[mlpack] branch svn-trunk updated (5071776 -> c80e63e)

[Barak A. Pearlmutter]

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bap pushed a change to branch svn-trunk
in repository mlpack.

      from  5071776   Modify test for new RangeSearch API.
       new  52b48ed   Add rank parameter.  This might not be applicable to when we have other decompositions, though.
       new  432f0bd   Minor documentation fix, and sometimes the labels need to be transposed.
       new  efa6d21   Don't transpose the labels upon loading; expect that they are going to be one line per label.
       new  201d543   Get the number of classes correctly.
       new  a281b09   Don't transpose on save; one point per line.
       new  727b070   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  a146972   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  80524d6   Test incremental variance functionality.
       new  8fbd237   Change to two-pass algorithm suggested by Vahab in #344.
       new  4505084   Add new contributor.
       new  81e0724   Add sparse autoencoder contribution by Siddharth.  This is the version given in ticket #345 as Changes3.tar.gz.
       new  f047378   Add test for sparse autoencoder, contributed by Siddharth.
       new  6256206   First pass: add file headers, include guards, and then my vimrc auto-stripped all trailing spaces.
       new  b31d18a   Minor (and ultimately trivial) documentation changes; add documentation for SparseAutoencoderFunction constructor.
       new  e8ba3ef   Syntax cleanup; just some spacing.  No functionality change.
       new  e1acf23   Adapt test to work in the larger framework of mlpack tests.
       new  803dc8f   Simple style changes; no functionality change.
       new  f4a989a   CMake configuration to compile sparse autoencoders.
       new  90c14b9   Build sparse autoencoder as part of mlpack.
       new  5a30d1e   Test sparse autoencoder.
       new  bdc8e80   Remove unused variables to fix warnings.
       new  c80e63e   Change Sigmoid() function to avoid matrix copies via the return value.

The 22 revisions listed above as "new" are entirely new to this
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Summary of changes:
 COPYRIGHT.txt                                      |   1 +
 src/mlpack/core.hpp                                |   1 +
 src/mlpack/methods/CMakeLists.txt                  |   1 +
 src/mlpack/methods/cf/cf_main.cpp                  |   4 +
 .../methods/naive_bayes/naive_bayes_classifier.hpp |   6 +-
 .../naive_bayes/naive_bayes_classifier_impl.hpp    | 119 ++++++---
 src/mlpack/methods/naive_bayes/nbc_main.cpp        |  32 ++-
 .../{mvu => sparse_autoencoder}/CMakeLists.txt     |  14 +-
 .../sparse_autoencoder/sparse_autoencoder.hpp      | 199 +++++++++++++++
 .../sparse_autoencoder_function.cpp                | 204 ++++++++++++++++
 .../sparse_autoencoder_function.hpp                | 162 +++++++++++++
 .../sparse_autoencoder/sparse_autoencoder_impl.hpp |  77 ++++++
 src/mlpack/tests/CMakeLists.txt                    |   1 +
 src/mlpack/tests/nbc_test.cpp                      |  55 +++++
 src/mlpack/tests/sparse_autoencoder_test.cpp       | 266 +++++++++++++++++++++
 15 files changed, 1084 insertions(+), 58 deletions(-)
 copy src/mlpack/methods/{mvu => sparse_autoencoder}/CMakeLists.txt (75%)
 create mode 100644 src/mlpack/methods/sparse_autoencoder/sparse_autoencoder.hpp
 create mode 100644 src/mlpack/methods/sparse_autoencoder/sparse_autoencoder_function.cpp
 create mode 100644 src/mlpack/methods/sparse_autoencoder/sparse_autoencoder_function.hpp
 create mode 100644 src/mlpack/methods/sparse_autoencoder/sparse_autoencoder_impl.hpp
 create mode 100644 src/mlpack/tests/sparse_autoencoder_test.cpp

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