[mlpack] 03/06: Merge tag 'upstream/1.0.9'
Barak A. Pearlmutter
barak+git at cs.nuim.ie
Sun Aug 17 08:21:49 UTC 2014
This is an automated email from the git hooks/post-receive script.
bap pushed a commit to branch master
in repository mlpack.
commit 49c1d57d8ba556c6708442353c02162f66174197
Merge: 05c1219 7dab9ac
Author: Barak A. Pearlmutter <barak+git at cs.nuim.ie>
Date: Sun Aug 17 08:19:36 2014 +0200
Merge tag 'upstream/1.0.9'
Upstream version 1.0.9
CMake/GenerateDoxyfile.cmake | 9 +-
CMake/exec2man.sh | 4 +-
CMakeLists.txt | 38 +-
COPYRIGHT.txt | 9 +
Doxyfile | 5 +-
HISTORY.txt | 54 +
README.txt | 2 +-
doc/guide/build.hpp | 7 +-
doc/guide/iodoc.hpp | 4 +-
doc/guide/version.hpp | 2 +-
doc/tutorials/emst/emst.txt | 24 +-
doc/tutorials/neighbor_search/neighbor_search.txt | 8 +-
doc/tutorials/range_search/range_search.txt | 32 +-
src/mlpack/CMakeLists.txt | 7 +-
src/mlpack/core.hpp | 59 +-
src/mlpack/core/data/load.hpp | 2 +-
src/mlpack/core/data/load_impl.hpp | 13 +-
src/mlpack/core/data/normalize_labels.hpp | 4 +-
src/mlpack/core/data/normalize_labels_impl.hpp | 5 +-
src/mlpack/core/data/save.hpp | 2 +-
src/mlpack/core/data/save_impl.hpp | 14 +-
src/mlpack/core/dists/CMakeLists.txt | 2 +
src/mlpack/core/dists/discrete_distribution.cpp | 10 +-
src/mlpack/core/dists/discrete_distribution.hpp | 2 +-
src/mlpack/core/dists/gaussian_distribution.cpp | 13 +-
src/mlpack/core/dists/gaussian_distribution.hpp | 20 +-
src/mlpack/core/dists/laplace_distribution.cpp | 106 +
src/mlpack/core/dists/laplace_distribution.hpp | 161 +
src/mlpack/core/kernels/cosine_distance.hpp | 12 +-
src/mlpack/core/kernels/cosine_distance_impl.hpp | 2 +-
src/mlpack/core/kernels/epanechnikov_kernel.cpp | 13 +-
src/mlpack/core/kernels/epanechnikov_kernel.hpp | 7 +-
.../core/kernels/epanechnikov_kernel_impl.hpp | 4 +-
src/mlpack/core/kernels/example_kernel.hpp | 20 +-
src/mlpack/core/kernels/gaussian_kernel.hpp | 17 +-
.../core/kernels/hyperbolic_tangent_kernel.hpp | 12 +-
src/mlpack/core/kernels/kernel_traits.hpp | 2 +-
src/mlpack/core/kernels/laplacian_kernel.hpp | 11 +-
src/mlpack/core/kernels/linear_kernel.hpp | 10 +-
src/mlpack/core/kernels/polynomial_kernel.hpp | 12 +-
.../core/kernels/pspectrum_string_kernel.cpp | 2 +-
.../core/kernels/pspectrum_string_kernel.hpp | 16 +-
.../core/kernels/pspectrum_string_kernel_impl.hpp | 3 +-
src/mlpack/core/kernels/spherical_kernel.hpp | 11 +-
src/mlpack/core/kernels/triangular_kernel.hpp | 11 +-
src/mlpack/core/math/clamp.hpp | 2 +-
src/mlpack/core/math/lin_alg.cpp | 7 +-
src/mlpack/core/math/lin_alg.hpp | 6 +-
src/mlpack/core/math/random.cpp | 2 +-
src/mlpack/core/math/random.hpp | 7 +-
src/mlpack/core/math/range.hpp | 2 +-
src/mlpack/core/math/range_impl.hpp | 3 +-
src/mlpack/core/math/round.hpp | 2 +-
src/mlpack/core/metrics/ip_metric.hpp | 7 +-
src/mlpack/core/metrics/ip_metric_impl.hpp | 13 +-
src/mlpack/core/metrics/lmetric.hpp | 6 +-
src/mlpack/core/metrics/lmetric_impl.hpp | 13 +-
src/mlpack/core/metrics/mahalanobis_distance.hpp | 12 +-
.../core/metrics/mahalanobis_distance_impl.hpp | 27 +-
src/mlpack/core/optimizers/CMakeLists.txt | 2 +
.../optimizers/aug_lagrangian/aug_lagrangian.hpp | 6 +-
.../aug_lagrangian/aug_lagrangian_function.hpp | 6 +-
.../aug_lagrangian_function_impl.hpp | 15 +-
.../aug_lagrangian/aug_lagrangian_impl.hpp | 16 +-
.../aug_lagrangian_test_functions.cpp | 10 +-
.../aug_lagrangian_test_functions.hpp | 5 +-
src/mlpack/core/optimizers/lbfgs/lbfgs.hpp | 6 +-
src/mlpack/core/optimizers/lbfgs/lbfgs_impl.hpp | 23 +-
.../core/optimizers/lbfgs/test_functions.cpp | 2 +-
.../core/optimizers/lbfgs/test_functions.hpp | 2 +-
src/mlpack/core/optimizers/lrsdp/CMakeLists.txt | 13 +
src/mlpack/core/optimizers/lrsdp/lrsdp.cpp | 50 +
src/mlpack/core/optimizers/lrsdp/lrsdp.hpp | 95 +-
.../lrsdp/{lrsdp_impl.hpp => lrsdp_function.cpp} | 96 +-
.../lrsdp/{lrsdp.hpp => lrsdp_function.hpp} | 89 +-
src/mlpack/core/optimizers/sa/CMakeLists.txt | 12 +
.../core/optimizers/sa/exponential_schedule.hpp | 79 +
src/mlpack/core/optimizers/sa/sa.hpp | 240 +
src/mlpack/core/optimizers/sa/sa_impl.hpp | 244 +
src/mlpack/core/optimizers/sgd/sgd.hpp | 7 +-
src/mlpack/core/optimizers/sgd/sgd_impl.hpp | 18 +-
src/mlpack/core/optimizers/sgd/test_function.cpp | 2 +-
src/mlpack/core/optimizers/sgd/test_function.hpp | 2 +-
src/mlpack/core/tree/CMakeLists.txt | 10 +-
src/mlpack/core/tree/TREE_EXPLANATION.txt | 101 +
src/mlpack/core/tree/ballbound.hpp | 91 +-
src/mlpack/core/tree/ballbound_impl.hpp | 189 +-
src/mlpack/core/tree/binary_space_tree.hpp | 4 +-
.../tree/binary_space_tree/binary_space_tree.hpp | 113 +-
.../binary_space_tree/binary_space_tree_impl.hpp | 491 +-
.../tree/binary_space_tree/dual_tree_traverser.hpp | 18 +-
.../binary_space_tree/dual_tree_traverser_impl.hpp | 121 +-
.../core/tree/binary_space_tree/mean_split.hpp | 133 +
.../tree/binary_space_tree/mean_split_impl.hpp | 210 +
.../binary_space_tree/single_tree_traverser.hpp | 10 +-
.../single_tree_traverser_impl.hpp | 119 +-
src/mlpack/core/tree/binary_space_tree/traits.hpp | 13 +-
src/mlpack/core/tree/bounds.hpp | 3 +-
src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 440 +
src/mlpack/core/tree/cosine_tree/cosine_tree.hpp | 279 +-
.../core/tree/cosine_tree/cosine_tree_builder.hpp | 123 -
.../tree/cosine_tree/cosine_tree_builder_impl.hpp | 187 -
.../core/tree/cosine_tree/cosine_tree_impl.hpp | 123 -
src/mlpack/core/tree/cover_tree.hpp | 4 +-
src/mlpack/core/tree/cover_tree/cover_tree.hpp | 6 +-
.../core/tree/cover_tree/cover_tree_impl.hpp | 7 +-
.../core/tree/cover_tree/dual_tree_traverser.hpp | 53 +-
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.../core/tree/cover_tree/first_point_is_root.hpp | 2 +-
.../core/tree/cover_tree/single_tree_traverser.hpp | 2 +-
.../tree/cover_tree/single_tree_traverser_impl.hpp | 2 +-
src/mlpack/core/tree/cover_tree/traits.hpp | 14 +-
src/mlpack/core/tree/example_tree.hpp | 250 +
src/mlpack/core/tree/hrectbound.hpp | 22 +-
src/mlpack/core/tree/hrectbound_impl.hpp | 46 +-
src/mlpack/core/tree/mrkd_statistic.cpp | 2 +-
src/mlpack/core/tree/mrkd_statistic.hpp | 2 +-
src/mlpack/core/tree/mrkd_statistic_impl.hpp | 2 +-
src/mlpack/core/tree/periodichrectbound.hpp | 165 -
src/mlpack/core/tree/periodichrectbound_impl.hpp | 600 -
src/mlpack/core/tree/rectangle_tree.hpp | 41 +
src/mlpack/core/tree/statistic.hpp | 2 +-
src/mlpack/core/tree/traversal_info.hpp | 100 +
src/mlpack/core/tree/tree_traits.hpp | 23 +-
src/mlpack/core/util/arma_traits.hpp | 104 +
src/mlpack/core/util/cli.cpp | 2 +-
src/mlpack/core/util/cli.hpp | 2 +-
src/mlpack/core/util/cli_deleter.cpp | 2 +-
src/mlpack/core/util/cli_deleter.hpp | 2 +-
src/mlpack/core/util/cli_impl.hpp | 2 +-
src/mlpack/core/util/log.cpp | 2 +-
src/mlpack/core/util/log.hpp | 6 +-
src/mlpack/core/util/nulloutstream.hpp | 49 +-
src/mlpack/core/util/option.cpp | 2 +-
src/mlpack/core/util/option.hpp | 6 +-
src/mlpack/core/util/option_impl.hpp | 6 +-
src/mlpack/core/util/prefixedoutstream.cpp | 2 +-
src/mlpack/core/util/prefixedoutstream.hpp | 6 +-
src/mlpack/core/util/prefixedoutstream_impl.hpp | 6 +-
src/mlpack/core/util/save_restore_utility.cpp | 8 +-
src/mlpack/core/util/save_restore_utility.hpp | 8 +-
src/mlpack/core/util/save_restore_utility_impl.hpp | 7 +-
src/mlpack/core/util/sfinae_utility.hpp | 2 +-
src/mlpack/core/util/string_util.cpp | 29 +-
src/mlpack/core/util/string_util.hpp | 6 +-
src/mlpack/core/util/timers.cpp | 2 +-
src/mlpack/core/util/timers.hpp | 2 +-
src/mlpack/core/util/version.cpp | 2 +-
src/mlpack/core/util/version.hpp | 4 +-
src/mlpack/methods/CMakeLists.txt | 8 +
src/mlpack/methods/{cf => amf}/CMakeLists.txt | 14 +-
src/mlpack/methods/amf/amf.hpp | 147 +
src/mlpack/methods/amf/amf_impl.hpp | 85 +
.../methods/{nmf/nmf_main.cpp => amf/amf_main.cpp} | 73 +-
.../methods/{cf => amf/init_rules}/CMakeLists.txt | 12 +-
.../{nmf => amf/init_rules}/random_acol_init.hpp | 10 +-
.../{nmf => amf/init_rules}/random_init.hpp | 10 +-
.../termination_policies}/CMakeLists.txt | 15 +-
.../complete_incremental_termination.hpp | 88 +
.../incomplete_incremental_termination.hpp | 76 +
.../simple_residue_termination.hpp | 89 +
.../simple_tolerance_termination.hpp | 148 +
.../validation_RMSE_termination.hpp | 174 +
.../{cf => amf/update_rules}/CMakeLists.txt | 16 +-
.../update_rules/nmf_als.hpp} | 71 +-
.../update_rules/nmf_mult_dist.hpp} | 71 +-
.../update_rules/nmf_mult_div.hpp} | 68 +-
.../amf/update_rules/svd_batch_learning.hpp | 211 +
.../svd_complete_incremental_learning.hpp | 236 +
.../svd_incomplete_incremental_learning.hpp | 162 +
src/mlpack/methods/cf/CMakeLists.txt | 2 +-
src/mlpack/methods/cf/cf.hpp | 145 +-
src/mlpack/methods/cf/{cf.cpp => cf_impl.hpp} | 181 +-
src/mlpack/methods/cf/cf_main.cpp | 16 +-
.../{kernel_pca => decision_stump}/CMakeLists.txt | 17 +-
.../methods/decision_stump/decision_stump.hpp | 176 +
.../methods/decision_stump/decision_stump_impl.hpp | 444 +
.../methods/decision_stump/decision_stump_main.cpp | 127 +
src/mlpack/methods/det/det_main.cpp | 6 +-
src/mlpack/methods/det/dt_utils.cpp | 13 +-
src/mlpack/methods/det/dt_utils.hpp | 2 +-
src/mlpack/methods/det/dtree.cpp | 25 +-
src/mlpack/methods/det/dtree.hpp | 8 +-
src/mlpack/methods/emst/dtb.hpp | 13 +-
src/mlpack/methods/emst/dtb_impl.hpp | 163 +-
src/mlpack/methods/emst/dtb_rules.hpp | 30 +-
src/mlpack/methods/emst/dtb_rules_impl.hpp | 13 +-
src/mlpack/methods/emst/dtb_stat.hpp | 16 +-
src/mlpack/methods/emst/edge_pair.hpp | 2 +-
src/mlpack/methods/emst/emst_main.cpp | 38 +-
src/mlpack/methods/emst/union_find.hpp | 5 +-
src/mlpack/methods/fastmks/fastmks.hpp | 7 +-
src/mlpack/methods/fastmks/fastmks_impl.hpp | 16 +-
src/mlpack/methods/fastmks/fastmks_main.cpp | 9 +-
src/mlpack/methods/fastmks/fastmks_rules.hpp | 11 +-
src/mlpack/methods/fastmks/fastmks_rules_impl.hpp | 194 +-
src/mlpack/methods/fastmks/fastmks_stat.hpp | 2 +-
src/mlpack/methods/gmm/diagonal_constraint.hpp | 2 +-
.../methods/gmm/eigenvalue_ratio_constraint.hpp | 2 +-
src/mlpack/methods/gmm/em_fit.hpp | 2 +-
src/mlpack/methods/gmm/em_fit_impl.hpp | 2 +-
src/mlpack/methods/gmm/gmm.hpp | 27 +-
src/mlpack/methods/gmm/gmm_impl.hpp | 88 +-
src/mlpack/methods/gmm/gmm_main.cpp | 2 +-
src/mlpack/methods/gmm/no_constraint.hpp | 2 +-
src/mlpack/methods/gmm/phi.hpp | 2 +-
.../methods/gmm/positive_definite_constraint.hpp | 9 +-
src/mlpack/methods/hmm/hmm.hpp | 35 +-
src/mlpack/methods/hmm/hmm_generate_main.cpp | 2 +-
src/mlpack/methods/hmm/hmm_impl.hpp | 70 +-
src/mlpack/methods/hmm/hmm_loglik_main.cpp | 2 +-
src/mlpack/methods/hmm/hmm_train_main.cpp | 2 +-
src/mlpack/methods/hmm/hmm_util.hpp | 2 +-
src/mlpack/methods/hmm/hmm_util_impl.hpp | 2 +-
src/mlpack/methods/hmm/hmm_viterbi_main.cpp | 2 +-
src/mlpack/methods/kernel_pca/CMakeLists.txt | 2 +
src/mlpack/methods/kernel_pca/kernel_pca.hpp | 37 +-
src/mlpack/methods/kernel_pca/kernel_pca_impl.hpp | 105 +-
src/mlpack/methods/kernel_pca/kernel_pca_main.cpp | 104 +-
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.../kernel_pca/kernel_rules/nystroem_method.hpp | 86 +
src/mlpack/methods/kmeans/allow_empty_clusters.hpp | 2 +-
src/mlpack/methods/kmeans/kmeans.hpp | 15 +-
src/mlpack/methods/kmeans/kmeans_impl.hpp | 452 +-
src/mlpack/methods/kmeans/kmeans_main.cpp | 28 +-
.../methods/kmeans/max_variance_new_cluster.hpp | 2 +-
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src/mlpack/methods/kmeans/random_partition.hpp | 2 +-
src/mlpack/methods/kmeans/refined_start.hpp | 2 +-
src/mlpack/methods/kmeans/refined_start_impl.hpp | 2 +-
src/mlpack/methods/lars/lars.cpp | 105 +-
src/mlpack/methods/lars/lars.hpp | 25 +-
src/mlpack/methods/lars/lars_main.cpp | 2 +-
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src/mlpack/methods/local_coordinate_coding/lcc.hpp | 5 +-
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.../logistic_regression/logistic_regression.hpp | 5 +-
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.../logistic_regression_main.cpp | 16 +-
src/mlpack/methods/lsh/lsh_main.cpp | 2 +-
src/mlpack/methods/lsh/lsh_search.hpp | 6 +-
src/mlpack/methods/lsh/lsh_search_impl.hpp | 24 +-
src/mlpack/methods/{cf => mvu}/CMakeLists.txt | 14 +-
src/mlpack/methods/mvu/mvu.cpp | 122 +
src/mlpack/methods/mvu/mvu.hpp | 58 +
src/mlpack/methods/mvu/mvu_main.cpp | 86 +
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src/mlpack/methods/naive_bayes/nbc_main.cpp | 34 +-
src/mlpack/methods/nca/nca.hpp | 5 +-
src/mlpack/methods/nca/nca_impl.hpp | 15 +-
src/mlpack/methods/nca/nca_main.cpp | 2 +-
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src/mlpack/methods/neighbor_search/CMakeLists.txt | 1 +
src/mlpack/methods/neighbor_search/allkfn_main.cpp | 2 +-
src/mlpack/methods/neighbor_search/allknn_main.cpp | 12 +-
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src/mlpack/methods/neighbor_search/typedef.hpp | 2 +-
src/mlpack/methods/neighbor_search/unmap.cpp | 2 +-
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src/mlpack/methods/nmf/CMakeLists.txt | 21 -
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src/mlpack/methods/nmf/nmf_main.cpp | 39 +-
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src/mlpack/methods/pca/pca_main.cpp | 2 +-
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src/mlpack/methods/perceptron/perceptron.hpp | 109 +
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src/mlpack/methods/perceptron/perceptron_main.cpp | 139 +
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src/mlpack/methods/rann/allkrann_main.cpp | 2 +-
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src/mlpack/methods/rann/ra_search.hpp | 67 +-
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src/mlpack/methods/rann/ra_search_rules.hpp | 38 +-
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src/mlpack/tests/allkfn_test.cpp | 609 +-
src/mlpack/tests/allknn_test.cpp | 637 +-
src/mlpack/tests/allkrann_search_test.cpp | 147 +-
src/mlpack/tests/arma_extend_test.cpp | 1 +
src/mlpack/tests/aug_lagrangian_test.cpp | 3 +-
src/mlpack/tests/cf_test.cpp | 34 +-
src/mlpack/tests/cli_test.cpp | 2 +-
src/mlpack/tests/cosine_tree_test.cpp | 201 +
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src/mlpack/tests/data/german.csv | 1000 +
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src/mlpack/tests/data/lars_dependent_x.csv | 200 +
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src/mlpack/tests/decision_stump_test.cpp | 325 +
src/mlpack/tests/det_test.cpp | 4 +-
src/mlpack/tests/distribution_test.cpp | 2 +-
src/mlpack/tests/emst_test.cpp | 212 +-
src/mlpack/tests/fastmks_test.cpp | 2 +-
src/mlpack/tests/gmm_test.cpp | 2 +-
src/mlpack/tests/hmm_test.cpp | 88 +-
src/mlpack/tests/kernel_pca_test.cpp | 72 +-
src/mlpack/tests/kernel_test.cpp | 2 +-
src/mlpack/tests/kernel_traits_test.cpp | 2 +-
src/mlpack/tests/kmeans_test.cpp | 2 +-
src/mlpack/tests/lars_test.cpp | 58 +-
src/mlpack/tests/lbfgs_test.cpp | 2 +-
src/mlpack/tests/lin_alg_test.cpp | 2 +-
src/mlpack/tests/linear_regression_test.cpp | 2 +-
src/mlpack/tests/load_save_test.cpp | 2 +-
src/mlpack/tests/local_coordinate_coding_test.cpp | 6 +-
src/mlpack/tests/logistic_regression_test.cpp | 2 +-
src/mlpack/tests/lrsdp_test.cpp | 2 +-
src/mlpack/tests/lsh_test.cpp | 2 +-
src/mlpack/tests/math_test.cpp | 2 +-
src/mlpack/tests/metric_test.cpp | 2 +-
src/mlpack/tests/mlpack_test.cpp | 2 +-
src/mlpack/tests/nbc_test.cpp | 57 +-
src/mlpack/tests/nca_test.cpp | 2 +-
src/mlpack/tests/nmf_test.cpp | 282 +-
src/mlpack/tests/nystroem_method_test.cpp | 197 +
src/mlpack/tests/old_boost_test_definitions.hpp | 2 +-
src/mlpack/tests/pca_test.cpp | 2 +-
src/mlpack/tests/perceptron_test.cpp | 184 +
src/mlpack/tests/quic_svd_test.cpp | 57 +
src/mlpack/tests/radical_test.cpp | 5 +-
src/mlpack/tests/range_search_test.cpp | 773 +-
src/mlpack/tests/regularized_svd_test.cpp | 255 +
src/mlpack/tests/sa_test.cpp | 132 +
src/mlpack/tests/save_restore_utility_test.cpp | 2 +-
src/mlpack/tests/sgd_test.cpp | 7 +-
src/mlpack/tests/sort_policy_test.cpp | 30 +-
src/mlpack/tests/sparse_autoencoder_test.cpp | 281 +
src/mlpack/tests/sparse_coding_test.cpp | 2 +-
src/mlpack/tests/svd_batch_test.cpp | 190 +
src/mlpack/tests/svd_incremental_test.cpp | 134 +
src/mlpack/tests/to_string_test.cpp | 516 +
src/mlpack/tests/tree_test.cpp | 903 +-
src/mlpack/tests/tree_traits_test.cpp | 19 +-
src/mlpack/tests/union_find_test.cpp | 2 +-
398 files changed, 117872 insertions(+), 106256 deletions(-)
--
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