primal dual method now takes adv of sparse constraints
new 6641bab use glibc constants
new fca638d make the SDP objective matrix type a template parameter
new 1457061 iteration check is now iteration != maxIterations
new a76f469 Port LR-SDP to use the new SDP problem object
new 736f62c fix up PrimalDualSolver::Optimize() return value
new e7e1721 Merge remote-tracking branch 'mlpack/master' into ip
new e183e8a remove unused variable
new 827c49f expose SDP object directly for LRSDPFunction
new f1beedd use builtin diagmat
new b29b5ae Inline alphahat into alpha
new 6f0c814 iteration=1 to allow maxIterations=0 to work
new 73da878 some comments for the algorithm implementation
new 3564151 Merge branch 'ip' of https://github.com/stephentu/mlpack into stephentu-ip
new 0195f97 Merge branch 'stephentu-ip'
new 07b0cbc Refactor to access SDPs through LRSDP::SDP(). (also change everything that used direct access through LRSDP.)
new 1913154 Better commenting of the SDP class. Make the dangers of invalid SDPs documented, among other things.
new 2969438 Slight code cleanups for style. No functionality changes.
new dd6ee23 .so problem fixed
new 8869b45 .so problem fixed
new 1a598d3 .so problem fixed
new 41d34cb Merge pull request #398 from jaskaran1/master
new 9984629 Refactor notice about LD_LIBRARY_PATH.
new a6e5686 Add new contributor.
new 59c7595 Updated path of install in Readme
new 5b313de Merge branch 'master' of https://github.com/jaskaran1/mlpack into jaskaran1-master
new bb79a6a Merge branch 'jaskaran1-master'
new d48cf44 Fix documentation, thanks to Squalluca.
new 4b4d22b older versions of arma do not support unary minus on sparse matrices
new 2bfe20d cov matrices should be symmetric- fixes error in gaussian test case
new cc6199a Comment out SDP test which is failing randomly
new ea795f1 Revert "older versions of arma do not support unary minus on sparse matrices"
new 22ae38a Remove tab character.
new 62def05 Backport operator-(sp_mat) for Armadillo <= 4.000.
new da3c955 Standardize name of test suite.
new c0f44ee Fix syntax.
new d67726d We're not using Java. There's no need for new. Stack, heap, what's the difference anyway? I like stacking things, but I don't know how to heap things, so we should be stacking them.
new a808a56 Fix #400 -- remove unneeded specializations. Also, refactor LoadParameter(arma::mat&) because you can't just empty streams into them (maybe this should change?).
new c7a3aa7 Fix documentation; thanks to Kumar.
new d398b95 Fix minor misspelling.
new a526a31 Code cleanup; better documentation.
new 609a49c Fix stray forward-slash.
new d27eb05 Refactoring.
new c998010 Fix incorrect variable name.
new 59d721b Refactoring and code cleanup.
new 73a9bd3 Remove unneeded semicolons at end of namespace.
new 58d48bb Code cleanup.
new 165977e Refactor and code cleanup. Sparse matrix overloads are untouched -- for now.
new 93a21fc Suppress non-bad warnings; they confuse people. The homebrew-science folks are confused by these.
new 660aa77 SDP primal-dual: use a more numerically stable starting point
new 62618f1 iterator counter was off by 1
new 81a0f57 WIP: test out this travis.yml
new c04b6af travis.yml: add armadillo dep
new f34f516 travis.yml: maybe this will let us get the right version of arma?
new 8d22eb5 travis.yml: add libboost-dev dep
new 76ca1cf travis.yml: add a newer version of boost
new 3b9cfef travis.yml: hopefully this includes all the relevant boost libs
new 0c6aa64 travis.yml: cat arma_config.hpp for debug
new d346878 travis.yml: we really want config.hpp
new 6ef2e47 travis.yml: add custom config.hpp
new 0c13d7e travis.yml: don't die when diff reports diff
new 7915012 travis.yml: i hate you
new 59beaf1 travis: try ARMA_64BIT_WORD
new 6335967 travis.yml: make test
new 15fdced travis.yml: pwd for debug
new 986736f travis.yml: log level all for tests
new d091d37 travis.yml: try travis_wait
new 817c8b5 travis.yml: don't use travis_wait
new ce93257 Force high-precision Armadillo saves. This will fix the failing tests in GMMTest and HMMTest. We now use enable_if_c<> to catch when an Armadillo dense or sparse object is being saved/loaded, and use Armadillo's diskio functionality to write to (or read from) a stream. This allows high-precision saving, whereas just printing via `stream << mat` is pretty low-precision and can't be changed with setwidth().
new d5f5b9b Update TREE_EXPLANATION.txt
new 23c21da Merge pull request #407 from hritik25/patch-1
new 581667c better boost test output
new 5f26cb0 Merge pull request #409 from apir8181/issue-344
new 869bb06 Non-important spelling and style fixes.
new 7881c3e Adds inplace transpose method and some tests. This method used in Load() now.
new 73d5ff9 inpace transpoce moved to load_impl.cpp
new decc21e Merge pull request #408 from VladimirGl/Issue#203
new 704718e The connection type defines how to multiply the input activation and the delta.
new 3a1a98d Use Gradient() to get the gradient.
new 440c555 Set a default value for the seqnumer.
new 55f9309 Minor style fixes.
new 924da7b Add function to evaluate the network.
new 22c413f Use the correct number of epochs.
new e933c9b Properly handle the rnn structure.
new 9233324 Add test cases for the recurrent neural network.
new 196cd87 Merge branch from github.com:zoq/mlpack to address structure issues.
new bd36cd0 added vim temp files to gitignore
new fb5fec3 Merge pull request #411 from VladimirGl/master
new f5c8e3c Minor style changes.
new 1703198 Ensmallen dataset; test speedup about 25x. The cost may be the possibility of a bug going unnoticed, but given that this is a random test anyway, we're basically just slightly increasing P(fastmks is wrong | test passes), but that should be quite small anyway.
new 2b76e6d This isn't warning output. Make it "info" instead.
new b7769dc I've concluded that this test isn't useful. Basically, the test is just checking that the implementation is exactly the same as in the test, and that's not actually a great test, because the implementation may change without breaking anything.
new 35bd45c use std random module instead of boost
new bca4027 Merge pull request #410 from VladimirGl/randoms
new 534c7d3 Remove references to Boost.Random.
new df09588 arma::inplace_trans is not available for older versions of arma
new 0a7c4f4 Armadillo 3.930+ supports inplace_trans() too.
new 3642663 Fix documentation, pointed out by Marcus. Also fix the return type when we can't transpose.
new a62991a Add new contributors.
new 918df71 add intercept term to softmax regression
new 672d8f0 Merge pull request #418 from apir8181/issue-332
new 1d19aa1 Add new contributor.
new f529c50 Trivial spelling fix (why am I even bothering?).
new 251fb8f Change API slightly to match other code. Realistically, this probably needs further thought: C++11 gives us rvalue references, so we can do something a bit smarter to validate parameters without any unnecessary copies that would result from Mutator(const T&) (or whatever).
new 3e4a3c8 Note that softmax regression is done.
new 757c92a Adjust the rnn class and LSTM layer to handle sequences of different lengths.
new 4389c0c Add embedded Reber Grammar test to test the LSTM layer.
new 4d2caf8 Inplace gradient calculation for peephole connections.
new 270c76e The class template auto_ptr is deprecated, use std::unique_ptr instead.
new 3760035 Add test case for the LSTM peephole connections.
new 5e2f4f2 Add distracted sequence recall test (LSTM architecture).
new b73773f Minor style changes.
new f349aa7 Add support for 3rd order tensors as input to train neural networks.
new d6c23a4 Add function to get the number of cols/slices. Thanks Shangtong for pointing this out.
new eddd716 Adapted Shangtongs naming schema to distingush between layer and connections.
new bc3f605 Fix commenting before patch application.
new c63a518 Slight refactoring of dual-tree k-means rules.
new ee45212 Beginning to refactor dual-tree k-means. So far the Pelleg-Moore rule is properly refactored (well, sort of, at least). Try to move IterationUpdate() into DualTreeKMeans::TreeUpdate(); for now this will make the algorithm simpler: instead of updating on the fly, update after an iteration. It may make more sense to do updates on demand later, but let's make the algorithm work first...
new 347b8c0 Refactor to perform allknn on the clusters. This is done at the start of each iteration. This allows Elkan pruning without an additional distance calculation.
new 6366cc9 Fix all -Wunused-parameter.
new 44fa159 Perform the top-level scoring too.
new 56cbc1c Some fairly serious refactoring, but it works.
new e72ab4c Use ClosestQueryNode() not MaxQueryNodeDistance(). Eventually MaxQueryNodeDistance() will not be reset to DBL_MAX every iteration.
new 1072053 This output is less useful right now.
new 581a4a0 Don't accidentally take results before finished. We have to wait until all clusters are pruned, not all except one.
new 4a5add5 Avoid calculating distances after an Elkan prune. Slight, nearly negligible performance gains.
new 61f6552 Don't calculate MaxDistance() unless we have to. Fairly significant time savings on this one.
new 393be90 Count the base cases and scores of the kNN run.
new 37436c3 Remove unnecessary check; that can never happen.
new 8a76218 Try to do an Elkan prune not at a query leaf. It doesn't seem to work right now, though.
new f9c48d2 Fix warning for unused parameter.
new fd948ea Fix typo, which actually gives a speedup. A fairly trivial speedup, but a speedup nonetheless.
new ee7eb43 Set FirstBound() after the allknn. Now, checking if FirstBound() == DBL_MAX is unnecessary, although this doesn't (yet) seem to give any additional prunes.
new dea4b29 Update FirstBound correctly. Trivial speedup.
new f8a73a3 Elkan pruning can't prune the best query node. Bugfix. Trivial slowdown.
new 9515f01 New stub method for (hopefully) good Elkan prune. This allows us to prune without even needing to recurse.
new 6ad3f73 Oops, bad parameter name.
new cd1765c Rename to Hamerly-type score. Because that's what it is. Although Elkan's algorithm has a type of score that's sort of like this, it's Hamerly's algorithm that only keeps track of the second-closest cluster distance, and that's what we're doing here.
new 83f4201 Add second bound.
new 96bcad5 Fix invalid memory access.
new 727714e Avoid uninitialized owner field.
new c83b94b A first attempt at a working Hamerly prune. The bounds tighten too much and don't reset, so there's not much speedup, but it's a start.
new 772dc74 Add debug output; don't adjust second bound. This provides another minor speedup, but this still is nowhere near as fast as it should be with a properly working Hamerly prune.
new db0d792 Handle SecondClosestBound() a little better. Debugging information is still there, and it is going to need to be seriously refactored. We still don't have properly working Hamerly prunes; they go away after a couple iterations incorrectly.
new abfc0b8 Be more careful about when to take the last SCB. This gives a trivial speedup, but hey, speedup! Hamerly prunes are still not working properly, but I'm getting there.
new 994b485 Remove unnecessary check for parent's SCB. There actually isn't a need to take the parent's second closest bound preferentially, and it was preventing some valid prunes. This gives a little more (but not enough) Hamerly pruning, and provides (as usual) trivial speedup---but more than none!
new 79379ee Um, I made it faster. We're well into the land of confusion. Confusion will reign until eventual refactoring. Hamerly prunes still don't appear to be working properly after a couple iterations.
new eba305d Comment out most of the debugging output. It still shows you what's been Hamerly pruned and what hasn't, which is what's important right now.
new 27f3a36 Count number of points that are Hamerly pruned.
new 2913684 Fix compilation warnings. secondClosest will eventually be removed but is commented for now.
new b6a1c36 Unset Owner() after failed Hamerly prune. This is better than setting it by hand when we're checking if we can prune.
new 87ea896 Remove some debug output we don't need anymore.
new ca4066a Don't set CQN to NULL before recursing. This was an error in TreeUpdate() that caused... some problems that I'm only vaguely aware of as problems. Also refactor one of the second bound rules and comment it so that it makes some semblance of sense.
new a06391e Fix second bound to not be the first bound. In some situations, MinQueryNodeDistance() was equal to SecondClosestBound(). This fixes that. This also resolves an issue where SecondClosestBound() wasn't properly updated after an Elkan prune.
new ca7b1a3 Last changes for a little while.
new de01b8f I don't think this is worth saving. It also doesn't work very well, but I learned a lot about the bookkeeping I need to do.
new 2633583 Refactor into UpdateOwner(), instead of an ugly loop at the beginning of TreeUpdate().
new 50d4a32 Remove debug output; implement Pelleg-Moore prune. Now this is faster than the regular dtkm branch. Sometimes starting over is a good thing.
new c413ad2 Better speedups, provide more output on prunes.
new b094362 Add some debugging output. This makes it a bit easier to figure out what is going wrong.
new 6300189 Correct Pelleg-Moore prunes that finish a node. There were cases where a Pelleg-Moore prune would happen before committing the point. This is actually getting pretty fast in terms of base cases, so I am happy with that (for once).
new 5a4b15c Remove vestigial code. After all, this code isn't generated by genetic algorithms. (Maybe it should be?)
new cf56ad4 A start at implementing pointwise Hamerly bounds.
new aa36ea4 Shitty implementation of Elkan-type prune. It makes things faster... a little...
new bce6482 Slightly tighter prune.
new 4db93bf Refactor to use new set of rules. How many times will I restart writing this algorithm until I actually get it working well?
new b068d3c Add a StatisticType for DTNN.
new 181942e Revert back to one point per node.
new 29a7f5f Refactor UpdateTree() to sometimes Hamerly prune. We aren't properly retaining pruned nodes between iterations, but this is definitely a start and it's basically as fast as any of these attempted algorithms I've written.
new de0a5f1 More reasonable handling of bound updating. This speeds things up.
new 0a71f31 Better handling of cover trees.
new 2453a81 Run NNS on the centroids. No prune yet.
new 2a3f6f1 Apply another prune, but it isn't very effective. Maybe that's an artifact of the datasets I'm currently playing with.
new 33ebcd5 Cache mappings from new to old. Slows it down...? Not sure why there's a slowdown. Doesn't make much sense to me.
new a0a6bc1 Perform prunes on individual points. Significant speedup with respect to number of calculations, no real speedup for runtime. But there is still time to optimize it.
new a09c3e3 Also use between-cluster-distance prune for points.
new 7aac685 No need to reset the bounds when un-pruning. They've been updated correctly all along, even when the node is pruned.
new cad4791 Prune parents when children are pruned.
new d631986 Refactor: do tree update before kNN search. This will allow us to make tighter prunes.
new e4b3d87 Recalculate upper bound before giving up on prune. This is done by Hamerly's algorithm and we obtain minor speedup as a result.
new cc0aec0 Prune a node when all its points are pruned.
new 0968f53 Mark parent as pruned if its children are pruned.
new 9ffe06d Force four-point leaves. This is generally faster than one point. More points are probably even better (to a point... hah) but that requires a large k.
new acd8db8 Refactor BaseCase() to apply mappings. This reduces memory usage.
new 76e10e0 Refactor to re-use distances to clusters. This is better than setting the distances to DBL_MAX every iteration, and provides reasonable speedup.
new 27c0096 Use tighter bounds for distances. More speedup. Only increase the distances by the maximum amount those particular clusters could have moved.
new d6d0d78 Use distances instead of upperBounds. Remove upperBounds entirely. Minor speed improvement (not 100% sure why).
new b3c521f Refactor: remove unnecessary temporary.
new 72f2ddd Refactoring to reduce runtime of tree update. It speeds things up in terms of distance computations too, a bit.
new 820ba74 Refactoring, and tighten a bound for minor speedup.
new e36e25f Coalesce the tree before kNN. Speedup! This is a fairly significant speedup, actually.
new e2be4fb Compute max cluster distance after failed prune. This gives us another chance at a prune, and gives very minor speedup.
new 506c405 Make the 'clustering' timer encompass everything. Including the tree building time.
new 70deac5 Allow autodetection of number of centroids.
new 076fceb Update reference to Github.
new 3dc8249 Use existing bounds, if we can.
new 595ae21 Try to keep the query and reference levels equal.
new 55c72af Use default leaf size.
new 540480e Round four. Start over. This time, I proved that the algorithm is right before implementing it. This should help make debugging a lot easier.
new 905be1e Test with regular kd-trees and cover trees. The test conditions for the cover tree need to be adapted a little bit.
new 06b279c Handle cover trees. They don't have two leaves. This still won't work *quite* right for coalescing/decoalescing though.
new 1d2edb9 Refactor DTNNKMeans according to the new algorithm. Lots of stuff torn out. It'll go back in when the time is right.
new 45a731f Make DTNNKMeans work again. Next up, tree coalescion. (Is that a word?)
new 2201a2f Do mapping correctly; handle cover trees right.
new 670a56a Refactor to apply mappings earlier.
new 853b4bf Basic static pruning. Minor speedup.
new 51e14ec Fix a bug. And LastUpperBound() doesn't work. The bugfix speeds thigns up, too.
new 99b8d56 Add static point prunes. Fairly significant runtime improvement.
new 4ab1226 Avoid iterating over every point when pruned. Cache the amount the upper bounds and lower bounds must change when the node becomes unpruned.
new 928fd6d Coalesce and decoalesce the tree.
new f440ca0 Perform tree update at start of iteration. Cache some variables inside DTNNKMeans.
new 95cb008 Start applying prune on intercluster distances. Not quite done yet.
new e650149 Unmap intercluster distances (oops). Minor speedup.
new ba7f71b Don't perform cluster 1-NN unless we have to.
new 078eef0 Update lower bounds when possible. Surprisingly, no speedup anywhere?
new 536c639 Prune nodes whose points and children are pruned. This gives significant speedup, and on my little test dataset, this is the fastest algorithm yet that I have created.
new 030d36d Implement Rescore(). Minor speedup.
new b2fc22a Pre-emptive prunes. Potentially a slowdown. Not always, though, I don't think. I may revert this.
new 01ec8a5 A tighter, but random, prune. Minor speedup. Also add a commented-out check for the lower bounds, and fix a minor bug that screwed them up.
new 727edc7 Use one-leaf trees for better performance.
new 4003537 Make the search *actually* breadth-first. Significant speedups result!
new 8d30f34 More accurate counting of calculations.
new 5ee125c Fix a bug where we pruned too tightly. Provide a little more debugging output for errors, too (but this debugging is commented out by default).
new 43ab267 Make traversal depth-first in the queries. This results in less memory usage, and some amount of speedup.
new 3f76388 Always mark the owner. This fixes some unusual and unexpected floating point errors where the owner will not actually be set.
new 8c7c819 An attempt at making things faster. Might work?
new 2c3c33d Revert "An attempt at making things faster. Might work?" It didn't.
new 70342dd Comment out failing tests; to be fixed shortly.
new 3c32013 Remove un-necessary string copy for GetTimer()
new 507f913 Cleanup: remove trailing whitespace in source files
new b9edf2b Merge pull request #419 from stephentu/master
new a120654 Undef max first (thabks Joseph for pointing this out).
new 8bd3f96 Attempt 2: avoid min/max definitions.
new 732598d Minor cleanup of backtrace code; all style fixes.
new 9ea13de fix unused parameter warning
new 1588ab0 FindPackageHandleStandardArgs.cmake ships with CMake from version 2.8 onwards, since we require CMake 2.8.5 delete the outdated copy.
new 2adbba4 Using backtrace() become somewhat tricky when going multi-platform. Use CMake to figure out the correct header and library.
new 3b9e6e3 Minor cleanup of double header inclusion and file comments.
new e0e54db Add simple Log::Assert test case.
new 98fd81b I was not going to revert the last commit.
new bff92b7 Don't include inside the mlpack namespace. A downstream user may try to re-include execinfo and get very confused when it silently fails.
new 02a4f44 Link mlpack against backtrace, but not everything.
new cbccdc7 Include default unconfigured backtrace.hpp file.
new d34523a Update comments.
new 15c5546 Refactor CMake to get version info from git. Instead of subversion. This has been a long time coming...
new 9724d6c Add a comment, and fix macro name.
new 73b48dd Refactor tests to eliminate random failures. The tolerance is looser, but the tests now checks whether or not using momentum gives close to the same results as without momentum (s/momentum/regularization/, too). Fixes #417.
new aaa17fc Avoid generation of the backtrace.hpp entirely.
new 870007c Minor cleanup (svn -> git transition).
new 7ec665b Tiny misspelling fix.
new 672f0f9 add notifications to travis.yml
new dac00b2 Explicitly include the CreateGitVersionHeader module.
new 3a364a7 Reference Github ticket numbers, not Trac. That was a huge amount of manual labor, wow.
new 5982300 Minor cleanup of the local coordinate coding test;
new 8aa3abb Link against libc++ when using clang on OSX.
new 648651e the CMake flags are newline sensitive
new 7ba52f5 Add new(ish) executables to 'make man' target.
new 5c00312 Don't forget the perceptron.
new ff46b74 initialize tree pointer
new 0c14444 Merge pull request #429 from HurricaneTong/latest
new 90a9d93 Refactor CoverTree to allow sparse datasets.
new a8c7bca Put the documentation in a more relevant place.
new 60010ca When compiling, see if ARMA_64BIT_WORD is enabled. Store it in a file. This will tell the user (or us, the bug receivers) later if libmlpack.so has 32-bit uword or 64-bit uword.
new 857328f Check arma_config.hpp when compiling with mlpack. This is for downstream users, not for during the build of mlpack.
new 17f0148 Ignore auto-generated files, so they don't get checked in.
new 2eddaf1 Remove trash bloated not-working DualTreeKMeans. As noted above, it didn't work.
new 6805075 Rename DTNNKMeans to DualTreeKMeans.
new 1fbd646 Fix uncommitted class name change.
new 06b6a04 What? What is this file? Why is it here? This looks like it dates back to 2009 or earlier.
new a23e498 Use CMake to figure out if we need to link against libc++ or libstdc++.
new 845367e Remove tab characters; use spaces.
new 3d8fab0 The compiler should automatically select the right stdlib on most systems.
new 8540c1b Minor cleanup (tutorials link, git commit mailing list link).
new c41bc8d Highlight some commands.
new 5431f2a Make sure we use the complete type.
new 532101e Use complete type, which simplifies code too.
new 3e7d8bc Take different types for each kernel and metric argument.
new f602725 Don't overwrite arma_config.hpp unless needed. This should keep the build from being a complete rebuild every time 'make' is typed.
new 4da2228 Allow Centroid() with sparse vectors.
new a62125b Make sure traits are active for all cover trees.
new a8637c1 Refactor FastMKS to allow sparse datasets.
new 81fe638 Add a test for sparse FastMKS.
new 46e038c Remove unnecessary splitDimension and maxLeafSize. This results in a pretty trivial speedup (like, 0.5%?), but it makes the tree require less memory. Also I've removed a couple of entirely unused functions.
new 9e3dd12 Fix change I left in that I meant to take out.
new 6dd7d3e Don't call exit(1); throw an exception. That was a bad decision, and I'm sorry, and I promise that I've learned my lesson.
new aaa19c9 Make Assert() throw an exception too.
new 3673579 Preliminary refactoring of RangeSearch.
new 2916ec7 Update documentation for functionality change.
new a7fecec Update output for Log::Fatal crash.
new 8732174 Update links to Github.
new 9a55cac Update documentation: program no longer exits.
new ea0d81f If we are using Armadillo 5+, ARMA_64BIT_WORD is implicit.
new 861ac83 Fix warning.
new c260f6e Update documentation.
new e2beb21 This constructor doesn't take a set.
new 1e30b68 Add implementation of convolution using the naive approach (it's pretty fast for small filter).
new 72e1621 Add implementation of convolution through fft.
new 003ff89 Add border modes (valid convolution, full convolution).
new 1068cf5 Add implementation of convolution using svd to speeded up the computation.
new 066d860 Add 3rd order tensors support (convolution).
new 8f85309 A test for convolution algorithms.
new 805d71a Remove unused class member.
new 8573522 Fix bug where query set gets modified.
new eabdec3 Add sameSet parameter. This properly handles when the query and reference set are the same (i.e. when Search() is called without a query set).
new 80650d4 Refactor NeighborSearch like RangeSearch. Now Search() takes the query set.
new 4ea89a8 Refactor for new NeighborSearch API.
new 46831bd Fix traits, other slight bugs. I'm not sure this is ready for production yet.
new 03b73c6 Refactor tests for NeighborSearch API.
new 505c723 Document API change.
new 57d0567 Refactor executables for new NeighborSearch API.
new 0c9af65 Document when singleMode is useful and add SingleMode().
new 3ad3877 Refactor FastMKS to take individual queries in Search().
new 7983ad4 Tiny spelling fix.
new da47b6e Refactor RASearch to take queries in Search().
new 3977306 Refactor test.
new 9763c57 Update history.
new 340a6d1 add pooling rules
new 5d820f8 Merge pull request #433 from HurricaneTong/pooling_rule
new de78ad8 Add comments, and minor cleanup.
new 97f2c92 A test for the pooling methods.
new 86f647c Return MatType instead of arma::mat.
new 44308fa add two layers
new fbd6b1f Merge pull request #434 from HurricaneTong/latest
new c122d05 Add convolution batch mode.
new 1e5ff62 Add test case for the convolution batch mode.
new 8394ec0 Add 3rd order tensors support (weight init methods).
new 2eb28bc Adjust weight init methods.
new 025d3b2 add pooling connection for CNN
new 59a05b8 Merge pull request #435 from HurricaneTong/cnn_pool_connection
new 897499b Fix glaringly obvious memory leaks.
new fbdc8d4 Fix #406.
new 89a7fe8 add can network
new cc153b0 Merge pull request #436 from HurricaneTong/add-cnn-network
new 1352c1d Add arma_config.hpp so that it gets installed.
new 191713c Add Predict() method for predicting individual ratings.
new 724a353 A struct is better here...
new cdab225 Add a tutorial for CF.
new 96e6efc Remove unnecessary period.
new 997aec8 Fix filename.
new ee38465 Add batch Predict() method.
new 1bada6d xcode
new 6c004a8 Revert "xcode"
new daf77e7 implement mean shift algorithm
new 9543f79 support for selecting kernel
new cd4c0ed delete unused header file
new edbc0f1 template order
new 51a0896 Add test case
new 1ea40f2 estimation of duplicate thresh
new 0347c76 optimization
new 8121657 add metric
new 96895bd zero duplicate thresh test
new 34ac131 make test in correct order
new 6e1e8a9 only consider points within radius
new 7a9485b implement Gradient()
new 22ef07f use SquaredEuclideanDistance
new 1df8dc0 remove unnecessary kernel traits
new dfc6156 Remove 'metric' member; we can use it statically.
new 96d437b Add header guards.
new 481aa09 Style overhaul, and clarify some comments.
new 8612608 Style fixes for main file. Also give a bit of informational output when running.
new 12ca0b6 Specify namespace.
new 51248e4 Set radius in initialization list.
new ee55885 Minor speedup.
new 823b8d7 Fix -Wreorder and simplify AllkNN type.
new f381fe8 use unsafe_col to speed up
new 04d234b generate seeds as initial centroids to speed up
new 6511938 involve mean to calculate new centroid
new 182d4a6 delete obsolete paramater
new d0a3e9a Fix merge failures.
new e06ce8f Adapt to new NeighborSearch API.
new 4379c33 Revert to older Armadillo syntax.
new 0f31abb Allow the dual-tree traverser to be changed easily. This probably should be done for the single-tree traverser too, but we'll start here for now.
new c1bfdf3 Rename pooling connection.
new f9d6162 Swap naming convention.
new 9d714f7 Minor style fix.
new f84079f Clean the steepest descent optimizer class and add tensor support.
new f2dcb8f Adapt new design pattern.
new d60fca2 Add new connection trait.
new 174d2de Fix ambiguous constructor.
new e603caa Refactor BinarySpaceTree to use instantiated splitter. This isn't currently user-passable, but, maybe later.
new 77893ce Make sure the tree doesn't split on the same dimension over and over again when there's a tie.
new 076156d This wasn't actually mean split before. Now it is.
new 9d8c552 Oops, did not apply changes to other overload.
new 744b326 Count base cases and scores correctly.
new acbf832 Add a BoundTraits<> class for template metaprogramming.
new b9d5716 Refactor to use BoundTraits. Remove nextDimension.
new 6caf31a Fix memory leak and bug.
new 609ee9c Refactor pooling connection to support 3rd order tensors.
new 89fb9ec Style overhaul, and clarify some comments.
new 2c868b6 Rename the conv connection class.
new 47dd33d Refactor conv connection to support 3rd order tensors.
new 5b5e1cf Add method to get the number of slices.
new 6137e52 Refactor neuron layer class to support 3rd order tensors.
new 66341ba Add methods for counting distance computations.
new 9c34c98 Refactor LSH. Don't used squared distances.
new b0ab609 Add the convolution neural network to the network traits.
new 237ab40 Refactor the convolutional neural network class, it's almost idenical with the ffnn code, but we add more features in the future, so copy the code right away.
new 34eb8da Remove pedantic ;s.
new 07a099f Add midpoint split. This often produces better trees than mean split...
new 148bfca Use MidpointSplit by default.
new bece04a Fix header guard.
new dde839e Don't specify the exact type; that's superfluous.
new f7c45b2 When BinarySpaceTree was refactored, its traits were not. And thus the traits didn't work unless you were using the default SplitType.
new a1ff4e1 Add convenience typedefs: ConvLayer, PoolingLayer.
new 8fce908 Handle 3rd tensors, when calculating the first derivatives of the identity function.
new 322deab Fix typo/bug and memory leak.
new fecccd3 Add OpenMP support to density estimation tree code
new 340b34b Optimize small things in density estimation trees
new a63ddcd Replace unsupported array operation with arma::vec
new 77d750c Merge pull request #438 from jahabrewer/master
new 55a7ba8 Adapt to trees that aren't just binary.
new 5538fb0 Remove self-flagellation; no longer necessary.
new ac2d3a0 Only unmap if necessary.
new 37c5173 Fix includes.
new fc38043 Fix centroid calculation for cover tree.
new 64b52e0 Refactor UpdateTree() to pass parent bounds. This is a little bit tighter, I think, and is necessary for cover trees, where the MaxDistance() to a node is not necessarily bounded above by the MaxDistance() to the node's parent.
new 1915392 Fix typo.
new 722d375 Remove debugging output. Cover trees work.
new 644dfd9 Fix unnecessary copy.
new 8943424 Fix include ordering.
new cdb9c34 Fix include ordering.
new 4c71640 Fix unnecessary copy.
new 6c7ac8c Reinclude dual-tree cover tree test for k-means.
new 822efa5 Add new tree trait.
new 7811d53 Document new feature.
new 431392d Add new contributor.
new 334d8df Add new utility functions for coalescion. Is coalescion even a word?
new 7e9cd46 Remove unnecessary debugging output.
new b28b2de * Adding support for user cleaned matrix in CF
new 436c65b * Refactoring CF module * CleanData function made static * Added overload of CF constructor which accepts user cleaned matrix if supported by the factorizer
new d2f2976 Merge pull request #437 from sumedhghaisas/master
new 362b6b0 Refactor to use SFINAE for both constructors.
new 802ead7 Refactor input a bit. We don't take dense matrices for CF.
new 29ab461 Slight refactorization for speed.
new 3d23964 Provide per-iteration information; avoid W*H.
new db7f910 Add sanity check for #428.
new 5249c0f Fix typo that caused rank to be 0 by default.
new 7872202 When coalescing implicit nodes, be sure to rebuild the statistic. This was causing a problem in k-means.
new a5b9c34 Optimization: don't needlessly tighten point bounds.
new 803224f Update children before pruning points. This is an improvement for the cover tree.
new 35c0f04 Refactor to precalculate variances.
new 0495b6b Refactor to avoid issues with empty cluster action refactoring.
new 7011dd8 Adjust to new EmptyClusterAction API.
new cd08c87 Use a sane strategy for normalizing variances.
new c0a0045 Don't give up if the residue is NaN or inf.
new f07048b Oops, bad paste.
new f8b5416 Fix the include guards to avoid the problem of double inclusion.
new 0547fb7 Don't make OpenMP a requirement to build the source.
new 38ac5cc Simplify the usage of the performance function by reducing the template parameter.
new fa9937b Use the simplified performance function.
new 61d7876 Adjust the performance function test; use the simplified performance function.
new 2f479f3 Refactor to support convolutional neural networks.
new ad5c77b Slight refactorization for simplicity. No need to specify additional template parameter.
new 6644370 Refactor the bias-, softmax- and lstm-layer to pass the convolutional neural network change.
new 3967b1e Populate the matrix with the entries of the max value.
new c354986 Make sure we calculate the correct delta when using convolutional neural network.
new 296c951 Add batch support. In batch mode, the convolution runs on a batch of images.
new 7fb3213 Reset the delta before calling the unsampling method.
new 25f1f5e Use the rotated filter to calculate the delta.
new e958e66 Refactor to support 3rd order tensors.
new b5fbcaa Use the number of rows and cols to initialize the optimizer.
new 7d6afa5 Add a test for the convolutional neural network.
new 90309ec Fix unused parameter warning.
new 1d5349c Oops, use the right test file.
new 3ade929 The gradient to update the weight depends on the number of output maps.
new c8d5b3d Fix typo and minor style change.
new f4d8e70 Add bias connection, that works with convolutional neural networks.
new 4156e3f Make a note that feature-sign search isn't used.
new 9264f75 Refactor EmptyClusterPolicy to use both the old and the new clusters.
new 37c89a5 Use bias connection and decrease number of epochs.
new 69439c2 Fix typo.
new cd9fb08 Add RmsProp optimizer.
new 40d3a41 Fix typo.
new 9d6469e Use RmsProp and decrease the number of epochs.
new e565147 Add function to update/reset the optimizer object.
new e03cc28 Use the new optimizer interface.
new 3533b01 Adjust connections; use new optimzer.
new 7df836c Refactor for new optimizer API.
new ee7c82d Fix changed EmptyClusterAction API for the tests too.
new a96b462 Add another test to mean shift, which should cluster 4 Gaussians.
new 98c0c48 Format fixes for mean shift.
new 6e98f6d Minor/trivial speedup: preallocate the matrix.
new c56829b Use the complete dataset.
new b421424 Use MaxPooling as default pooling rule.
new ebede26 Refactor for new optimizer API.
new da10c65 Add update formula.
new 292420f Fix the name of the input parameter.
new 0aa8749 Add Adadelta optimizer.
new 60a4d92 Refactor to support 3rd-order tensors.
new 90163a1 Make the layer independent regarding the datatype.
new 7de290f Add dropout layer; regularizer that randomly sets units to zero.
new 15c86b8 Allow the Intel compiler too... not that it works. "internal error: null pointer"
new aee90c3 Update documentation, and fail on invalid algorithm.
new f9a6cd5 Update code style.
new 614f7a9 Switch to residue termination, because it's *much* faster. Maybe to be switched back later, but I doubt it, kind of.
new 6d2e43d Print iteration and residue for tolerance termination.
new 14366a2 Allow calculation of RMSE.
new 9f0d3b3 Old Armadillo versions needed a second parameter for norm, it seems.
new b9ac6ef Add identity connection.
new a7a6856 Add weight zero initialization rule.
new cf08dc9 Rescale the input unless the user explicitly requested not to.
new 63b8c8e Add new connection trait (identity connection).
new 67ab14a Update the connection trait and there is no need to reset the delta, we already reset the delta in the network class (cnn, ffn).
new 6de6a0b Update the all connection traits; including the self and fullself connection.
new 2598e5a Use the naive convolution method as default.
new 222a7e1 Handle the identity connection.
new d9e984e Avoid overflow by subtracting the maximum of the input values from each input.
new d5dd528 Gradient calculation speedup by iterating over the output maps.
new e58937c Use the rectifier function for the whole test and decrease the overall error tolerance.
new d712369 Set the current evaluation mode.
new 267bf1f Add convolutional neural network dropout test.
new 9e80681 Add as-of-yet untested termination policy. Tests will come soon, but I want to work from a different system...
new 651e224 Add tests for MaxIterationTermination.
new ef5540f Add MaxIterationTermination to list of files.
new da092bd Add Index(), and make convergence occur for all iterations after the maximum iteration.
new ddb8ae9 Refactor CF program to allow specifying the maximum number of iterations.
new ca9c4c7 Time the factorization.
new 9e00b42 Allow the random seed to be set.
new 53a93a0 Switch to random Acol initialization by default.
new 408e7ea Include acol init.
new baeb388 Use correct signature.
new f530120 Add feedforward neural network dropout test.
new 6b6a446 No need to specify the size of the delta parameter.
new c326043 Simplify the training process.
new 4a97187 Set the correct evaluation mode.
new 2fecd93 Add wrapper for boost::serialization. This means we can write Serialize() not serialize(). (And thus we stay in accordance with the style guidelines.)
new 666e7fe Add list of formats we can load.
new 3de074b Update CMakeLists.txt.
new b100468 Convenience function for extracting extensions.
new 8514fd5 Add Load() and Save() for models.
new 19ef551 Move serialization shim to data/.
new 6d9a46d Fix syntax and include errors.
new 3e43461 Add boost::serialization to dependencies.
new bab1de6 A few first tests for serialization.
new 22d6906 Add serialization for arma::mat.
new 7686349 Add serialization for sparse matrices.
new 840f1cf Refactor includes to include serialization code.
new ee916cd Add Serialize() to distributions.
new 2236fe0 Add tests for distribution Serialize().
new 264ef97 Add Serialize() to kernels; not yet tested. Also I didn't do the p-spectrum string kernel yet.
new 88f8ef2 Add Range::Serialize().
new 40b8a61 Refactor and add Serialize(). Don't hold a reference to the kernel, hold a pointer and use it internally.
new bcd1570 Add Serialize() to MahalanobisDistance.
new e294504 Clarify comments, fix accessors.
new a255049 Add BallBound<>::Serialize().
new 676b003 Some serialization changes.
new d90f8ff Allow serialization of linear regression.
new 036ed5c Add shims for arrays.
new 6851133 Fix typo.
new dc49c0e Comment out unused member.
new 7f1b9d0 Fix memory misuse.
new ca35a6a Add shims for pointers.
new 2cd4052 Update comment for serialize() interception.
new a2579f3 Add Serialize() for empty class.
new 960e017 Be safer with memory usage.
new 1b62937 Add Serialize() for HRectBound<>.
new 7c7add5 Add some more tests.
new 4329aa9 A first pass at refactoring BinarySpaceTree.
new 8998cd7 Refactor tree test.
new 4972219 Merge branch 'master' into serialize
new e7890e2 Refactor NeighborSearch internals to deal with the tree holding the dataset internally.
new 9690b45 Refactor tests to deal with modified NeighborSearch.
new 3063668 Merge branch 'master' into serialize
new 826c5e8 Add serialization for statistic.
new d86e4e5 Fix memory leak when overwriting bounds.
new 763f377 Add BinarySpaceTree::Serialize() and tests. Also add a constructor to allow constructing from an iarchive.
new f852bc7 Fix some style.
new 4a17756 Remove unnecessary LastDistanceNode().
new 5611e1f Add Serialize(); remove unnecessary LastDistanceNode().
new d470910 Merge branch 'serialize' of https://github.com/rcurtin/mlpack into rcurtin-serialize
new c2cf437 80 columns max.
new e5905e6 Merge branch 'rcurtin-serialize'
new 551f803 Add deterministic parameter to distinguish between trainign and testing.
new 8b2ca72 Handle the identity connection.
new efbddf2 Remove SaveRestoreUtility. An ignominious end to an ambitious idea.
new df80baa Remove libxml2 dependency (awesome!).
new 16a6d65 First pass at Serialize().
new cb2b579 Remove hmm_convert, since boost::serialization makes it unnecessary. If someone wants it back someday, we can address the issue then, but I don't think anyone is trying to convert old HMM models in mlpack to new ones, so this is kind of dead code.
new 05db9c3 Remove old load/save utilities.
new 0a265e1 Remove save_restore_utility*
new 494a04c Refactor serialization shim to handle static methods. Also make it shorter by removing a bunch of CreateNVP() overloads.
new f5f930f Don't include SaveRestoreUtility.
new b51b276 Remove Save() and Load() calls.
new ea1f8fd Remove tests for SaveRestoreUtility.
new 73f01e6 Add Serialize() to KMeans and related classes.
new 076afb4 Add Serialize() to GMM and refactor to not use references. This is because references make serialization really hard. As a second though, it may actually be better to not hold the FittingType internally but only pass it when the model is being trained. Needs more thought (and someone to make the change).
new 8ee48b4 Add (mostly empty) Serialize() methods to classes related to GMM.
new ad4f7b3 Refactor main program to use boost::serialization for saving.
new 2dfad1a Remove deprecated conversion utility. I don't think anyone was using it anyway, and like the HMM conversion utility, we can reimplement it if someone complains.
new 9986769 Allow default construction, and fix syntax for Serialize().
new ac2031c Remove gmm_convert from list of targets.
new 7f3c228 Refactor HMM programs to use boost::serialization.
new 17874a8 Fix particularly subtle bug that tried to free statically-allocated memory.
new 45ccf16 Alias properly.
new 2cbfd1a Fix type error.
new 19c2c44 Refactor GMMTest for boost::serialization.
new b4659b6 Refactor HMMTest for boost::serialization.
new a84f602 Remove unused bool.
new 24f0dde Allow access to 'naive'.
new a7ee285 Minor style fix.
new 3a83a18 Fix typo in documentation.
new 02c5995 The beginning of a document about the TreeType API.
new 2965415 Fix somehow truncated comment.
new a6709aa Remove some crufty unused functions from BinarySpaceTree.
new 6f0bb75 Add policies/ to Doxygen output.
new 54c32b8 Refactor to use Center() instead of Centroid().
new 0d9213f Use Center() instead of Centroid().
new d49e069 Refactor to use Center().
new 015d791 Re-add Center() to the API.
new 7b0b67d Fix typo (thanks Ryan Birmingham for pointing it out).
new b2578f6 Minor misspelling fix.
new b3bf0db Refactor to match TreeType API.
new 9c8e313 Add typedefs for common tree types.
new 47cc6fe Refactor to take a MetricType.
new 02af1b5 Make Power and TakeRoot available for other classes.
new e61252a Refactor to handle new HRectBound API.
new 7662ee3 Further fixes for new TreeType API. typedef.hpp needs better comments.
new b37e976 Refactor DTB to use new TreeType API.
new f6a65f3 Specify metric:: namespace.
new afd3f9d Specify metric:: namespace.
new 66a1a52 Refactor for new TreeType API. Also some syntax convention fixes...
new f7c1693 Refactor FastMKS to new TreeType API.
new aa28b5e Refactor NeighborSearch to new TreeType API.
new 6e3f49e Refactor CoverTree to new TreeType API.
new 9e3550b Minor refactorings and fixes.
new fac56f6 Include template typedefs.
new 3485da0 Add default template arguments.
new fceb010 Update documentation.
new 7b433e5 Update documentation.
new 0a32987 Missed a function for the changed HRectBound API.
new b0f82db Refactor for new TreeType API. Also handle the fact that trees now copy the dataset internally (this will be changed again).
new 4af30af Refactor for new TreeType API.
new 5ee25ba Refactor for new TreeType API.
new 48a4fef Refactor for new TreeType API.
new 16e3f2b Refactor all tests for new TreeType API.
new b1616c0 Add convenience template typedefs.
new 9768ed1 Refactor utility functionality into RAUtil class.
new 45d9117 Refactor to handle interally-copying trees correctly.
new b3d3eb8 Refactor test to handle internally-copying trees correctly.
new 90c67e8 Refactor for non-modifying TreeTypes.
new fa72b45 Refactor for non-modifying TreeTypes.
new f8ceffa Add a constructor that takes ownership of the data.
new 6ee2187 Remove stray space.
new dd18858 No need to specify the type of the input data.
new c49adea Add function to get the current gradient.
new 36324dc Update Doxyfile generation and list of trees.
new d968f73 Refactor for new multiclass output layer.
new 9cd66cc Fix build failure with clang.
new 9f25296 Merge pull request #446 from trungda/trungda
new 4c63ae5 Fix linkage discrepancy that produces a clang warning.
new 3f01d81 Compress if statement.
new d40f24a Apply Marcus' suggestion for better template template parameter template parameter names (that sentence is not redundant).
new 43e1d09 Add new contributor.
new 80adf7a Add convenience template typedefs to the CMakeLists.
new 7485dfc Add documentation for tree typedefs.
new f10c2d7 We transitioned from svn to git a long time ago...
new 3e452e0 No need for non-functional @defn command.
new 71ea42f Fix some non-compiling Doxygen Latex documentation.
new a8dd81b Fix weird formatting.
new 7d64cd6 Add a Predict() method to LARS.
new 4842fa9 Allow passing a row-major matrix to Predict() to save time.
new 2849148 Add option to predict values on test points.
new 6382806 Mark down the changes I made to lars.
new 98ecfbc Minor misspelling fix (use 'Optimizer' instead of 'Optimzer').
new 1ed600c Include the connection traits.
new c7e0481 Refactor test for the network API.
new d2a1ec1 Include stdexcept (compilation fails on gcc 4.7 without this fix).
new 10c5788 Update obsolete reference to svn trunk.
new 6ba560b The collaboration graph is confusing. Disable.
new 6f8a54c Reduce namespace cruft in output.
new ea45ace Hiding scope names has a bug: https://bugzilla.gnome.org/show_bug.cgi?id=676971
new 9ca0d78 Build the activation functions.
new cf92267 Add linear layer.
new 1ffcc65 Add base layer.
new 7f4b0f8 Minor style fix (80 character limit).
new baf438b Minor misspelling fix.
new 2d515f7 Refactor for new network API.
new da50cb5 Refactor feedforward network test for new network API.
new ba83352 Replacement for the FFNN class using the new network API.
new de29ef6 Refactor to handle 3rd order tensors correctly.
new d15ff95 Add SFINAE pattern for the Gradient and Deterministic function.
new dac2a6f Refactor bias layer for new network API.
new e1977d2 Replacement for the convolution connection class using the new network API.
new 1b88e29 Refactor to handle 3rd order tensors correctly.
new 345645d Minor misspelling and style fix.
new d7dc773 Update Layer traits for the multiclass classification layer.
new ce0d0fa Updated layer traits (binary classification layer and one hot layer).
new 8161193 Replacement for the pooling connection class using the new network API.
new 5891e88 Decrease the overall test time by decreasing the layer size and number of epochs.
new 87deb9a Distinguish between OutputParameter and InputParamater.
new fd33623 Refactor dropout layer for new network API.
new 3413a77 Remove the no longer needed connections.
new 967adc4 Refactor feedforward network test for new network API.
new 459b7fe Add CMake files to build and test the activation functions.
new be6fe1f Remove subfolders from the CMake file that doesn't contain a CMakeLists.txt file.
new f601eae The transform() function isn't available on armadillo 3.6 so we move back to a standard for loop.
new f2758b2 The transform() function isn't available on armadillo 3.6 so we move back to a standard for loop.
new 3375caa Refactor all activation functions and layer which uses the transform() function.
new ad4cc1b Comment out the ann code.
new becde5b Document the MetricType policy.
new 89b6cb8 Make sure doxygen picks up info on typedefs.
new dd38d5c Reference the MetricType documentation where possible.
new e7ab269 Add an actual example.
new 07f205f Add documentation for the KernelType policy.
new 49d726c Do some documentation refactoring.
new 4630d8d Use at least armadillo 4.x to build mlpack.
new fbb25be Add travis ubuntu trusty repository.
new fab25ea Document the KernelTraits struct.
new 661cf30 We use C++11 now; update the comment.
new 3b44f3d Switch to struct to be in line with other trait structs.
new 8110b5c Revert "Switch to struct to be in line with other trait structs." I'd rather just switch the documentation, because it turns out the other trait structs are actually classes too.
new 316ef33 class instead of struct.
new 30db4e2 Make build directory Doxyfile update itself when root Doxyfile changes.
new 0e03ed7 Document TreeTraits.
new b34381d \b -> **, \e -> * (Newer doxygen versions don't seem to play nice with \b and \e.)
new 7b68ca3 Compile in non-debug mode for faster tests.
new 5e395bd Refactor softmax layer for new network API.
new 236d5bc Use the correct filter/kernel parameter.
new 86771a4 Feel-stupid moment of the day: these unintentional loops have been here for months, causing tests to fail, which I never investigated. Bonus: I'm the one who made this change months ago. I think I can take this as proof that I had too much going on over the summer.
new 7eece24 Provide a few convenience typedefs.
new 4c0c618 Build the neural network code.
new 2da470c Limit training epochs and add thyroid dataset.
new 5235578 Decrease the overall test time by decreasing the layer size and number of epochs.
new 9e6c0fe Widen tolerance for the network decreasing error test.
new 49d765c Fix two FastMKS bugs.
new c5dbcc0 Remove unused layer and optimizer classes.
new 91ae106 Remove unused header.
new 1c6e9f7 Refactor convolutional network test for new network API.
new 4a7b633 Refactor convolutional network main class for new network API.
new 24f8733 Use mean pooling as default pooling rule.
new 98b6773 Refactor optimizer for new network API.
new 4618086 Remove unused function; we only need to support 3rd-order tensors.
new 6c4bcf6 Add 3rd-order tensor support (Dropout layer).
new 7dcf30a Use the filter matrix for the convolution function instead of the 3rd-order tensor.
new 42d61df Build the convolutional neural network code.
new c55ce61 Widen convolutional test tolerance.
new df9446c Comment out the convolution test.
new 952cc39 Use the logistic function and the RMSProp optimizer because the combination tends to be more stable and in most cases it converges faster using the specified architecture.
new ef29032 Fix 'no known conversion from arma::Mat<double> to arma::Cube<double>' error that occurred on some systems. Actually the build should be fine even without the change, but I guess some systems like to draw our attention on some 'incredibly long' templates in the error log.
new f5893d5 Use static weights for the network decreasing error test.
new 80feca5 Add Serialize() (unimplemented) to the perceptron.
new 424383c Refactor perceptron to not modify input dataset. Minimize internally-held variables.
new 19a4620 Refactor weight vectors to be column-major.
new 105a30f Simplify expression.
new a961350 Split biases into separate vector (speedup).
new f3bd5e8 Fix bug introduced in previous commits.
new 8ace79e Rename weightVectors to weights and simplify API.
new 2bd5e78 Refactor to make instance weights optional.
new 980b66c Rename iter -> maxIterations.
new 16cb76a Require specification of number of classes.
new d6a5f70 fix #449
new 4bcc6e6 Merge pull request #450 from thirdwing/master
new 14e1f4f Fix Adaboost executable for Perceptron API change.
new ee732ca Allow .tsv extension too.
new a4d2dc2 Update documentation.
new 3ee916e Add DatasetInfo class for categorical features.
new 59d841b Add tests for DatasetInfo.
new fcf3425 Rename to match other enums.
new 431fcef Stub of new Load().
new 15faffe Add Load() overload with DatasetInfo.
new da12bda Count lines by hand; and trim whitespace from tokens.
new ae7f38a Flesh out tests for DatasetInfo Load() functions.
new 2135073 Rename .txt to .csvs where necessary.
new f8be407 A first pass at the abstractions for VFDT.
new d39a6b2 Add a basic comment.
new 8d33d0a Implement the Gini impurity.
new 6ffeae2 Add tests for Gini impurity.
new 3385f80 A base class for information after the split has been made.
new 0a6b3a2 A pass at VFDT implementation.
new 34d521c Simple tests for the HoeffdingCategoricalSplit.
new 4713e20 Incremental check-in so I can work from a different system.
new 81c8dc8 Make NumMappings() const.
new 2d0fe63 Fix build with newer Boost versions.
new bdb55da New boost versions don't take kindly to comparing DatasetInfos.
new 22ada51 Fix compilation with newer Boost on OS X.
new 33bb754 Actually create the correct number of children.
new 924d086 Add Range() to GiniImpurity, and test HoeffdingSplit.
new 90d3b42 Clean up Evaluate() and fix test.
new fa1153b Finish Range test.
new 338c9dc Fix compilation warnings.
new fae71d0 Remove debugging output.
new b742e17 Fix epsilon calculation.
new a5ddd52 Add some more tests for HoeffdingSplit.
new a77b9f3 Get HoeffdingSplit and StreamingDecisionTree to compile.
new c5a27c2 Add numeric split info.
new a897380 Fix test number of classes.
new 2eece86 Use explicit mlpack namespace.
new 87e9623 Fix test input.
new 7c9f5b6 Make sure training propagates through the tree.
new 0e795f3 Refactor so that dimensionality is a parameter.
new 2d5fb03 Add test: equally good features should not split.
new 1f936fd Implement numeric feature support (though stupidly).
new ebc6c94 A more complex test for HoeffdingNumericSplit.
new dd83d57 Fix build warnings.
new 8d51657 Add another test for the numeric feature splitting.
new cf6f031 Add a command-line program for streaming decision trees.
new 55dfc55 Handle numeric and categorical attributes simultaneously.
new d48fd3f Force splitting after enough samples.
new c76e8f3 Make sure that we don't run out of samples.
new 845218e Set majority class when making children.
new 17a7986 Mild refactoring; Split() instead of CreateChildren().
new 1ff6f2f Eliminate redundant classCounts.
new 953f96e Add (unused) test set parameter.
new a4415f3 Avoid copies of dimensionMappings.
new 4fadecf Fix ambiguities and use of at().
new 71aca20 First pass at serialization.
new 3122b83 Fix serialization bug.
new 28f45c6 Fix compilation issue.
new b2b1939 Serialization support.
new d0823e6 Add serialization prerequisites.
new d58d318 Add Serialize().
new 7534316 Test HoeffdingNumericSplit<>::Serialize().
new 5c8603b Add test for HoeffdingCategoricalSplit.
new f416d2d Fix (kind of) serialization for HoeffdingSplit.
new 2b1828e Fix a really, really stupid bug.
new 929f86a Hold a pointer to the dataset info, and serialize accordingly. This is a bit hackish.
new 3225f14 Allow serialization of dataset information.
new 475edaa Serialize correctly.
new 22c32fb Don't overwrite majorityClass.
new e0bd80a Save the tree.
new 68fe2da Test StreamingDecisionTree::Serialize().
new 5268e55 Add a way to get the probability at each node.
new daceb0f Revert unintentional commit.
new 413456a Backport unordered_map serialization from boost 1.56.
new 18415db Revert syntax for older Armadillo versions.
new 67314c1 Fix -Wuninitialized.
new 522cf72 Add convenience typedef.
new 6647d1b Fix include for typedef.
new 6c63405 Make sure memory is initialized before loading/saving.
new 6cdc7c5 Better main executable.
new 650e752 A first pass at a better numeric split.
new 06eff7a Fix compilation errors; add a first test.
new 1687a1c Add better test; fix bug.
new d904de6 Add NumChildren() to use instead of Bins().
new 08478f6 Add test for binary numeric split.
new 0dc2bf5 Remove debugging output.
new ad904dc Allow specification of dimensionality.
new 5cb6f8d Sometimes the template recursion during builds goes very deep...
new 51441e2 Re-initialize DatasetInfo on load.
new 1e07979 Fix backwards initialization.
new 736df58 Don't save observations we haven't seen yet.
new 39b1bd7 Fix tests that rely on DatasetInfo.
new 5d89077 Smarter serialization; modest size decrease in output.
new 8153570 Only serialize the necessary split.
new 65bcfb2 Shorten names to reduce file size.
new 06a6879 Refactor to use template template parameters.
new f03ae5b Allow large speedups by not requiring split checks every training point.
new 1a19ef9 Add support for the BinaryNumericSplit.
new 133f036 Fix tests to new API.
new 4e212e1 Handle when we have both categorical and numeric features.
new 1c9ad21 Add a primitive ARFF reader.
new 6d96f3a Add a test for the ARFF reader.
new 929a657 Add another test.
new e99c387 Merge branch 'vfdt' of https://github.com/rcurtin/mlpack into vfdt
new 1b32dab Fix for new DatasetInfo API.
new c13ca51 Split correctly on comments too.
new 535f0aa Add a harder ARFF test.
new 3f9cb06 Test Classify().
new b48e9a9 Fix bug that could cause a hang.
new 1a55288 Serialize number of classes correctly.
new 093579b Fix invalid accesses by reordering loop conditionals.
new 567f212 Use a const datasetInfo.
new eca9af0 Comment the HoeffdingSplit class.
new 70a8e70 Add some documentation (finally).
new 2bff3d7 Refactor: HoeffdingSplit -> HoeffdingTree.
new b0cbd59 Fix names of constructor/destructor.
new d925afc Fix -Wreorder.
new 50b2c03 Update include paths.
new 676f406 Add (unimplemented) batch training functionality.
new f8db920 Remove unnecessary dimensionality parameter.
new 9b4453a Use Row for labels.
new 29160cf Slightly better documentation.
new 8b10332 Fix API; prepare for deletion.
new b0d8816 Remove StreamingDecisionTree; refactor main executable.
new 62d6f47 Update configuration.
new f0abc60 Refactor HoeffdingTree to replace StreamingDecisionTree.
new 6622778 Take ownership of DatasetInfo struct when needed.
new 6e25f79 Don't use StreamingDecisionTree anymore.
new 5ec6e31 Refactor tests for new HoeffdingTree API.
new b841b13 First pass at batch training.
new 4233cd4 Add batch mode and a test for it.
new e7294b8 Add batch training option.
new 26ba0e2 A better attempt at batch training.
new cb3522e Add separate split info for binary splits.
new 21456cf Make sure the split improves things.
new 9a4fb1d Clarify where splitting actually occurs; fix bugs.
new dfba0d5 Fix tests for changed APIs.
new 91a5ff3 Add minSamples for splitting.
new 66592fa Add information gain and tests.
new e00a29a Fix -Wreorder.
new 1196eaa Add flag for using information gain.
new e7b0e4e Make children pointers, so serialization doesn't copy dimensionMappings and datasetInfo.
new 81a8b6c Refactor EvaluateFitnessFunction().
new 278a5f8 Refactor for changed EvaluateFitnessFunction().
new 0e93455 Fix -Wuninitialized.
new 7bd2144 Add the number of passes to the program.
new c8511e6 Make parameter name unambiguous.
new 06eeee1 Handle non-new DatasetInfo objects better.
new d118921 Actually take multiple passes over the data when streaming.
new 967e230 Yes, this is the problem I've been chasing for weeks.
new 7a5ef89 A smarter splitting criteria that works right.
new b69fc07 Refactor to allow passing parameters of splits to children.
new 00c77fc Allow specification of the number of bins and observations before binning.
new 5129152 Merge branch 'vfdt' of http://github.com/rcurtin/mlpack into vfdt
new b2079b6 Add min_samples option.
new a00f5df Print test and training error.
new d65abd5 Fix segfault.
new 41bf107 An optimization to speed up the binary split -- but it's still slow...
new 92ade97 Print the number of nodes in the tree.
new 4909f53 Install the hoeffding_tree program.
new a33bc45 Add non-training constructor and write Serialize().
new aef3619 Refactor perceptron program to load/save models.
new 763f54c Add Serialize() to LogisticRegression.
new 754ff98 Build the convolution test.
new ebfe0c0 Wow, this was an incredibly stupid bug.
new bbe9cd1 Refactor LogisticRegressionFunction to work with arbitrary matrix types.
new 600b2f5 Refactor so that OptimizerType is only needed sometimes.
new b34bb0f Add and implement Train() methods.
new e67787e Refactor logistic_regression to allow persistent models.
new f379ee2 Add another Train(); remove templated constructors.
new 14d8551 Add tests for new LogisticRegression functionality.
new d6e9b1b Refactor main executable. Still needs documentation.
new 1eec7b7 Note the changes that have been made.
new 273401e Update documentation for logistic_regression.
new 9295469 Fix bugs in logistic_regression.
new 3ba7a67 When the user requests single-tree, actually do it.
new 7e682d5 Deal with newer Boost versions nicely.
new 7bd9c95 Fix unused parameter warning.
new fa45524 Handle empty datasets.
new 60c8170 Add Train() functions to NeighborSearch for consistency.
new 2fa4ba2 Test empty NeighborSearch objects and Train().
new df2dac2 Add unfinished serialization test.
new 14e794d Add empty Serialize() methods to initialization policies.
new 5cfb713 Add Serialize().
new 075383b Fix AllkNN serialization test.
new 5b61871 Include std::vector serialization support.
new 4a469b2 Refactor to add Train() and empty constructor.
new 0ae0b1a Refactor tests for changed NBC API.
new e59d52d Refactor for new NBC API. Not yet tested.
new 7b28dce Fix incremental single-point training.
new 3464c8e Add tests for Naive Bayes classifier.
new ec1f8d7 Add separate Train() method.
new c8cdc77 Refactor main executable.
new 5be6093 Don't set MLPACK_USE_64BIT_WORD when on a 32-bit system.
new 0e910b1 Add serialization to DTree.
new 11746e9 1 : add function Serialize 2 : add function Train 3 : fix bug--did not initialize fitIntercept
new e1320b7 make codes follows the style guide
new 96af50b Merge pull request #456 from stereomatchingkiss/softmax_enhance
new cbeb3ea Style fixes. Remove constructor that takes a file.
new 050bc70 Add test for new constructor, Train(), and fix compilation error.
new 5866674 Add tests for new Train() functions.
new 754bf15 Add serialization test for SoftmaxRegression.
new f85a9b2 Add new contributor.
new 8a8b708 Set initial parameters correctly; restore tolerances.
new 7a8b85c 1 : remove inputSize from the constructors and data member 2 : provide static function initializeWeight to simplify constructor task 3 : change labels from arma::vec to arma::Row<size_t> 4 : update test cases
new a4d925c refine test cases
new e5c2e71 1 : add read only function FeatureSize 2 : add function InitializeWeights to avoid the case when RVO fail
new 8692a76 fix bug--return wrong feature size
new dc2c5c6 Merge pull request #457 from stereomatchingkiss/softmax_enhance
new 7a8b0e1 Minor syntax and formatting changes.
new de88672 Merge branch 'master' of https://github.com/mlpack/mlpack
new 7e6fe3f Fix failed merge.
new 405bf73 This appears to be a failed merge; fix it.
new 997d03b Refactor so holding a dataset internally is possible.
new 95088aa Add Serialize() to CoverTree and tests too.
new b4b7e8a Remove using declaration.
new f499e5c Minor style fix/change.
new 6e9a746 Refactor to hold dataset internally (for serialization).
new 0672de4 fix vc2015 compile issue
new c700949 Merge pull request #459 from stereomatchingkiss/ann_workaround
new 81e72d4 Minor syntax and formatting changes.
new 168a49a Serialization for RectangleTree. Not working---committed in order to work on another system. Also has debugging output.
new c60e531 Refactor Serialize(); don't duplicate the parent.
new edf35a0 Remove debugging output.
new 35e8c77 Clean up memory afterwards.
new f60f59c Remove unused field.
new c50f6a9 Refactor to avoid duplication of root during serialization.
new e6491c3 Don't check localDataset because sometimes it is NULL.
new ce49a4b Fix uninitialized values.
new 90f9f8f Minor documentation updates and formatting changes.
new 68157b9 Add ADAM optimizer.
new 54f77d3 Add a test for RMSProp.
new 1190791 Use the correct number of feature maps in the network description (thanks Ngap wei Tham for pointing it out).
new 069911f fix constructor bug
new badba65 remove data member epsilon since it only needed by constructor
new 6e86d10 Merge pull request #462 from stereomatchingkiss/FixOIVSInitBug
new ecf36c5 Use easier-to-understand isnan().
new 09cd0d6 Check isinf() too.
new b44979b Add access to the reference set.
new 9ed5c23 Add a helper class for knn model saving.
new 25fde1e Fix extraneous template parameter list.
new 55ea6aa Add move constructors.
new 9f51ae1 Test move constructors.
new 4956dca The minimum Armadillo requirement is now 3.6.0. So the ifdefs aren't necessary.
new 10d7140 Add rvalue reference constructors.
new 7ec97d0 Add rvalue reference constructor.
new 852571a Fix casting error.
new d9d69fc Make some test sets smaller for speed.
new 1b1a3fa Fix mappings for rvalue reference constructors.
new 89e4f43 Add std::move constructor for datasets.
new 95d1357 Use rvalue references to prevent copies.
new 2e50e03 Update test API.
new fffc24d Fix initialization.
new 3f4e6a8 Handle zero-size cover trees... sort of.
new fecf119 Complete refactoring of allknn program. Allows saving models and selection of different tree types.
new 612affd Add a test for AdaDelta.
new a8215ba Add a test for ADAM.
new 67e0a13 Widen tolerance slightly and disable non-deterministic behavior by setting the shuffle parameter to false.
new c7f92a5 Give name of tree in output.
new abce060 Add ball tree support to NSModel.
new c75abf2 Fix -Wunused.
new 609fddb Add 'ball' option for -t.
new 9c5b690 Fix definition.
new eadb92a Fix grammar issue.
new b25508f Fix function signature.
new 00eccfd Refactor allkfn program.
new d02f7c4 For monochromatic dual-tree search, the bounds may need to be reset.
new c818933 Add a test to ensure that doing monochromatic dual-tree search resets bounds.
new 5584483 Allow access to number of base cases and scores.
new 757971a Initialize baseCases and scores correctly.
new 9ae893e Allow ownership of data matrix.
new d1dfaa8 Add Serialize().
new 29b89eb Don't issue a warning for one-column CSVs.
new 22cf1a3 Minor style fixes.
new 4db02b1 Use a pointer to the dataset.
new f86acf8 Fix #464: the assert was not valid.
new 742e8f2 Update documentation.
new b959363 Add a function to create a random basis.
new c702342 Fix documentation.
new 06b2e58 Add move constructors and Train() functions.
new 752b783 Add Serialize().
new 156787d Add RSModel (not yet tested).
new 04ff436 Fix formatting.
new 3e9b914 Fix casting issues.
new bd3fd9b Add tests for Train() and move constructors.
new 1eb721c Add Serialization() to NaiveBayesClassifier.
new aa19d06 Fix collision of variable names.
new e248946 Do unmapping correctly.
new e09d6a4 Test RSModel.
new c3b6a9b Be more clear with the warning.
new a9d64fc Refactor range search program. Allow model saving/loading.
new 9bd2063 Force settings of --single and --naive.
new 78cc694 Make query set a parameter to Search().
new 24b66d4 Add Serialize() for RASearch.
new a9dcd68 Serialize all search preferences, not just some.
new 0f4e83d Check for correct neighbors correctly.
new 9d29ede Add convenience typedefs (ReLULayer, TanHLayer).
new 7e645b5 Add tests for the current init rules.
new a410bf5 Minor formatting change.
new 99de0b6 Use the new optimizer interface.
new 0642d66 Refactor recurrent network main class for new network API.
new 2e59b7d Add SFINAE pattern for the RecurrentParameter function.
new 263688c Add SFINAE pattern for the SeqLen function.
new 605697f Set the sequence length if necessary.
new a2b7c9b Reset the recurrent delta at the beginning of a new sequence.
new d77572e Refactor LSTM layer for new network API.
new 423fc62 Use the correct number of parameters for the LSTM LayerTraits.
new 9ea11b8 We can't initialize a matrix with an uninitialized matrix.
new dafade6 Add recurrent layer.
new c13f764 Minor style and formatting changes.
new 7388de7 Refactor recurrent network test for new network API.
new 633c18c Minor style and formatting changes.
new 69b969b Fix the include guards to avoid the problem ofdouble inclusion.
new 9d882d9 Remove extra space.
new ec4bdf2 implement command line programs of softmaxRegression
new 60fcc4b refine messages
new 2fc0278 1 : change file name 2 : fix make file, should not add the cpp into SOURCES
new c1e25a3 1 : change the option name of command line 2 : allow users to reuse trained results 3 : allow users to test the predict results of test data
new 3d1aae4 change Predict to const function
new ceeb19f const correctness
new 7983dc9 Merge pull request #466 from stereomatchingkiss/softmaxExe
new 589f13b Minor style changes; no functionality changes.
new 01f5c60 Add note about runtime_error exception
new 03fadcf Add test for twice start/stop timer
new 7d4d0a7 Add changes for runtime_error exception.
new 607a132 Throw a runtime_error exception for start/stop
new d0d8284 Change contributors list
new 4e4588e Merge pull request #472 from Kirizaki/master
new 325348b Tiny minor documentation changes.
new af2e6e8 Add new contributor to copyright list.
new a435e75 Move timerState to Timers, instead of the static Timer class.
new 22fd94d Add breaks in switch statement.
new 7bbe735 Serialize tolerance and initial states.
new 713fa60 Use CLI parameters correctly.
new b661f1f Slightly increased number of training epochs in the SequenceClassificationTest.
new 319205b Build the recurrent neural network code.
new 2dbcd01 Check the feature size.
new d2bcc6b Use Row, not vec, for predictions.
new a1dada8 Refactor main program, add documentation, slightly improve functionality.
new c992568 Add changes to HISTORY and document new program.
new 6e7239c fix bug--forgot to initialize parameter scale
new 8e8166f adjust format
new be45bc4 1 : add function Ratio to set the ratio parameter and set the scale parameter 2 : avoid passing input matrix twice
new d69ac29 Merge pull request #463 from stereomatchingkiss/FixDropOutLayer
new fdd2ae0 No need to reset the scale parameter in the forward pass of the dropout layer.
new 2eface7 Issue a warning when observations are not given for all classes.
new fa89192 Fail when invalid labels are specified.
new 962a37f Fix #478 and add tests.
new 9b75b38 Use a pointer to the reference set, so it can be changed.
new b4c2948 Add Train() method.
new 8f9a75b Fix typo.
new c84287b Handle the k == 0 case without crashing.
new 2dbeb4e Add empty constructor.
new 8c514fd Add some accessors to internal LSH fields.
new 43c57aa Fix ownership bug: we don't own when we Train().
new 70871c6 Add some warnings, and make some minor fixes.
new 05cb18d Add Serialize() and test for LSH.
new a7d8231 Test the empty constructor.
new b243c2d kmeans: small fix with inf variance
new 1bb8434 Merge pull request #481 from arnike/master
new ec8a151 Force re-Precalculate() when we run out of points in one cluster.
new d4e6af5 Compiles on VC14
new c627ed7 arma_config.hpp is auto-generated; don't keep it in the repo.
new 2d9ef25 mlpack build
new 79e4132 Remove build artifact.
new 0dc380d Formatting fixes.
new c265e57 Serialisation tests pass except DET
new e0191b7 Revert DETTest.
new 449b660 all tests are passing
new 4ce2fc6 Open .bin models in binary mode on Windows.
new 4f97fdf Add new contributor.
new bec1b58 Initialize variables more nicely.
new 5aaf0e4 Don't transpose columns on save (#484).
new a484241 first commit
new 2aea096 add example
new c4a2e5a add example
new fc58d77 add the link to UFLDL
new 07df2ce add the link to UFLDL
new 6ec2a93 refine comments
new 779437e 1 : Transpose the input 2 : Reduce copy
new e4294dd can adjust the output range
new 71ef0e4 adjust format
new ab850a1 extract the part of encoder
new 3044ad9 use arma::uword to replace int
new 612e562 make MaximalInputs become more general
new b317138 fix bug--range error
new 7615ed3 fix bug--sign error
new d967335 first commit
new 5a470ed fix compile error and comments
new 86306c9 Merge https://github.com/mlpack/mlpack into visualizeEncoder
new 662d770 1 : change ColumnsToBlocks from function to class(place in core/math) 2 : make NormalizeColByMax as public function(old name is MaximizeHiddenInputs)
new e0f2225 first commit
new 346a52f refine test case
new 8ad13ee able to set block width and block height
new ed9ce37 add new test case
new e4519fc Merge pull request #465 from stereomatchingkiss/visualizeEncoder
new 995e0c0 Cast to fix std::min() call.
new e0eba3f Rewrite and elaborate on documentation significantly.
new 86b368b Fix -Wreorder.
new a03808a The positivity check is unnecessary -- it's a size_t.
new 3bd24c8 Fix -Wreorder and provide better documentation.
new 10b9d45 Document what the file is.
new 52d7f6e Standardize terminology.
new 6f16ab3 Refactor main program to allow saving/loading LSH models.
new 60a0798 Update history for LSH changes.
new e409e3e 80-column maximum.
new cca2005 Refactor DecisionStump significantly.
new c20bcdc Add serialization to DecisionStump.
new cb948db Always resize the labels vector when Classify() is called!
new 38a1905 Clarify or fix documentation for API changes.
new 48fcbbc Add tests for empty DecisionStump constructor and serialization.
new cb74433 Change 'attribute' to 'dimension' for consistency.
new 07888b3 Refactor decision_stump to allow saving/loading of models.
new 8931c87 Remove superfluous semicolons for -pedantic.
new 74f5ac9 Style and documentation consistency fixes.
new 293241e Refactor AdaBoost constructor to allow default parameters.
new da1c9a6 Add Train() and a test for it.
new 5bbce1c Make tolerance private; add accessor/mutator.
new c7bde94 Initialize size of predicted labels correctly.
new c10cc27 Performance improvments. BuildWeightMatrix() is probably unnecessary entirely.
new 31c557d Don't use finalHypothesis.
new 907420a Remove unnecessary BuildWeightMatrix().
new abd5fdc Code and speed cleanups: make things column-major, etc.
new 5480ea7 Add getter for timerState.
new 127de5f Definition of GetState().
new ca5ba7c Terminate the program timers.
new 924425c Merge pull request #488 from Kirizaki/master
new 29e612e Trivial style fix.
new c6c04e6 Clean up documentation.
new 1b34ae0 Minor style fixes.
new f11208f Add file header.
new 5858f46 Braindead refactoring strikes again.
new fd41611 Rename Regress() to Train(), and allow retraining.
new 516ef59 Update API, and add tests for retraining.
new c829fc1 Update for API change.
new e3c3f78 Add Serialize() and a test.
new 9e76f0b Refactor executable to allow saving/loading models.
new 458bd20 Refactor constructors; rename Encode() to Train().
new 2720ddc Add error handling when streams fail to open.
new 1efafa1 Be more clear with error message.
new 61f9a47 Remove data and codes members from SparseCoding.
new a265ddb Refactor so only the training is templatized.
new b463081 Use double, not size_t.
new 8164c9d Fix Classify().
new 2d89f15 Refactor tests to avoid finalHypothesis; use Classify() instead.
new 127a426 Remove finalHypothesis.
new c2d22d6 Add some more documentation.
new de31c15 How did I forget to add Shangtong to the list of contributors? :(
new 157595c Add empty constructor, rvalue reference constructor, and tests.
new f0c32e8 Add Serialize() and other accessors.
new e5a3884 Allow this constructor to be a default constructor.
new c2107ad Test Serialize(). Clean up test, too.
new fc50782 Refactor serialization tests; add SparseCoding implementation.
new b597aa4 Remove tab character; reformat.
new d2e08ad Syntax fix.
new 371e7dc Add RAModel.
new b0f81c8 Add test for RAModel. (does not yet work, still debugging)
new efffb9f Remove tab character; reformat.
new 3b15ce2 Syntax fix.
new 26e8560 Add RAModel.
new c7b4744 Add test for RAModel. (does not yet work, still debugging)
new e839902 This is a more correct implementation. But it isn't efficient and it may fail on corner cases.
new 9576004 Fix bug in test by initializing leafSize.
new cec4ac4 Issue an error if config.hpp is not found.
new 4a39d47 Merge branch 'master' of https://github.com/mlpack/mlpack
new bb63250 Refactor main program.
new dd7c8b9 Add newline after message output.
new 439fec9 Use Row instead of Col.
new fb3a4ad Use Row instead of Col for labels.
new 782e446 Reorder template parameters for consistency.
new 88d5114 Refactor main executable. Allow saving models.
new 1543ee8 Fix transpose issues.
new 99b6dd6 Add default parameter.
new cc794a7 Fix transpose issues.
new 4fb456e Add Serialize() to SparseCoding.
new 64901be Move Serialize() to _impl file.
new a03c124 Add model save/load support to sparse_coding.
new 3b926fd Rename OptimizeCode() to Encode().
new d7d3493 Fix classification error
new f535c29 Merge pull request #492 from MooNDeaR/patch-1
new 1058c4c Merge branch 'master' of https://github.com/mlpack/mlpack
new c673742 Remove ToString() from everything.
new 3d5d9f2 Update HISTORY.md.
new a693c72 Remove special handling for ToString().
new 4326b99 Merge branch 'no-to-string' of https://github.com/rcurtin/mlpack into rcurtin-no-to-string
new 21b198b Merge branch 'rcurtin-no-to-string'
new d3b7d2f Add new contributor.
new 672786f Make lines 80 columns wide.
new 7467dd4 Merge branch 'master' of https://github.com/mlpack/mlpack
new 7e9529e Okay, so it turns out I'm not very good at git merge.
new 714d6b7 Remove unnecessary includes.
new 2736a29 Remove extra line.
new abb4c64 Fix documentation typo.
new 0ec523d This constructor actually does not initialize the dictionary.
new d37d1cd Remove unnecessary parameters.
new efb930e Refactor LCC to same API as SparseCoding.
new cd5986e Finish transition to Row<size_t> for labels.
new 5ebb080 Merge branch 'master' of https://github.com/mlpack/mlpack
new 982e17e Add _impl.hpp file and serialization.
new 443b00a Refactor lcc program.
new 31c10fe Better casting, remove std::.
new 5ba11bc Add additional parameter validation.
new f1f75c8 Rename Estimate() to Train().
new 9999ec9 Rename Estimate() to Train().
new e444bd0 Update documentation and use Train() not Estimate() for distributions.
new 1a0a4ce Update tests to use Train().
new dde8e7b Use Train() not Estimate().
new e08a8ff A smarter strategy for checking positive-definiteness.
new 15b41bb Fix syntax.
new d924562 Refactor GMM: only use FittingType template parameter for Train().
new 09f9c3e Add more useful GMM programs.
new df229e4 Update lists of programs.
new 09cbc6e Refactor nbc program to allow loading/saving models.
new 3ae72c5 Don't print "Required options:" unless we need to.
new f601e99 Standardize options.
new b7911f9 Better documentation of save failures.
new 7d0b607 Better program documentation.
new a990392 Refactor main det program.
new be72510 Better documentation.
new 341414b Only use template parameter for training.
new 0206156 Add default template parameters for Train() overloads.
new 93c0f0d Add tests for Train().
new 51205e0 Add tests for Train() overloads and empty constructor.
new 6a9ab72 Remove unused rating matrix.
new f3c84b4 Update documentation.
new e01baa6 Add Serialize() implementation.
new f86d10c Add serialization test.
new 6ab20af Fix dependencies.
new a8222e0 Refactor main CF program to allow loading/saving of models.
new 62eb2db Don't use a reference internally.
new a33dfc3 Add empty constructor and test.
new 7d68833 Add Train() and tests.
new 31b8022 Update documentation.
new 5a444b0 Fix memory leak.
new 360e78b Remove unused amf program.
new 74846d3 const Serialize() functions don't get picked up right by the compiler.
new b2a108f A better memory leak fix.
new eb41f4b Add Serialize() and tests.
new 2865496 Allow access to naive.
new da8ed43 Add Train() with a tree.
new 48b4706 Add a model for FastMKS, to be used by the command-line program for serialization.
new 0f4fd99 Add tests for FastMKSModel.
new d2ffa5d Fix -Wunused.
new 977afbe Add tests for FastMKSModel.
new fbc045a Refactor main executable.
new 42a94db Fix bugs; add KernelType().
new c0a1500 Fix #229.
new cf72555 Update tutorials.
new de9cc4b Properly list all available algorithms.
new 6070527 Merge branch 'master' into vfdt
new 01558b8 Use mlpack_ prefix.
new 3ff35ba Add mlpack_hoeffding_tree to list of targets.
new 7e6f53b Add PROGRAM_INFO() documentation.
new 5a0370e Update HISTORY.md.
new c9b86e4 Outline the versioning policy. (This can change, of course, but I think this is a good start.)
new d640209 Bump version; everything from here is 2.x.x or higher.
new 83a189a Fix dependency documentation.
new b8508a6 Fix build bug.
new 114d432 Standardize: 'mlpack' instead of 'MLPACK'.
new 734a0b1 Use .csv extensions not .txt extensions.
new c525694 Fix test condition.
new 46c2d4a Wait for long tests with no output.
new a263be4 Test with arma::chol() not arma::det().
new 5919cc0 Loosen bound since it is probabilistic and we have many tests.
new 0c3faf2 Initialize dsPrediction to fix failing test and uninitialized memory.
new a6b57a4 Further loosening of tolerances to increase probability of success.
new f1e8487 Fix test filenames.
new 17d319d Loosen test tolerance slightly.
new a50bd2a Make Newton tolerance larger so the method actually converges most of the time...
new 396f7f2 Ensure a larger set of original singular values.
new 84b9d42 Fix -Wmaybe-uninitialized.
new 858342e Due to technicalities, the tree we load back may not be exactly the same.
new bcabda7 Update required dependency versions.
new e27f1e6 Use right call to chol() depending on Armadillo version.
new dd268fe Relax tolerance for test.
new 1e5443b Loosen tolerances to reduce failure rate.
new 0af5e8c Loosen matrix tolerance checks a bit for floating-point errors.
new cfb5983 Relax tolerance.
new 703c241 Add headers for files missing headers.
new a3eae70 Add header.
new cef372f Add license information.
new c651ad6 Add date of release.
new d33596f Remove unreleased features.
new f965ee3 Update version numbers.
new acee2f7 Compile without debugging symbols.
new 5f39b02 Remove ANN tests.
new 0539869 Remove build artifacts / git artifacts.
new 6dbef35 merge upstream/2.0.0 carrying along only debian/*
new f36a5ce forward port quilt patches
new aeef194 bump to libmlpack.so.2
new b6af25e augment spelling patch
new 9d5e847 build dependency on libboost-serialization-dev
new 6565b24 upstream README.txt now README.md
new bd8b07e remove obsolete field DM-Upload-Allowed
new 10a3099 dh_install --list-missing
new 3a6d5cc patch to silence lintian warning binary-compiled-with-profiling-enabled
new 0ec68da upstream now prefixes binaries with mlpack_
new c8916ed hdf5 include directory debian/rules tweak seems unnecessary
new 091ee6c install generated html documentation
new eeb919e update debian/copyright per upstream COPYRIGHT.txt
new 76b8849 log changes
The 14049 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 9 +-
.travis.yml | 21 +
.travis/config.hpp | 143 +
CMake/ARMA_FindARPACK.cmake | 78 +-
CMake/CXX11.cmake | 48 +
CMake/CompilerFlags.cmake | 16 -
CMake/CreateArmaConfigInfo.cmake | 83 +
CMake/CreateGitVersionHeader.cmake | 29 +
CMake/CreateSVNVersionHeader.cmake | 25 -
CMake/FindArmadillo.cmake | 23 +-
CMake/FindBacktrace.cmake | 106 +
CMake/FindPackageHandleStandardArgs.cmake | 296 --
CMake/GenerateDoxyfile.cmake | 9 +-
CMakeLists.txt | 303 +-
COPYRIGHT.txt | 15 +-
Doxyfile | 9 +-
HISTORY.txt => HISTORY.md | 185 +-
README.md | 225 ++
README.txt | 216 --
UPDATING.txt | 35 +
debian/.gitignore | 2 +-
debian/changelog | 26 +
debian/control | 8 +-
debian/copyright | 110 +-
debian/{libmlpack1.install => libmlpack2.install} | 0
debian/mlpack-doc.docs | 3 +-
debian/patches/0001-build-Doxygen.patch | 4 +-
debian/patches/0002-spelling.patch | 275 +-
debian/patches/0003-Doxygen-timestamp.patch | 2 +-
debian/patches/0004-default-profile-off.patch | 21 +
debian/patches/series | 1 +
debian/rules | 15 +-
debian/shlibs.local | 2 +-
doc/guide/build.hpp | 59 +-
doc/guide/iodoc.hpp | 19 +-
doc/guide/matrices.hpp | 10 +-
doc/guide/sample.hpp | 6 +-
doc/guide/timer.hpp | 9 +-
doc/guide/version.hpp | 2 +-
doc/policies/kernels.hpp | 167 +
doc/policies/metrics.hpp | 113 +
doc/policies/trees.hpp | 901 +++++
doc/tutorials/README.md | 20 +
doc/tutorials/amf/amf.txt | 108 +-
doc/tutorials/cf/cf.txt | 470 +++
doc/tutorials/det/det.txt | 129 +-
doc/tutorials/emst/emst.txt | 28 +-
doc/tutorials/fastmks/fastmks.txt | 126 +-
doc/tutorials/kmeans/kmeans.txt | 205 +-
.../linear_regression/linear_regression.txt | 190 +-
doc/tutorials/neighbor_search/neighbor_search.txt | 188 +-
doc/tutorials/range_search/range_search.txt | 190 +-
doc/tutorials/tutorials.txt | 10 +-
src/mlpack/CMakeLists.txt | 15 +-
src/mlpack/bindings/CMakeLists.txt | 4 +
src/mlpack/bindings/matlab/CMakeLists.txt | 154 +
src/mlpack/bindings/matlab/allkfn/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/allkfn/allkfn.cpp | 194 +
src/mlpack/bindings/matlab/allkfn/allkfn.m | 58 +
src/mlpack/bindings/matlab/allknn/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/allknn/allknn.cpp | 279 ++
src/mlpack/bindings/matlab/allknn/allknn.m | 60 +
src/mlpack/bindings/matlab/emst/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/emst/emst.cpp | 72 +
src/mlpack/bindings/matlab/emst/emst.m | 52 +
src/mlpack/bindings/matlab/gmm/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/gmm/gmm.cpp | 129 +
src/mlpack/bindings/matlab/gmm/gmm.m | 28 +
src/mlpack/bindings/matlab/hmm/hmm_generate.cpp | 373 ++
src/mlpack/bindings/matlab/hmm/hmm_generate.m | 28 +
.../bindings/matlab/kernel_pca/CMakeLists.txt | 19 +
.../bindings/matlab/kernel_pca/kernel_pca.cpp | 136 +
src/mlpack/bindings/matlab/kernel_pca/kernel_pca.m | 71 +
src/mlpack/bindings/matlab/kmeans/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/kmeans/kmeans.cpp | 175 +
src/mlpack/bindings/matlab/kmeans/kmeans.m | 28 +
src/mlpack/bindings/matlab/lars/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/lars/lars.cpp | 58 +
src/mlpack/bindings/matlab/lars/lars.m | 48 +
src/mlpack/bindings/matlab/nca/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/nca/nca.cpp | 55 +
src/mlpack/bindings/matlab/nca/nca.m | 24 +
src/mlpack/bindings/matlab/nmf/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/nmf/nmf.cpp | 106 +
src/mlpack/bindings/matlab/nmf/nmf.m | 58 +
src/mlpack/bindings/matlab/pca/CMakeLists.txt | 19 +
src/mlpack/bindings/matlab/pca/pca.cpp | 62 +
src/mlpack/bindings/matlab/pca/pca.m | 33 +
.../bindings/matlab/range_search/CMakeLists.txt | 19 +
.../bindings/matlab/range_search/range_search.cpp | 325 ++
.../bindings/matlab/range_search/range_search.m | 47 +
src/mlpack/core.hpp | 107 +-
src/mlpack/core/CMakeLists.txt | 1 +
src/mlpack/core/arma_extend/CMakeLists.txt | 5 +-
src/mlpack/core/arma_extend/Mat_extra_bones.hpp | 4 +
src/mlpack/core/arma_extend/Mat_extra_meat.hpp | 35 +
src/mlpack/core/arma_extend/SpMat_extra_bones.hpp | 6 +-
src/mlpack/core/arma_extend/SpMat_extra_meat.hpp | 34 +-
src/mlpack/core/arma_extend/arma_extend.hpp | 17 +
src/mlpack/core/arma_extend/fn_ccov.hpp | 24 +-
src/mlpack/core/arma_extend/fn_inplace_reshape.hpp | 16 -
src/mlpack/core/arma_extend/glue_ccov_meat.hpp | 30 +-
src/mlpack/core/arma_extend/glue_ccov_proto.hpp | 21 +-
src/mlpack/core/arma_extend/op_ccov_meat.hpp | 34 +-
src/mlpack/core/arma_extend/op_ccov_proto.hpp | 22 +-
src/mlpack/core/arma_extend/operator_minus.hpp | 25 +
.../core/{data => boost_backport}/CMakeLists.txt | 13 +-
src/mlpack/core/boost_backport/README.md | 3 +
.../unordered_collections_load_imp.hpp | 74 +
.../unordered_collections_save_imp.hpp | 86 +
src/mlpack/core/boost_backport/unordered_map.hpp | 231 ++
src/mlpack/core/data/CMakeLists.txt | 11 +-
src/mlpack/core/data/dataset_info.hpp | 89 +
src/mlpack/core/data/dataset_info_impl.hpp | 100 +
src/mlpack/core/data/extension.hpp | 33 +
src/mlpack/core/data/format.hpp | 26 +
src/mlpack/core/data/load.hpp | 107 +-
src/mlpack/core/data/load_arff.hpp | 56 +
src/mlpack/core/data/load_arff_impl.hpp | 206 ++
src/mlpack/core/data/load_impl.hpp | 417 ++-
src/mlpack/core/data/normalize_labels.hpp | 21 +-
src/mlpack/core/data/normalize_labels_impl.hpp | 21 +-
src/mlpack/core/data/save.hpp | 57 +-
src/mlpack/core/data/save_impl.hpp | 119 +-
src/mlpack/core/data/serialization_shim.hpp | 505 +++
src/mlpack/core/dists/CMakeLists.txt | 6 +-
src/mlpack/core/dists/discrete_distribution.cpp | 33 +-
src/mlpack/core/dists/discrete_distribution.hpp | 50 +-
src/mlpack/core/dists/gaussian_distribution.cpp | 105 +-
src/mlpack/core/dists/gaussian_distribution.hpp | 143 +-
src/mlpack/core/dists/laplace_distribution.cpp | 29 +-
src/mlpack/core/dists/laplace_distribution.hpp | 44 +-
src/mlpack/core/dists/regression_distribution.cpp | 60 +
src/mlpack/core/dists/regression_distribution.hpp | 125 +
src/mlpack/core/kernels/CMakeLists.txt | 4 +-
src/mlpack/core/kernels/cosine_distance.hpp | 30 +-
src/mlpack/core/kernels/cosine_distance_impl.hpp | 15 +-
src/mlpack/core/kernels/epanechnikov_kernel.cpp | 47 +-
src/mlpack/core/kernels/epanechnikov_kernel.hpp | 46 +-
.../core/kernels/epanechnikov_kernel_impl.hpp | 36 +-
src/mlpack/core/kernels/example_kernel.hpp | 69 +-
src/mlpack/core/kernels/gaussian_kernel.hpp | 64 +-
.../core/kernels/hyperbolic_tangent_kernel.hpp | 31 +-
src/mlpack/core/kernels/kernel_traits.hpp | 16 +-
src/mlpack/core/kernels/laplacian_kernel.hpp | 45 +-
src/mlpack/core/kernels/linear_kernel.hpp | 29 +-
src/mlpack/core/kernels/polynomial_kernel.hpp | 31 +-
.../core/kernels/pspectrum_string_kernel.cpp | 7 -
.../core/kernels/pspectrum_string_kernel.hpp | 27 +-
.../core/kernels/pspectrum_string_kernel_impl.hpp | 11 +-
src/mlpack/core/kernels/spherical_kernel.hpp | 89 +-
src/mlpack/core/kernels/triangular_kernel.hpp | 46 +-
src/mlpack/core/math/CMakeLists.txt | 9 +-
src/mlpack/core/math/clamp.hpp | 11 +-
src/mlpack/core/math/columns_to_blocks.cpp | 94 +
src/mlpack/core/math/columns_to_blocks.hpp | 222 ++
src/mlpack/core/math/lin_alg.cpp | 94 +-
src/mlpack/core/math/lin_alg.hpp | 57 +-
src/mlpack/core/math/lin_alg_impl.hpp | 23 +
src/mlpack/core/math/random.cpp | 44 +-
src/mlpack/core/math/random.hpp | 70 +-
src/mlpack/core/math/random_basis.cpp | 44 +
src/mlpack/core/math/random_basis.hpp | 27 +
src/mlpack/core/math/range.hpp | 17 +-
src/mlpack/core/math/range_impl.hpp | 24 +-
src/mlpack/core/math/round.hpp | 7 -
src/mlpack/core/metrics/CMakeLists.txt | 4 +-
src/mlpack/core/metrics/ip_metric.hpp | 54 +-
src/mlpack/core/metrics/ip_metric_impl.hpp | 44 +-
src/mlpack/core/metrics/lmetric.hpp | 51 +-
src/mlpack/core/metrics/lmetric_impl.hpp | 56 +-
src/mlpack/core/metrics/mahalanobis_distance.hpp | 23 +-
.../core/metrics/mahalanobis_distance_impl.hpp | 48 +-
src/mlpack/core/optimizers/CMakeLists.txt | 2 +-
.../optimizers/aug_lagrangian/aug_lagrangian.hpp | 14 +-
.../aug_lagrangian/aug_lagrangian_function.hpp | 14 +-
.../aug_lagrangian_function_impl.hpp | 23 +-
.../aug_lagrangian/aug_lagrangian_impl.hpp | 38 +-
.../aug_lagrangian_test_functions.cpp | 38 +-
.../aug_lagrangian_test_functions.hpp | 14 +-
src/mlpack/core/optimizers/lbfgs/lbfgs.hpp | 26 +-
src/mlpack/core/optimizers/lbfgs/lbfgs_impl.hpp | 73 +-
.../core/optimizers/lbfgs/test_functions.cpp | 7 -
.../core/optimizers/lbfgs/test_functions.hpp | 13 +-
src/mlpack/core/optimizers/lrsdp/CMakeLists.txt | 13 -
src/mlpack/core/optimizers/lrsdp/lrsdp.cpp | 42 -
src/mlpack/core/optimizers/lrsdp/lrsdp.hpp | 111 -
.../core/optimizers/lrsdp/lrsdp_function.cpp | 176 -
.../core/optimizers/lrsdp/lrsdp_function.hpp | 119 -
.../core/optimizers/sa/exponential_schedule.hpp | 11 +-
src/mlpack/core/optimizers/sa/sa.hpp | 13 +-
src/mlpack/core/optimizers/sa/sa_impl.hpp | 35 +-
.../core/optimizers/{sgd => sdp}/CMakeLists.txt | 12 +-
src/mlpack/core/optimizers/sdp/lrsdp.hpp | 89 +
src/mlpack/core/optimizers/sdp/lrsdp_function.hpp | 121 +
.../core/optimizers/sdp/lrsdp_function_impl.hpp | 212 ++
src/mlpack/core/optimizers/sdp/lrsdp_impl.hpp | 36 +
src/mlpack/core/optimizers/sdp/primal_dual.hpp | 133 +
.../core/optimizers/sdp/primal_dual_impl.hpp | 458 +++
src/mlpack/core/optimizers/sdp/sdp.hpp | 138 +
src/mlpack/core/optimizers/sdp/sdp_impl.hpp | 71 +
src/mlpack/core/optimizers/sgd/sgd.hpp | 14 +-
src/mlpack/core/optimizers/sgd/sgd_impl.hpp | 28 +-
src/mlpack/core/optimizers/sgd/test_function.cpp | 7 -
src/mlpack/core/optimizers/sgd/test_function.hpp | 13 +-
src/mlpack/core/tree/CMakeLists.txt | 32 +-
src/mlpack/core/tree/TREE_EXPLANATION.txt | 2 +-
src/mlpack/core/tree/ballbound.hpp | 51 +-
src/mlpack/core/tree/ballbound_impl.hpp | 56 +-
src/mlpack/core/tree/binary_space_tree.hpp | 13 +-
.../tree/binary_space_tree/binary_space_tree.hpp | 306 +-
.../binary_space_tree/binary_space_tree_impl.hpp | 783 ++--
...r.hpp => breadth_first_dual_tree_traverser.hpp} | 59 +-
.../breadth_first_dual_tree_traverser_impl.hpp | 205 ++
.../tree/binary_space_tree/dual_tree_traverser.hpp | 21 +-
.../binary_space_tree/dual_tree_traverser_impl.hpp | 42 +-
.../core/tree/binary_space_tree/mean_split.hpp | 13 +-
.../tree/binary_space_tree/mean_split_impl.hpp | 136 +-
.../{mean_split.hpp => midpoint_split.hpp} | 30 +-
...mean_split_impl.hpp => midpoint_split_impl.hpp} | 177 +-
.../binary_space_tree/single_tree_traverser.hpp | 21 +-
.../single_tree_traverser_impl.hpp | 130 +-
src/mlpack/core/tree/binary_space_tree/traits.hpp | 26 +-
src/mlpack/core/tree/binary_space_tree/typedef.hpp | 141 +
src/mlpack/core/tree/bound_traits.hpp | 32 +
src/mlpack/core/tree/bounds.hpp | 8 +-
src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 13 +-
src/mlpack/core/tree/cosine_tree/cosine_tree.hpp | 32 +-
src/mlpack/core/tree/cover_tree.hpp | 11 +-
src/mlpack/core/tree/cover_tree/cover_tree.hpp | 113 +-
.../core/tree/cover_tree/cover_tree_impl.hpp | 718 +++-
.../core/tree/cover_tree/dual_tree_traverser.hpp | 24 +-
.../tree/cover_tree/dual_tree_traverser_impl.hpp | 75 +-
.../core/tree/cover_tree/first_point_is_root.hpp | 14 +-
.../core/tree/cover_tree/single_tree_traverser.hpp | 21 +-
.../tree/cover_tree/single_tree_traverser_impl.hpp | 46 +-
src/mlpack/core/tree/cover_tree/traits.hpp | 23 +-
src/mlpack/core/tree/cover_tree/typedef.hpp | 42 +
src/mlpack/core/tree/example_tree.hpp | 11 +-
src/mlpack/core/tree/hrectbound.hpp | 76 +-
src/mlpack/core/tree/hrectbound_impl.hpp | 210 +-
src/mlpack/core/tree/mrkd_statistic.cpp | 50 -
src/mlpack/core/tree/mrkd_statistic.hpp | 105 -
src/mlpack/core/tree/mrkd_statistic_impl.hpp | 100 -
src/mlpack/core/tree/rectangle_tree.hpp | 17 +-
.../dual_tree_traverser.hpp | 63 +-
.../rectangle_tree/dual_tree_traverser_impl.hpp | 166 +
.../tree/rectangle_tree/hilbert_r_tree_split.hpp | 1 +
.../rectangle_tree/hilbert_r_tree_split_impl.hpp | 1 +
.../r_star_tree_descent_heuristic.hpp | 48 +
.../r_star_tree_descent_heuristic_impl.hpp | 200 ++
.../core/tree/rectangle_tree/r_star_tree_split.hpp | 70 +
.../tree/rectangle_tree/r_star_tree_split_impl.hpp | 679 ++++
.../rectangle_tree/r_tree_descent_heuristic.hpp | 58 +
.../r_tree_descent_heuristic_impl.hpp | 103 +
.../core/tree/rectangle_tree/r_tree_split.hpp | 86 +
.../core/tree/rectangle_tree/r_tree_split_impl.hpp | 525 +++
.../core/tree/rectangle_tree/rectangle_tree.hpp | 614 ++++
.../tree/rectangle_tree/rectangle_tree_impl.hpp | 1045 ++++++
.../tree/rectangle_tree/single_tree_traverser.hpp | 76 +
.../rectangle_tree/single_tree_traverser_impl.hpp | 84 +
src/mlpack/core/tree/rectangle_tree/traits.hpp | 61 +
src/mlpack/core/tree/rectangle_tree/typedef.hpp | 84 +
.../core/tree/rectangle_tree/x_tree_split.hpp | 81 +
.../core/tree/rectangle_tree/x_tree_split_impl.hpp | 832 +++++
src/mlpack/core/tree/statistic.hpp | 23 +-
src/mlpack/core/tree/traversal_info.hpp | 7 -
src/mlpack/core/tree/tree_traits.hpp | 27 +-
src/mlpack/core/util/CMakeLists.txt | 9 +-
src/mlpack/core/util/arma_config_check.hpp | 34 +
src/mlpack/core/util/arma_traits.hpp | 9 +-
src/mlpack/core/util/cli.cpp | 34 +-
src/mlpack/core/util/cli.hpp | 37 +-
src/mlpack/core/util/cli_deleter.cpp | 7 -
src/mlpack/core/util/cli_deleter.hpp | 11 +-
src/mlpack/core/util/cli_impl.hpp | 9 +-
src/mlpack/core/util/log.cpp | 34 +-
src/mlpack/core/util/log.hpp | 7 -
src/mlpack/core/util/nulloutstream.hpp | 7 -
src/mlpack/core/util/option.cpp | 7 -
src/mlpack/core/util/option.hpp | 11 +-
src/mlpack/core/util/option_impl.hpp | 11 +-
src/mlpack/core/util/prefixedoutstream.cpp | 7 -
src/mlpack/core/util/prefixedoutstream.hpp | 50 +-
src/mlpack/core/util/prefixedoutstream_impl.hpp | 56 +-
src/mlpack/core/util/save_restore_utility.cpp | 213 --
src/mlpack/core/util/save_restore_utility.hpp | 129 -
src/mlpack/core/util/save_restore_utility_impl.hpp | 100 -
src/mlpack/core/util/sfinae_utility.hpp | 10 +-
src/mlpack/core/util/string_util.cpp | 7 -
src/mlpack/core/util/string_util.hpp | 11 +-
src/mlpack/core/util/timers.cpp | 75 +-
src/mlpack/core/util/timers.hpp | 37 +-
src/mlpack/core/util/version.cpp | 15 +-
src/mlpack/core/util/version.hpp | 23 +-
src/mlpack/methods/CMakeLists.txt | 7 +-
.../{decision_stump => adaboost}/CMakeLists.txt | 17 +-
src/mlpack/methods/adaboost/adaboost.hpp | 180 +
src/mlpack/methods/adaboost/adaboost_impl.hpp | 251 ++
src/mlpack/methods/adaboost/adaboost_main.cpp | 361 ++
src/mlpack/methods/amf/CMakeLists.txt | 4 +-
src/mlpack/methods/amf/amf.hpp | 152 +-
src/mlpack/methods/amf/amf_impl.hpp | 15 +-
src/mlpack/methods/amf/amf_main.cpp | 146 -
src/mlpack/methods/amf/init_rules/CMakeLists.txt | 6 +-
src/mlpack/methods/amf/init_rules/average_init.hpp | 64 +-
.../methods/amf/init_rules/random_acol_init.hpp | 53 +-
src/mlpack/methods/amf/init_rules/random_init.hpp | 33 +-
.../amf/termination_policies/CMakeLists.txt | 5 +-
.../complete_incremental_termination.hpp | 118 +-
.../incomplete_incremental_termination.hpp | 91 +-
.../max_iteration_termination.hpp | 80 +
.../simple_residue_termination.hpp | 21 +-
.../simple_tolerance_termination.hpp | 13 +-
.../validation_RMSE_termination.hpp | 114 +-
src/mlpack/methods/amf/update_rules/CMakeLists.txt | 4 +-
src/mlpack/methods/amf/update_rules/nmf_als.hpp | 71 +-
.../methods/amf/update_rules/nmf_mult_dist.hpp | 63 +-
.../methods/amf/update_rules/nmf_mult_div.hpp | 68 +-
.../amf/update_rules/svd_batch_learning.hpp | 178 +-
.../svd_complete_incremental_learning.hpp | 159 +-
.../svd_incomplete_incremental_learning.hpp | 140 +-
src/mlpack/methods/ann/CMakeLists.txt | 26 +
.../activation_functions}/CMakeLists.txt | 11 +-
.../ann/activation_functions/identity_function.hpp | 91 +
.../ann/activation_functions/logistic_function.hpp | 112 +
.../activation_functions/rectifier_function.hpp | 110 +
.../ann/activation_functions/softsign_function.hpp | 129 +
.../ann/activation_functions/tanh_function.hpp | 100 +
src/mlpack/methods/ann/cnn.hpp | 419 +++
.../convolution_rules}/CMakeLists.txt | 9 +-
.../methods/ann/convolution_rules/border_modes.hpp | 28 +
.../ann/convolution_rules/fft_convolution.hpp | 216 ++
.../ann/convolution_rules/naive_convolution.hpp | 185 +
.../ann/convolution_rules/svd_convolution.hpp | 194 +
src/mlpack/methods/ann/ffn.hpp | 418 +++
.../init_rules}/CMakeLists.txt | 7 +-
.../kathirvalavakumar_subavathi_init.hpp | 117 +
.../methods/ann/init_rules/nguyen_widrow_init.hpp | 112 +
src/mlpack/methods/ann/init_rules/oivs_init.hpp | 125 +
.../methods/ann/init_rules/orthogonal_init.hpp | 77 +
src/mlpack/methods/ann/init_rules/random_init.hpp | 87 +
src/mlpack/methods/ann/init_rules/zero_init.hpp | 60 +
src/mlpack/methods/ann/layer/CMakeLists.txt | 23 +
src/mlpack/methods/ann/layer/base_layer.hpp | 223 ++
src/mlpack/methods/ann/layer/bias_layer.hpp | 280 ++
.../ann/layer/binary_classification_layer.hpp | 80 +
src/mlpack/methods/ann/layer/conv_layer.hpp | 394 ++
src/mlpack/methods/ann/layer/dropout_layer.hpp | 256 ++
src/mlpack/methods/ann/layer/layer_traits.hpp | 74 +
src/mlpack/methods/ann/layer/linear_layer.hpp | 351 ++
src/mlpack/methods/ann/layer/lstm_layer.hpp | 464 +++
.../ann/layer/multiclass_classification_layer.hpp | 85 +
src/mlpack/methods/ann/layer/one_hot_layer.hpp | 82 +
src/mlpack/methods/ann/layer/pooling_layer.hpp | 257 ++
src/mlpack/methods/ann/layer/recurrent_layer.hpp | 264 ++
src/mlpack/methods/ann/layer/softmax_layer.hpp | 114 +
src/mlpack/methods/ann/network_traits.hpp | 45 +
.../optimizer}/CMakeLists.txt | 9 +-
src/mlpack/methods/ann/optimizer/ada_delta.hpp | 175 +
src/mlpack/methods/ann/optimizer/adam.hpp | 177 +
src/mlpack/methods/ann/optimizer/rmsprop.hpp | 163 +
.../methods/ann/optimizer/steepest_descent.hpp | 146 +
.../performance_functions}/CMakeLists.txt | 8 +-
.../ann/performance_functions/cee_function.hpp | 53 +
.../ann/performance_functions/mse_function.hpp | 40 +
.../ann/performance_functions/sse_function.hpp | 40 +
.../pooling_rules}/CMakeLists.txt | 7 +-
.../methods/ann/pooling_rules/max_pooling.hpp | 51 +
.../methods/ann/pooling_rules/mean_pooling.hpp | 51 +
src/mlpack/methods/ann/rnn.hpp | 785 ++++
.../trainer}/CMakeLists.txt | 6 +-
src/mlpack/methods/ann/trainer/trainer.hpp | 279 ++
src/mlpack/methods/cf/CMakeLists.txt | 13 +-
src/mlpack/methods/cf/cf.cpp | 283 ++
src/mlpack/methods/cf/cf.hpp | 168 +-
src/mlpack/methods/cf/cf_impl.hpp | 284 +-
src/mlpack/methods/cf/cf_main.cpp | 324 +-
src/mlpack/methods/cf/svd_wrapper.hpp | 86 +
src/mlpack/methods/cf/svd_wrapper_impl.hpp | 127 +
src/mlpack/methods/decision_stump/CMakeLists.txt | 11 +-
.../methods/decision_stump/decision_stump.hpp | 163 +-
.../methods/decision_stump/decision_stump_impl.hpp | 291 +-
.../methods/decision_stump/decision_stump_main.cpp | 229 +-
src/mlpack/methods/det/CMakeLists.txt | 8 +-
src/mlpack/methods/det/det_main.cpp | 247 +-
src/mlpack/methods/det/dt_utils.cpp | 64 +-
src/mlpack/methods/det/dt_utils.hpp | 11 +-
src/mlpack/methods/det/dtree.cpp | 70 +-
src/mlpack/methods/det/dtree.hpp | 45 +-
src/mlpack/methods/emst/CMakeLists.txt | 10 +-
src/mlpack/methods/emst/dtb.hpp | 56 +-
src/mlpack/methods/emst/dtb_impl.hpp | 161 +-
src/mlpack/methods/emst/dtb_rules.hpp | 7 -
src/mlpack/methods/emst/dtb_rules_impl.hpp | 13 +-
src/mlpack/methods/emst/dtb_stat.hpp | 13 +-
src/mlpack/methods/emst/edge_pair.hpp | 11 +-
src/mlpack/methods/emst/emst_main.cpp | 14 +-
src/mlpack/methods/emst/union_find.hpp | 11 +-
src/mlpack/methods/fastmks/CMakeLists.txt | 14 +-
src/mlpack/methods/fastmks/fastmks.hpp | 226 +-
src/mlpack/methods/fastmks/fastmks_impl.hpp | 715 ++--
src/mlpack/methods/fastmks/fastmks_main.cpp | 328 +-
src/mlpack/methods/fastmks/fastmks_model.cpp | 203 ++
src/mlpack/methods/fastmks/fastmks_model.hpp | 140 +
src/mlpack/methods/fastmks/fastmks_model_impl.hpp | 215 ++
src/mlpack/methods/fastmks/fastmks_rules.hpp | 19 +-
src/mlpack/methods/fastmks/fastmks_rules_impl.hpp | 88 +-
src/mlpack/methods/fastmks/fastmks_stat.hpp | 36 +-
src/mlpack/methods/gmm/CMakeLists.txt | 34 +-
src/mlpack/methods/gmm/diagonal_constraint.hpp | 15 +-
.../methods/gmm/eigenvalue_ratio_constraint.hpp | 28 +-
src/mlpack/methods/gmm/em_fit.hpp | 31 +-
src/mlpack/methods/gmm/em_fit_impl.hpp | 135 +-
src/mlpack/methods/gmm/gmm.cpp | 152 +
src/mlpack/methods/gmm/gmm.hpp | 214 +-
src/mlpack/methods/gmm/gmm_generate_main.cpp | 52 +
src/mlpack/methods/gmm/gmm_impl.hpp | 425 +--
src/mlpack/methods/gmm/gmm_probability_main.cpp | 45 +
.../gmm/{gmm_main.cpp => gmm_train_main.cpp} | 123 +-
src/mlpack/methods/gmm/no_constraint.hpp | 15 +-
src/mlpack/methods/gmm/phi.hpp | 154 -
.../methods/gmm/positive_definite_constraint.hpp | 52 +-
src/mlpack/methods/hmm/CMakeLists.txt | 28 +-
src/mlpack/methods/hmm/hmm.hpp | 79 +-
src/mlpack/methods/hmm/hmm_generate_main.cpp | 118 +-
src/mlpack/methods/hmm/hmm_impl.hpp | 121 +-
src/mlpack/methods/hmm/hmm_loglik_main.cpp | 103 +-
src/mlpack/methods/hmm/hmm_regression.hpp | 335 ++
src/mlpack/methods/hmm/hmm_regression_impl.hpp | 191 +
src/mlpack/methods/hmm/hmm_train_main.cpp | 400 +--
src/mlpack/methods/hmm/hmm_util.hpp | 52 +-
src/mlpack/methods/hmm/hmm_util_impl.hpp | 322 +-
src/mlpack/methods/hmm/hmm_viterbi_main.cpp | 96 +-
src/mlpack/methods/hoeffding_trees/CMakeLists.txt | 35 +
.../hoeffding_trees/binary_numeric_split.hpp | 131 +
.../hoeffding_trees/binary_numeric_split_impl.hpp | 181 +
.../hoeffding_trees/binary_numeric_split_info.hpp | 44 +
.../hoeffding_trees/categorical_split_info.hpp | 36 +
.../methods/hoeffding_trees/gini_impurity.hpp | 84 +
.../hoeffding_categorical_split.hpp | 124 +
.../hoeffding_categorical_split_impl.hpp | 95 +
.../hoeffding_trees/hoeffding_numeric_split.hpp | 151 +
.../hoeffding_numeric_split_impl.hpp | 249 ++
.../methods/hoeffding_trees/hoeffding_tree.hpp | 337 ++
.../hoeffding_trees/hoeffding_tree_impl.hpp | 804 +++++
.../hoeffding_trees/hoeffding_tree_main.cpp | 328 ++
.../methods/hoeffding_trees/information_gain.hpp | 91 +
.../methods/hoeffding_trees/numeric_split_info.hpp | 48 +
src/mlpack/methods/hoeffding_trees/typedef.hpp | 21 +
src/mlpack/methods/kernel_pca/CMakeLists.txt | 10 +-
src/mlpack/methods/kernel_pca/kernel_pca.hpp | 14 +-
src/mlpack/methods/kernel_pca/kernel_pca_impl.hpp | 24 +-
src/mlpack/methods/kernel_pca/kernel_pca_main.cpp | 23 +-
.../methods/kernel_pca/kernel_rules/CMakeLists.txt | 4 +-
.../kernel_pca/kernel_rules/naive_method.hpp | 17 +-
.../kernel_pca/kernel_rules/nystroem_method.hpp | 39 +-
src/mlpack/methods/kmeans/CMakeLists.txt | 26 +-
src/mlpack/methods/kmeans/allow_empty_clusters.hpp | 36 +-
src/mlpack/methods/kmeans/dual_tree_kmeans.hpp | 172 +
.../methods/kmeans/dual_tree_kmeans_impl.hpp | 691 ++++
.../methods/kmeans/dual_tree_kmeans_rules.hpp | 82 +
.../methods/kmeans/dual_tree_kmeans_rules_impl.hpp | 334 ++
.../methods/kmeans/dual_tree_kmeans_statistic.hpp | 118 +
src/mlpack/methods/kmeans/elkan_kmeans.hpp | 65 +
src/mlpack/methods/kmeans/elkan_kmeans_impl.hpp | 186 +
src/mlpack/methods/kmeans/hamerly_kmeans.hpp | 63 +
src/mlpack/methods/kmeans/hamerly_kmeans_impl.hpp | 175 +
src/mlpack/methods/kmeans/kmeans.hpp | 118 +-
src/mlpack/methods/kmeans/kmeans_impl.hpp | 429 +--
src/mlpack/methods/kmeans/kmeans_main.cpp | 303 +-
.../methods/kmeans/max_variance_new_cluster.hpp | 51 +-
.../kmeans/max_variance_new_cluster_impl.hpp | 133 +-
src/mlpack/methods/kmeans/naive_kmeans.hpp | 65 +
src/mlpack/methods/kmeans/naive_kmeans_impl.hpp | 84 +
src/mlpack/methods/kmeans/pelleg_moore_kmeans.hpp | 90 +
.../methods/kmeans/pelleg_moore_kmeans_impl.hpp | 83 +
.../methods/kmeans/pelleg_moore_kmeans_rules.hpp | 107 +
.../kmeans/pelleg_moore_kmeans_rules_impl.hpp | 178 +
.../kmeans/pelleg_moore_kmeans_statistic.hpp | 71 +
src/mlpack/methods/kmeans/random_partition.hpp | 19 +-
src/mlpack/methods/kmeans/refined_start.hpp | 21 +-
src/mlpack/methods/kmeans/refined_start_impl.hpp | 18 +-
src/mlpack/methods/lars/CMakeLists.txt | 13 +-
src/mlpack/methods/lars/lars.cpp | 60 +-
src/mlpack/methods/lars/lars.hpp | 52 +-
src/mlpack/methods/lars/lars_impl.hpp | 53 +
src/mlpack/methods/lars/lars_main.cpp | 168 +-
.../methods/linear_regression/CMakeLists.txt | 8 +-
.../linear_regression/linear_regression.cpp | 59 +-
.../linear_regression/linear_regression.hpp | 72 +-
.../linear_regression/linear_regression_main.cpp | 46 +-
.../methods/local_coordinate_coding/CMakeLists.txt | 16 +-
.../{lcc_impl.hpp => lcc.cpp} | 135 +-
src/mlpack/methods/local_coordinate_coding/lcc.hpp | 116 +-
.../methods/local_coordinate_coding/lcc_impl.hpp | 288 +-
.../methods/local_coordinate_coding/lcc_main.cpp | 214 +-
.../methods/logistic_regression/CMakeLists.txt | 10 +-
.../logistic_regression/logistic_regression.hpp | 121 +-
.../logistic_regression_function.hpp | 31 +-
...n.cpp => logistic_regression_function_impl.hpp} | 76 +-
.../logistic_regression_impl.hpp | 149 +-
.../logistic_regression_main.cpp | 285 +-
src/mlpack/methods/lsh/CMakeLists.txt | 13 +-
src/mlpack/methods/lsh/lsh_main.cpp | 146 +-
src/mlpack/methods/lsh/lsh_search.hpp | 209 +-
src/mlpack/methods/lsh/lsh_search_impl.hpp | 345 +-
.../{quic_svd => matrix_completion}/CMakeLists.txt | 8 +-
.../matrix_completion/matrix_completion.cpp | 109 +
.../matrix_completion/matrix_completion.hpp | 140 +
src/mlpack/methods/mean_shift/CMakeLists.txt | 24 +
src/mlpack/methods/mean_shift/mean_shift.hpp | 168 +
src/mlpack/methods/mean_shift/mean_shift_impl.hpp | 270 ++
src/mlpack/methods/mean_shift/mean_shift_main.cpp | 111 +
src/mlpack/methods/mvu/CMakeLists.txt | 4 +-
src/mlpack/methods/mvu/mvu.cpp | 11 +-
src/mlpack/methods/mvu/mvu.hpp | 11 +-
src/mlpack/methods/mvu/mvu_main.cpp | 7 -
src/mlpack/methods/naive_bayes/CMakeLists.txt | 10 +-
.../methods/naive_bayes/naive_bayes_classifier.hpp | 87 +-
.../naive_bayes/naive_bayes_classifier_impl.hpp | 111 +-
src/mlpack/methods/naive_bayes/nbc_main.cpp | 216 +-
src/mlpack/methods/nca/CMakeLists.txt | 10 +-
src/mlpack/methods/nca/nca.hpp | 20 +-
src/mlpack/methods/nca/nca_impl.hpp | 26 +-
src/mlpack/methods/nca/nca_main.cpp | 19 +-
.../methods/nca/nca_softmax_error_function.hpp | 20 +-
.../nca/nca_softmax_error_function_impl.hpp | 27 +-
src/mlpack/methods/neighbor_search/CMakeLists.txt | 16 +-
src/mlpack/methods/neighbor_search/allkfn_main.cpp | 306 +-
src/mlpack/methods/neighbor_search/allknn_main.cpp | 392 +-
.../methods/neighbor_search/neighbor_search.hpp | 279 +-
.../neighbor_search/neighbor_search_impl.hpp | 827 +++--
.../neighbor_search/neighbor_search_rules.hpp | 19 +-
.../neighbor_search/neighbor_search_rules_impl.hpp | 23 +-
.../neighbor_search/neighbor_search_stat.hpp | 29 +-
src/mlpack/methods/neighbor_search/ns_model.hpp | 138 +
.../methods/neighbor_search/ns_model_impl.hpp | 477 +++
.../methods/neighbor_search/ns_traversal_info.hpp | 11 +-
.../sort_policies/furthest_neighbor_sort.cpp | 7 -
.../sort_policies/furthest_neighbor_sort.hpp | 11 +-
.../sort_policies/furthest_neighbor_sort_impl.hpp | 11 +-
.../sort_policies/nearest_neighbor_sort.cpp | 7 -
.../sort_policies/nearest_neighbor_sort.hpp | 11 +-
.../sort_policies/nearest_neighbor_sort_impl.hpp | 11 +-
src/mlpack/methods/neighbor_search/typedef.hpp | 11 +-
src/mlpack/methods/neighbor_search/unmap.cpp | 11 +-
src/mlpack/methods/neighbor_search/unmap.hpp | 11 +-
src/mlpack/methods/nmf/CMakeLists.txt | 6 +-
src/mlpack/methods/nmf/nmf_main.cpp | 13 +-
src/mlpack/methods/nystroem_method/CMakeLists.txt | 4 +-
.../methods/nystroem_method/kmeans_selection.hpp | 25 +-
.../methods/nystroem_method/nystroem_method.hpp | 19 +-
.../nystroem_method/nystroem_method_impl.hpp | 17 +-
.../methods/nystroem_method/ordered_selection.hpp | 11 +-
.../methods/nystroem_method/random_selection.hpp | 11 +-
src/mlpack/methods/pca/CMakeLists.txt | 10 +-
src/mlpack/methods/pca/pca.cpp | 17 -
src/mlpack/methods/pca/pca.hpp | 16 +-
src/mlpack/methods/pca/pca_main.cpp | 7 -
src/mlpack/methods/perceptron/CMakeLists.txt | 10 +-
.../initialization_methods/CMakeLists.txt | 4 +-
.../initialization_methods/random_init.hpp | 25 +-
.../initialization_methods/zero_init.hpp | 28 +-
.../perceptron/learning_policies/CMakeLists.txt | 4 +-
.../learning_policies/simple_weight_update.hpp | 54 +-
src/mlpack/methods/perceptron/perceptron.hpp | 126 +-
src/mlpack/methods/perceptron/perceptron_impl.hpp | 200 +-
src/mlpack/methods/perceptron/perceptron_main.cpp | 305 +-
src/mlpack/methods/quic_svd/CMakeLists.txt | 4 +-
src/mlpack/methods/quic_svd/quic_svd.hpp | 48 +-
src/mlpack/methods/quic_svd/quic_svd_impl.hpp | 15 +-
src/mlpack/methods/radical/CMakeLists.txt | 8 +-
src/mlpack/methods/radical/radical.cpp | 19 -
src/mlpack/methods/radical/radical.hpp | 14 +-
src/mlpack/methods/radical/radical_main.cpp | 7 -
src/mlpack/methods/range_search/CMakeLists.txt | 13 +-
src/mlpack/methods/range_search/range_search.hpp | 303 +-
.../methods/range_search/range_search_impl.hpp | 710 +++-
.../methods/range_search/range_search_main.cpp | 427 +--
.../methods/range_search/range_search_rules.hpp | 29 +-
.../range_search/range_search_rules_impl.hpp | 24 +-
.../methods/range_search/range_search_stat.hpp | 27 +-
src/mlpack/methods/range_search/rs_model.cpp | 304 ++
src/mlpack/methods/range_search/rs_model.hpp | 171 +
src/mlpack/methods/range_search/rs_model_impl.hpp | 138 +
src/mlpack/methods/rann/CMakeLists.txt | 19 +-
src/mlpack/methods/rann/allkrann_main.cpp | 394 +-
src/mlpack/methods/rann/ra_model.hpp | 172 +
src/mlpack/methods/rann/ra_model_impl.hpp | 558 +++
src/mlpack/methods/rann/ra_query_stat.hpp | 20 +-
src/mlpack/methods/rann/ra_search.hpp | 457 ++-
src/mlpack/methods/rann/ra_search_impl.hpp | 787 ++--
src/mlpack/methods/rann/ra_search_rules.hpp | 66 +-
src/mlpack/methods/rann/ra_search_rules_impl.hpp | 248 +-
src/mlpack/methods/rann/ra_typedef.hpp | 11 +-
src/mlpack/methods/rann/ra_util.cpp | 182 +
src/mlpack/methods/rann/ra_util.hpp | 64 +
src/mlpack/methods/regularized_svd/CMakeLists.txt | 4 +-
.../methods/regularized_svd/regularized_svd.hpp | 96 +-
.../regularized_svd/regularized_svd_function.cpp | 33 +-
.../regularized_svd/regularized_svd_function.hpp | 39 +-
.../regularized_svd/regularized_svd_impl.hpp | 52 +-
.../methods/softmax_regression/CMakeLists.txt | 25 +
.../softmax_regression/softmax_regression.hpp | 200 ++
.../softmax_regression_function.cpp | 202 ++
.../softmax_regression_function.hpp | 148 +
.../softmax_regression/softmax_regression_impl.hpp | 167 +
.../softmax_regression/softmax_regression_main.cpp | 282 ++
.../methods/sparse_autoencoder/CMakeLists.txt | 6 +-
.../methods/sparse_autoencoder/maximal_inputs.cpp | 41 +
.../methods/sparse_autoencoder/maximal_inputs.hpp | 91 +
.../sparse_autoencoder/sparse_autoencoder.hpp | 11 +-
.../sparse_autoencoder_function.cpp | 7 -
.../sparse_autoencoder_function.hpp | 13 +-
.../sparse_autoencoder/sparse_autoencoder_impl.hpp | 11 +-
src/mlpack/methods/sparse_coding/CMakeLists.txt | 9 +-
.../data_dependent_random_initializer.hpp | 11 +-
.../methods/sparse_coding/nothing_initializer.hpp | 11 +-
.../methods/sparse_coding/random_initializer.hpp | 11 +-
.../{sparse_coding_impl.hpp => sparse_coding.cpp} | 155 +-
src/mlpack/methods/sparse_coding/sparse_coding.hpp | 157 +-
.../methods/sparse_coding/sparse_coding_impl.hpp | 323 +-
.../methods/sparse_coding/sparse_coding_main.cpp | 254 +-
src/mlpack/prereqs.hpp | 33 +-
src/mlpack/tests/CMakeLists.txt | 27 +-
src/mlpack/tests/activation_functions_test.cpp | 340 ++
src/mlpack/tests/ada_delta_test.cpp | 113 +
src/mlpack/tests/adaboost_test.cpp | 881 +++++
src/mlpack/tests/adam_test.cpp | 114 +
src/mlpack/tests/allkfn_test.cpp | 156 +-
src/mlpack/tests/allknn_test.cpp | 539 ++-
src/mlpack/tests/allkrann_search_test.cpp | 300 +-
src/mlpack/tests/arma_extend_test.cpp | 214 +-
src/mlpack/tests/armadillo_svd_test.cpp | 52 +
src/mlpack/tests/aug_lagrangian_test.cpp | 7 -
src/mlpack/tests/cf_test.cpp | 406 ++-
src/mlpack/tests/cli_test.cpp | 21 +-
src/mlpack/tests/connection_traits_test.cpp | 82 +
src/mlpack/tests/convolution_test.cpp | 372 ++
src/mlpack/tests/convolutional_network_test.cpp | 224 ++
src/mlpack/tests/cosine_tree_test.cpp | 19 +-
src/mlpack/tests/data/completion_X.csv | 20 +
src/mlpack/tests/data/completion_indices.csv | 2 +
src/mlpack/tests/data/erdosrenyi-n100.csv | 1440 ++++++++
src/mlpack/tests/data/{iris.txt => iris.csv} | 0
src/mlpack/tests/data/iris_labels.txt | 2 +-
src/mlpack/tests/data/iris_test.csv | 63 +
src/mlpack/tests/data/iris_test_labels.csv | 63 +
src/mlpack/tests/data/iris_train.csv | 87 +
.../{iris_labels.txt => iris_train_labels.csv} | 63 -
src/mlpack/tests/data/r10.txt | 10 +
src/mlpack/tests/data/sensing_A.csv | 200 ++
src/mlpack/tests/data/sensing_X.csv | 20 +
src/mlpack/tests/data/test_labels_nonlinsep.txt | 600 ++++
src/mlpack/tests/data/test_nonlinsep.txt | 600 ++++
src/mlpack/tests/data/thyroid_test.csv | 3428 ++++++++++++++++++
src/mlpack/tests/data/thyroid_train.csv | 3772 ++++++++++++++++++++
src/mlpack/tests/data/train_labels_nonlinsep.txt | 1200 +++++++
src/mlpack/tests/data/train_nonlinsep.txt | 1200 +++++++
src/mlpack/tests/data/vc2.csv | 207 ++
.../tests/data/{iris_labels.txt => vc2_labels.txt} | 77 +-
src/mlpack/tests/data/vc2_test.csv | 67 +
src/mlpack/tests/data/vc2_test_labels.txt | 67 +
src/mlpack/tests/decision_stump_test.cpp | 75 +-
src/mlpack/tests/det_test.cpp | 7 -
src/mlpack/tests/distribution_test.cpp | 171 +-
src/mlpack/tests/emst_test.cpp | 19 +-
src/mlpack/tests/fastmks_test.cpp | 845 ++++-
src/mlpack/tests/feedforward_network_test.cpp | 434 +++
src/mlpack/tests/gmm_test.cpp | 377 +-
src/mlpack/tests/hmm_test.cpp | 374 +-
src/mlpack/tests/hoeffding_tree_test.cpp | 1155 ++++++
src/mlpack/tests/init_rules_test.cpp | 125 +
src/mlpack/tests/kernel_pca_test.cpp | 7 -
src/mlpack/tests/kernel_test.cpp | 7 -
src/mlpack/tests/kernel_traits_test.cpp | 7 -
src/mlpack/tests/kmeans_test.cpp | 287 +-
src/mlpack/tests/lars_test.cpp | 145 +-
src/mlpack/tests/layer_traits_test.cpp | 68 +
src/mlpack/tests/lbfgs_test.cpp | 7 -
src/mlpack/tests/lin_alg_test.cpp | 106 +-
src/mlpack/tests/linear_regression_test.cpp | 28 +-
src/mlpack/tests/load_save_test.cpp | 774 +++-
src/mlpack/tests/local_coordinate_coding_test.cpp | 80 +-
src/mlpack/tests/log_test.cpp | 38 +
src/mlpack/tests/logistic_regression_test.cpp | 208 +-
src/mlpack/tests/lrsdp_test.cpp | 215 +-
src/mlpack/tests/lsh_test.cpp | 58 +-
src/mlpack/tests/lstm_peephole_test.cpp | 87 +
src/mlpack/tests/math_test.cpp | 7 -
src/mlpack/tests/matrix_completion_test.cpp | 62 +
src/mlpack/tests/maximal_inputs_test.cpp | 81 +
src/mlpack/tests/mean_shift_test.cpp | 146 +
src/mlpack/tests/metric_test.cpp | 7 -
src/mlpack/tests/mlpack_test.cpp | 46 +-
src/mlpack/tests/nbc_test.cpp | 178 +-
src/mlpack/tests/nca_test.cpp | 27 +-
src/mlpack/tests/nmf_test.cpp | 19 +-
src/mlpack/tests/nystroem_method_test.cpp | 12 +-
src/mlpack/tests/old_boost_test_definitions.hpp | 7 -
src/mlpack/tests/pca_test.cpp | 7 -
src/mlpack/tests/perceptron_test.cpp | 23 +-
src/mlpack/tests/performance_functions_test.cpp | 49 +
src/mlpack/tests/pooling_rules_test.cpp | 75 +
src/mlpack/tests/quic_svd_test.cpp | 40 +-
src/mlpack/tests/radical_test.cpp | 7 -
src/mlpack/tests/range_search_test.cpp | 587 ++-
src/mlpack/tests/rectangle_tree_test.cpp | 838 +++++
src/mlpack/tests/recurrent_network_test.cpp | 589 +++
src/mlpack/tests/regularized_svd_test.cpp | 7 -
src/mlpack/tests/rmsprop_test.cpp | 113 +
src/mlpack/tests/sa_test.cpp | 8 -
src/mlpack/tests/save_restore_utility_test.cpp | 181 -
src/mlpack/tests/sdp_primal_dual_test.cpp | 623 ++++
src/mlpack/tests/serialization.cpp | 76 +
src/mlpack/tests/serialization.hpp | 199 ++
src/mlpack/tests/serialization_test.cpp | 1658 +++++++++
src/mlpack/tests/sgd_test.cpp | 7 -
src/mlpack/tests/softmax_regression_test.cpp | 411 +++
src/mlpack/tests/sort_policy_test.cpp | 39 +-
src/mlpack/tests/sparse_autoencoder_test.cpp | 7 -
src/mlpack/tests/sparse_coding_test.cpp | 81 +-
src/mlpack/tests/svd_batch_test.cpp | 90 +-
src/mlpack/tests/svd_incremental_test.cpp | 93 +-
src/mlpack/tests/termination_policy_test.cpp | 61 +
src/mlpack/tests/to_string_test.cpp | 508 ---
src/mlpack/tests/tree_test.cpp | 495 ++-
src/mlpack/tests/tree_traits_test.cpp | 47 +-
src/mlpack/tests/union_find_test.cpp | 7 -
730 files changed, 77454 insertions(+), 17713 deletions(-)
create mode 100644 .travis.yml
create mode 100644 .travis/config.hpp
create mode 100644 CMake/CXX11.cmake
delete mode 100644 CMake/CompilerFlags.cmake
create mode 100644 CMake/CreateArmaConfigInfo.cmake
create mode 100644 CMake/CreateGitVersionHeader.cmake
delete mode 100644 CMake/CreateSVNVersionHeader.cmake
create mode 100644 CMake/FindBacktrace.cmake
delete mode 100644 CMake/FindPackageHandleStandardArgs.cmake
rename HISTORY.txt => HISTORY.md (59%)
create mode 100644 README.md
delete mode 100644 README.txt
create mode 100644 UPDATING.txt
rename debian/{libmlpack1.install => libmlpack2.install} (100%)
create mode 100644 debian/patches/0004-default-profile-off.patch
create mode 100644 doc/policies/kernels.hpp
create mode 100644 doc/policies/metrics.hpp
create mode 100644 doc/policies/trees.hpp
create mode 100644 doc/tutorials/README.md
create mode 100644 doc/tutorials/cf/cf.txt
create mode 100644 src/mlpack/bindings/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/allkfn/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/allkfn/allkfn.cpp
create mode 100644 src/mlpack/bindings/matlab/allkfn/allkfn.m
create mode 100644 src/mlpack/bindings/matlab/allknn/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/allknn/allknn.cpp
create mode 100644 src/mlpack/bindings/matlab/allknn/allknn.m
create mode 100644 src/mlpack/bindings/matlab/emst/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/emst/emst.cpp
create mode 100644 src/mlpack/bindings/matlab/emst/emst.m
create mode 100644 src/mlpack/bindings/matlab/gmm/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/gmm/gmm.cpp
create mode 100644 src/mlpack/bindings/matlab/gmm/gmm.m
create mode 100644 src/mlpack/bindings/matlab/hmm/hmm_generate.cpp
create mode 100644 src/mlpack/bindings/matlab/hmm/hmm_generate.m
create mode 100644 src/mlpack/bindings/matlab/kernel_pca/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/kernel_pca/kernel_pca.cpp
create mode 100644 src/mlpack/bindings/matlab/kernel_pca/kernel_pca.m
create mode 100644 src/mlpack/bindings/matlab/kmeans/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/kmeans/kmeans.cpp
create mode 100644 src/mlpack/bindings/matlab/kmeans/kmeans.m
create mode 100644 src/mlpack/bindings/matlab/lars/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/lars/lars.cpp
create mode 100644 src/mlpack/bindings/matlab/lars/lars.m
create mode 100644 src/mlpack/bindings/matlab/nca/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/nca/nca.cpp
create mode 100644 src/mlpack/bindings/matlab/nca/nca.m
create mode 100644 src/mlpack/bindings/matlab/nmf/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/nmf/nmf.cpp
create mode 100644 src/mlpack/bindings/matlab/nmf/nmf.m
create mode 100644 src/mlpack/bindings/matlab/pca/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/pca/pca.cpp
create mode 100644 src/mlpack/bindings/matlab/pca/pca.m
create mode 100644 src/mlpack/bindings/matlab/range_search/CMakeLists.txt
create mode 100644 src/mlpack/bindings/matlab/range_search/range_search.cpp
create mode 100644 src/mlpack/bindings/matlab/range_search/range_search.m
create mode 100644 src/mlpack/core/arma_extend/operator_minus.hpp
copy src/mlpack/core/{data => boost_backport}/CMakeLists.txt (56%)
create mode 100644 src/mlpack/core/boost_backport/README.md
create mode 100644 src/mlpack/core/boost_backport/unordered_collections_load_imp.hpp
create mode 100644 src/mlpack/core/boost_backport/unordered_collections_save_imp.hpp
create mode 100644 src/mlpack/core/boost_backport/unordered_map.hpp
create mode 100644 src/mlpack/core/data/dataset_info.hpp
create mode 100644 src/mlpack/core/data/dataset_info_impl.hpp
create mode 100644 src/mlpack/core/data/extension.hpp
create mode 100644 src/mlpack/core/data/format.hpp
create mode 100644 src/mlpack/core/data/load_arff.hpp
create mode 100644 src/mlpack/core/data/load_arff_impl.hpp
create mode 100644 src/mlpack/core/data/serialization_shim.hpp
create mode 100644 src/mlpack/core/dists/regression_distribution.cpp
create mode 100644 src/mlpack/core/dists/regression_distribution.hpp
create mode 100644 src/mlpack/core/math/columns_to_blocks.cpp
create mode 100644 src/mlpack/core/math/columns_to_blocks.hpp
create mode 100644 src/mlpack/core/math/lin_alg_impl.hpp
create mode 100644 src/mlpack/core/math/random_basis.cpp
create mode 100644 src/mlpack/core/math/random_basis.hpp
delete mode 100644 src/mlpack/core/optimizers/lrsdp/CMakeLists.txt
delete mode 100644 src/mlpack/core/optimizers/lrsdp/lrsdp.cpp
delete mode 100644 src/mlpack/core/optimizers/lrsdp/lrsdp.hpp
delete mode 100644 src/mlpack/core/optimizers/lrsdp/lrsdp_function.cpp
delete mode 100644 src/mlpack/core/optimizers/lrsdp/lrsdp_function.hpp
copy src/mlpack/core/optimizers/{sgd => sdp}/CMakeLists.txt (57%)
create mode 100644 src/mlpack/core/optimizers/sdp/lrsdp.hpp
create mode 100644 src/mlpack/core/optimizers/sdp/lrsdp_function.hpp
create mode 100644 src/mlpack/core/optimizers/sdp/lrsdp_function_impl.hpp
create mode 100644 src/mlpack/core/optimizers/sdp/lrsdp_impl.hpp
create mode 100644 src/mlpack/core/optimizers/sdp/primal_dual.hpp
create mode 100644 src/mlpack/core/optimizers/sdp/primal_dual_impl.hpp
create mode 100644 src/mlpack/core/optimizers/sdp/sdp.hpp
create mode 100644 src/mlpack/core/optimizers/sdp/sdp_impl.hpp
copy src/mlpack/core/tree/binary_space_tree/{dual_tree_traverser.hpp => breadth_first_dual_tree_traverser.hpp} (57%)
create mode 100644 src/mlpack/core/tree/binary_space_tree/breadth_first_dual_tree_traverser_impl.hpp
copy src/mlpack/core/tree/binary_space_tree/{mean_split.hpp => midpoint_split.hpp} (81%)
copy src/mlpack/core/tree/binary_space_tree/{mean_split_impl.hpp => midpoint_split_impl.hpp} (53%)
create mode 100644 src/mlpack/core/tree/binary_space_tree/typedef.hpp
create mode 100644 src/mlpack/core/tree/bound_traits.hpp
create mode 100644 src/mlpack/core/tree/cover_tree/typedef.hpp
delete mode 100644 src/mlpack/core/tree/mrkd_statistic.cpp
delete mode 100644 src/mlpack/core/tree/mrkd_statistic.hpp
delete mode 100644 src/mlpack/core/tree/mrkd_statistic_impl.hpp
copy src/mlpack/core/tree/{binary_space_tree => rectangle_tree}/dual_tree_traverser.hpp (62%)
create mode 100644 src/mlpack/core/tree/rectangle_tree/dual_tree_traverser_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/hilbert_r_tree_split.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/hilbert_r_tree_split_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_star_tree_descent_heuristic.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_star_tree_descent_heuristic_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_star_tree_split.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_star_tree_split_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_tree_descent_heuristic.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_tree_descent_heuristic_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_tree_split.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/r_tree_split_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/rectangle_tree.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/rectangle_tree_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/single_tree_traverser.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/single_tree_traverser_impl.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/traits.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/typedef.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/x_tree_split.hpp
create mode 100644 src/mlpack/core/tree/rectangle_tree/x_tree_split_impl.hpp
create mode 100644 src/mlpack/core/util/arma_config_check.hpp
delete mode 100644 src/mlpack/core/util/save_restore_utility.cpp
delete mode 100644 src/mlpack/core/util/save_restore_utility.hpp
delete mode 100644 src/mlpack/core/util/save_restore_utility_impl.hpp
copy src/mlpack/methods/{decision_stump => adaboost}/CMakeLists.txt (51%)
create mode 100644 src/mlpack/methods/adaboost/adaboost.hpp
create mode 100644 src/mlpack/methods/adaboost/adaboost_impl.hpp
create mode 100644 src/mlpack/methods/adaboost/adaboost_main.cpp
delete mode 100644 src/mlpack/methods/amf/amf_main.cpp
create mode 100644 src/mlpack/methods/amf/termination_policies/max_iteration_termination.hpp
create mode 100644 src/mlpack/methods/ann/CMakeLists.txt
copy src/mlpack/methods/{perceptron/initialization_methods => ann/activation_functions}/CMakeLists.txt (54%)
create mode 100644 src/mlpack/methods/ann/activation_functions/identity_function.hpp
create mode 100644 src/mlpack/methods/ann/activation_functions/logistic_function.hpp
create mode 100644 src/mlpack/methods/ann/activation_functions/rectifier_function.hpp
create mode 100644 src/mlpack/methods/ann/activation_functions/softsign_function.hpp
create mode 100644 src/mlpack/methods/ann/activation_functions/tanh_function.hpp
create mode 100644 src/mlpack/methods/ann/cnn.hpp
copy src/mlpack/methods/{perceptron/learning_policies => ann/convolution_rules}/CMakeLists.txt (57%)
create mode 100644 src/mlpack/methods/ann/convolution_rules/border_modes.hpp
create mode 100644 src/mlpack/methods/ann/convolution_rules/fft_convolution.hpp
create mode 100644 src/mlpack/methods/ann/convolution_rules/naive_convolution.hpp
create mode 100644 src/mlpack/methods/ann/convolution_rules/svd_convolution.hpp
create mode 100644 src/mlpack/methods/ann/ffn.hpp
copy src/mlpack/methods/{perceptron/initialization_methods => ann/init_rules}/CMakeLists.txt (61%)
create mode 100644 src/mlpack/methods/ann/init_rules/kathirvalavakumar_subavathi_init.hpp
create mode 100644 src/mlpack/methods/ann/init_rules/nguyen_widrow_init.hpp
create mode 100644 src/mlpack/methods/ann/init_rules/oivs_init.hpp
create mode 100644 src/mlpack/methods/ann/init_rules/orthogonal_init.hpp
create mode 100644 src/mlpack/methods/ann/init_rules/random_init.hpp
create mode 100644 src/mlpack/methods/ann/init_rules/zero_init.hpp
create mode 100644 src/mlpack/methods/ann/layer/CMakeLists.txt
create mode 100644 src/mlpack/methods/ann/layer/base_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/bias_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/binary_classification_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/conv_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/dropout_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/layer_traits.hpp
create mode 100644 src/mlpack/methods/ann/layer/linear_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/lstm_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/multiclass_classification_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/one_hot_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/pooling_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/recurrent_layer.hpp
create mode 100644 src/mlpack/methods/ann/layer/softmax_layer.hpp
create mode 100644 src/mlpack/methods/ann/network_traits.hpp
copy src/mlpack/methods/{perceptron/learning_policies => ann/optimizer}/CMakeLists.txt (60%)
create mode 100644 src/mlpack/methods/ann/optimizer/ada_delta.hpp
create mode 100644 src/mlpack/methods/ann/optimizer/adam.hpp
create mode 100644 src/mlpack/methods/ann/optimizer/rmsprop.hpp
create mode 100644 src/mlpack/methods/ann/optimizer/steepest_descent.hpp
copy src/mlpack/methods/{perceptron/learning_policies => ann/performance_functions}/CMakeLists.txt (61%)
create mode 100644 src/mlpack/methods/ann/performance_functions/cee_function.hpp
create mode 100644 src/mlpack/methods/ann/performance_functions/mse_function.hpp
create mode 100644 src/mlpack/methods/ann/performance_functions/sse_function.hpp
copy src/mlpack/methods/{perceptron/learning_policies => ann/pooling_rules}/CMakeLists.txt (64%)
create mode 100644 src/mlpack/methods/ann/pooling_rules/max_pooling.hpp
create mode 100644 src/mlpack/methods/ann/pooling_rules/mean_pooling.hpp
create mode 100644 src/mlpack/methods/ann/rnn.hpp
copy src/mlpack/methods/{perceptron/learning_policies => ann/trainer}/CMakeLists.txt (65%)
create mode 100644 src/mlpack/methods/ann/trainer/trainer.hpp
create mode 100644 src/mlpack/methods/cf/cf.cpp
create mode 100644 src/mlpack/methods/cf/svd_wrapper.hpp
create mode 100644 src/mlpack/methods/cf/svd_wrapper_impl.hpp
create mode 100644 src/mlpack/methods/fastmks/fastmks_model.cpp
create mode 100644 src/mlpack/methods/fastmks/fastmks_model.hpp
create mode 100644 src/mlpack/methods/fastmks/fastmks_model_impl.hpp
create mode 100644 src/mlpack/methods/gmm/gmm.cpp
create mode 100644 src/mlpack/methods/gmm/gmm_generate_main.cpp
create mode 100644 src/mlpack/methods/gmm/gmm_probability_main.cpp
rename src/mlpack/methods/gmm/{gmm_main.cpp => gmm_train_main.cpp} (70%)
delete mode 100644 src/mlpack/methods/gmm/phi.hpp
create mode 100644 src/mlpack/methods/hmm/hmm_regression.hpp
create mode 100644 src/mlpack/methods/hmm/hmm_regression_impl.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/CMakeLists.txt
create mode 100644 src/mlpack/methods/hoeffding_trees/binary_numeric_split.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/binary_numeric_split_impl.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/binary_numeric_split_info.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/categorical_split_info.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/gini_impurity.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/hoeffding_categorical_split.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/hoeffding_categorical_split_impl.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/hoeffding_numeric_split.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/hoeffding_numeric_split_impl.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/hoeffding_tree.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/hoeffding_tree_impl.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/hoeffding_tree_main.cpp
create mode 100644 src/mlpack/methods/hoeffding_trees/information_gain.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/numeric_split_info.hpp
create mode 100644 src/mlpack/methods/hoeffding_trees/typedef.hpp
create mode 100644 src/mlpack/methods/kmeans/dual_tree_kmeans.hpp
create mode 100644 src/mlpack/methods/kmeans/dual_tree_kmeans_impl.hpp
create mode 100644 src/mlpack/methods/kmeans/dual_tree_kmeans_rules.hpp
create mode 100644 src/mlpack/methods/kmeans/dual_tree_kmeans_rules_impl.hpp
create mode 100644 src/mlpack/methods/kmeans/dual_tree_kmeans_statistic.hpp
create mode 100644 src/mlpack/methods/kmeans/elkan_kmeans.hpp
create mode 100644 src/mlpack/methods/kmeans/elkan_kmeans_impl.hpp
create mode 100644 src/mlpack/methods/kmeans/hamerly_kmeans.hpp
create mode 100644 src/mlpack/methods/kmeans/hamerly_kmeans_impl.hpp
create mode 100644 src/mlpack/methods/kmeans/naive_kmeans.hpp
create mode 100644 src/mlpack/methods/kmeans/naive_kmeans_impl.hpp
create mode 100644 src/mlpack/methods/kmeans/pelleg_moore_kmeans.hpp
create mode 100644 src/mlpack/methods/kmeans/pelleg_moore_kmeans_impl.hpp
create mode 100644 src/mlpack/methods/kmeans/pelleg_moore_kmeans_rules.hpp
create mode 100644 src/mlpack/methods/kmeans/pelleg_moore_kmeans_rules_impl.hpp
create mode 100644 src/mlpack/methods/kmeans/pelleg_moore_kmeans_statistic.hpp
create mode 100644 src/mlpack/methods/lars/lars_impl.hpp
copy src/mlpack/methods/local_coordinate_coding/{lcc_impl.hpp => lcc.cpp} (63%)
rename src/mlpack/methods/logistic_regression/{logistic_regression_function.cpp => logistic_regression_function_impl.hpp} (70%)
copy src/mlpack/methods/{quic_svd => matrix_completion}/CMakeLists.txt (62%)
create mode 100644 src/mlpack/methods/matrix_completion/matrix_completion.cpp
create mode 100644 src/mlpack/methods/matrix_completion/matrix_completion.hpp
create mode 100644 src/mlpack/methods/mean_shift/CMakeLists.txt
create mode 100644 src/mlpack/methods/mean_shift/mean_shift.hpp
create mode 100644 src/mlpack/methods/mean_shift/mean_shift_impl.hpp
create mode 100644 src/mlpack/methods/mean_shift/mean_shift_main.cpp
create mode 100644 src/mlpack/methods/neighbor_search/ns_model.hpp
create mode 100644 src/mlpack/methods/neighbor_search/ns_model_impl.hpp
create mode 100644 src/mlpack/methods/range_search/rs_model.cpp
create mode 100644 src/mlpack/methods/range_search/rs_model.hpp
create mode 100644 src/mlpack/methods/range_search/rs_model_impl.hpp
create mode 100644 src/mlpack/methods/rann/ra_model.hpp
create mode 100644 src/mlpack/methods/rann/ra_model_impl.hpp
create mode 100644 src/mlpack/methods/rann/ra_util.cpp
create mode 100644 src/mlpack/methods/rann/ra_util.hpp
create mode 100644 src/mlpack/methods/softmax_regression/CMakeLists.txt
create mode 100644 src/mlpack/methods/softmax_regression/softmax_regression.hpp
create mode 100644 src/mlpack/methods/softmax_regression/softmax_regression_function.cpp
create mode 100644 src/mlpack/methods/softmax_regression/softmax_regression_function.hpp
create mode 100644 src/mlpack/methods/softmax_regression/softmax_regression_impl.hpp
create mode 100644 src/mlpack/methods/softmax_regression/softmax_regression_main.cpp
create mode 100644 src/mlpack/methods/sparse_autoencoder/maximal_inputs.cpp
create mode 100644 src/mlpack/methods/sparse_autoencoder/maximal_inputs.hpp
copy src/mlpack/methods/sparse_coding/{sparse_coding_impl.hpp => sparse_coding.cpp} (58%)
create mode 100644 src/mlpack/tests/activation_functions_test.cpp
create mode 100644 src/mlpack/tests/ada_delta_test.cpp
create mode 100644 src/mlpack/tests/adaboost_test.cpp
create mode 100644 src/mlpack/tests/adam_test.cpp
create mode 100644 src/mlpack/tests/armadillo_svd_test.cpp
create mode 100644 src/mlpack/tests/connection_traits_test.cpp
create mode 100644 src/mlpack/tests/convolution_test.cpp
create mode 100644 src/mlpack/tests/convolutional_network_test.cpp
create mode 100644 src/mlpack/tests/data/completion_X.csv
create mode 100644 src/mlpack/tests/data/completion_indices.csv
create mode 100644 src/mlpack/tests/data/erdosrenyi-n100.csv
rename src/mlpack/tests/data/{iris.txt => iris.csv} (100%)
create mode 100644 src/mlpack/tests/data/iris_test.csv
create mode 100644 src/mlpack/tests/data/iris_test_labels.csv
create mode 100644 src/mlpack/tests/data/iris_train.csv
copy src/mlpack/tests/data/{iris_labels.txt => iris_train_labels.csv} (58%)
create mode 100644 src/mlpack/tests/data/r10.txt
create mode 100644 src/mlpack/tests/data/sensing_A.csv
create mode 100644 src/mlpack/tests/data/sensing_X.csv
create mode 100644 src/mlpack/tests/data/test_labels_nonlinsep.txt
create mode 100644 src/mlpack/tests/data/test_nonlinsep.txt
create mode 100644 src/mlpack/tests/data/thyroid_test.csv
create mode 100644 src/mlpack/tests/data/thyroid_train.csv
create mode 100644 src/mlpack/tests/data/train_labels_nonlinsep.txt
create mode 100644 src/mlpack/tests/data/train_nonlinsep.txt
create mode 100644 src/mlpack/tests/data/vc2.csv
copy src/mlpack/tests/data/{iris_labels.txt => vc2_labels.txt} (67%)
create mode 100644 src/mlpack/tests/data/vc2_test.csv
create mode 100644 src/mlpack/tests/data/vc2_test_labels.txt
create mode 100644 src/mlpack/tests/feedforward_network_test.cpp
create mode 100644 src/mlpack/tests/hoeffding_tree_test.cpp
create mode 100644 src/mlpack/tests/init_rules_test.cpp
create mode 100644 src/mlpack/tests/layer_traits_test.cpp
create mode 100644 src/mlpack/tests/log_test.cpp
create mode 100644 src/mlpack/tests/lstm_peephole_test.cpp
create mode 100644 src/mlpack/tests/matrix_completion_test.cpp
create mode 100644 src/mlpack/tests/maximal_inputs_test.cpp
create mode 100644 src/mlpack/tests/mean_shift_test.cpp
create mode 100644 src/mlpack/tests/performance_functions_test.cpp
create mode 100644 src/mlpack/tests/pooling_rules_test.cpp
create mode 100644 src/mlpack/tests/rectangle_tree_test.cpp
create mode 100644 src/mlpack/tests/recurrent_network_test.cpp
create mode 100644 src/mlpack/tests/rmsprop_test.cpp
delete mode 100644 src/mlpack/tests/save_restore_utility_test.cpp
create mode 100644 src/mlpack/tests/sdp_primal_dual_test.cpp
create mode 100644 src/mlpack/tests/serialization.cpp
create mode 100644 src/mlpack/tests/serialization.hpp
create mode 100644 src/mlpack/tests/serialization_test.cpp
create mode 100644 src/mlpack/tests/softmax_regression_test.cpp
create mode 100644 src/mlpack/tests/termination_policy_test.cpp
delete mode 100644 src/mlpack/tests/to_string_test.cpp
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