rumale 0.23.3 → 0.24.0
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- checksums.yaml +4 -4
- data/LICENSE.txt +5 -1
- data/README.md +3 -288
- data/lib/rumale/version.rb +1 -1
- data/lib/rumale.rb +20 -131
- metadata +252 -150
- data/CHANGELOG.md +0 -643
- data/CODE_OF_CONDUCT.md +0 -74
- data/ext/rumale/extconf.rb +0 -37
- data/ext/rumale/rumaleext.c +0 -545
- data/ext/rumale/rumaleext.h +0 -12
- data/lib/rumale/base/base_estimator.rb +0 -49
- data/lib/rumale/base/classifier.rb +0 -36
- data/lib/rumale/base/cluster_analyzer.rb +0 -31
- data/lib/rumale/base/evaluator.rb +0 -17
- data/lib/rumale/base/regressor.rb +0 -36
- data/lib/rumale/base/splitter.rb +0 -21
- data/lib/rumale/base/transformer.rb +0 -22
- data/lib/rumale/clustering/dbscan.rb +0 -123
- data/lib/rumale/clustering/gaussian_mixture.rb +0 -218
- data/lib/rumale/clustering/hdbscan.rb +0 -291
- data/lib/rumale/clustering/k_means.rb +0 -122
- data/lib/rumale/clustering/k_medoids.rb +0 -141
- data/lib/rumale/clustering/mini_batch_k_means.rb +0 -139
- data/lib/rumale/clustering/power_iteration.rb +0 -127
- data/lib/rumale/clustering/single_linkage.rb +0 -203
- data/lib/rumale/clustering/snn.rb +0 -76
- data/lib/rumale/clustering/spectral_clustering.rb +0 -115
- data/lib/rumale/dataset.rb +0 -246
- data/lib/rumale/decomposition/factor_analysis.rb +0 -150
- data/lib/rumale/decomposition/fast_ica.rb +0 -188
- data/lib/rumale/decomposition/nmf.rb +0 -124
- data/lib/rumale/decomposition/pca.rb +0 -159
- data/lib/rumale/ensemble/ada_boost_classifier.rb +0 -179
- data/lib/rumale/ensemble/ada_boost_regressor.rb +0 -160
- data/lib/rumale/ensemble/extra_trees_classifier.rb +0 -139
- data/lib/rumale/ensemble/extra_trees_regressor.rb +0 -125
- data/lib/rumale/ensemble/gradient_boosting_classifier.rb +0 -306
- data/lib/rumale/ensemble/gradient_boosting_regressor.rb +0 -237
- data/lib/rumale/ensemble/random_forest_classifier.rb +0 -189
- data/lib/rumale/ensemble/random_forest_regressor.rb +0 -153
- data/lib/rumale/ensemble/stacking_classifier.rb +0 -215
- data/lib/rumale/ensemble/stacking_regressor.rb +0 -163
- data/lib/rumale/ensemble/voting_classifier.rb +0 -126
- data/lib/rumale/ensemble/voting_regressor.rb +0 -82
- data/lib/rumale/evaluation_measure/accuracy.rb +0 -29
- data/lib/rumale/evaluation_measure/adjusted_rand_score.rb +0 -74
- data/lib/rumale/evaluation_measure/calinski_harabasz_score.rb +0 -56
- data/lib/rumale/evaluation_measure/davies_bouldin_score.rb +0 -53
- data/lib/rumale/evaluation_measure/explained_variance_score.rb +0 -39
- data/lib/rumale/evaluation_measure/f_score.rb +0 -50
- data/lib/rumale/evaluation_measure/function.rb +0 -147
- data/lib/rumale/evaluation_measure/log_loss.rb +0 -45
- data/lib/rumale/evaluation_measure/mean_absolute_error.rb +0 -29
- data/lib/rumale/evaluation_measure/mean_squared_error.rb +0 -29
- data/lib/rumale/evaluation_measure/mean_squared_log_error.rb +0 -29
- data/lib/rumale/evaluation_measure/median_absolute_error.rb +0 -30
- data/lib/rumale/evaluation_measure/mutual_information.rb +0 -49
- data/lib/rumale/evaluation_measure/normalized_mutual_information.rb +0 -53
- data/lib/rumale/evaluation_measure/precision.rb +0 -50
- data/lib/rumale/evaluation_measure/precision_recall.rb +0 -96
- data/lib/rumale/evaluation_measure/purity.rb +0 -40
- data/lib/rumale/evaluation_measure/r2_score.rb +0 -43
- data/lib/rumale/evaluation_measure/recall.rb +0 -50
- data/lib/rumale/evaluation_measure/roc_auc.rb +0 -130
- data/lib/rumale/evaluation_measure/silhouette_score.rb +0 -82
- data/lib/rumale/feature_extraction/feature_hasher.rb +0 -110
- data/lib/rumale/feature_extraction/hash_vectorizer.rb +0 -155
- data/lib/rumale/feature_extraction/tfidf_transformer.rb +0 -113
- data/lib/rumale/kernel_approximation/nystroem.rb +0 -126
- data/lib/rumale/kernel_approximation/rbf.rb +0 -102
- data/lib/rumale/kernel_machine/kernel_fda.rb +0 -120
- data/lib/rumale/kernel_machine/kernel_pca.rb +0 -97
- data/lib/rumale/kernel_machine/kernel_ridge.rb +0 -82
- data/lib/rumale/kernel_machine/kernel_ridge_classifier.rb +0 -92
- data/lib/rumale/kernel_machine/kernel_svc.rb +0 -193
- data/lib/rumale/linear_model/base_sgd.rb +0 -285
- data/lib/rumale/linear_model/elastic_net.rb +0 -119
- data/lib/rumale/linear_model/lasso.rb +0 -115
- data/lib/rumale/linear_model/linear_regression.rb +0 -201
- data/lib/rumale/linear_model/logistic_regression.rb +0 -275
- data/lib/rumale/linear_model/nnls.rb +0 -137
- data/lib/rumale/linear_model/ridge.rb +0 -209
- data/lib/rumale/linear_model/svc.rb +0 -213
- data/lib/rumale/linear_model/svr.rb +0 -132
- data/lib/rumale/manifold/mds.rb +0 -155
- data/lib/rumale/manifold/tsne.rb +0 -222
- data/lib/rumale/metric_learning/fisher_discriminant_analysis.rb +0 -113
- data/lib/rumale/metric_learning/mlkr.rb +0 -161
- data/lib/rumale/metric_learning/neighbourhood_component_analysis.rb +0 -167
- data/lib/rumale/model_selection/cross_validation.rb +0 -125
- data/lib/rumale/model_selection/function.rb +0 -42
- data/lib/rumale/model_selection/grid_search_cv.rb +0 -225
- data/lib/rumale/model_selection/group_k_fold.rb +0 -93
- data/lib/rumale/model_selection/group_shuffle_split.rb +0 -115
- data/lib/rumale/model_selection/k_fold.rb +0 -81
- data/lib/rumale/model_selection/shuffle_split.rb +0 -90
- data/lib/rumale/model_selection/stratified_k_fold.rb +0 -99
- data/lib/rumale/model_selection/stratified_shuffle_split.rb +0 -118
- data/lib/rumale/model_selection/time_series_split.rb +0 -91
- data/lib/rumale/multiclass/one_vs_rest_classifier.rb +0 -83
- data/lib/rumale/naive_bayes/base_naive_bayes.rb +0 -47
- data/lib/rumale/naive_bayes/bernoulli_nb.rb +0 -82
- data/lib/rumale/naive_bayes/complement_nb.rb +0 -85
- data/lib/rumale/naive_bayes/gaussian_nb.rb +0 -69
- data/lib/rumale/naive_bayes/multinomial_nb.rb +0 -74
- data/lib/rumale/naive_bayes/negation_nb.rb +0 -71
- data/lib/rumale/nearest_neighbors/k_neighbors_classifier.rb +0 -133
- data/lib/rumale/nearest_neighbors/k_neighbors_regressor.rb +0 -108
- data/lib/rumale/nearest_neighbors/vp_tree.rb +0 -132
- data/lib/rumale/neural_network/adam.rb +0 -56
- data/lib/rumale/neural_network/base_mlp.rb +0 -248
- data/lib/rumale/neural_network/mlp_classifier.rb +0 -120
- data/lib/rumale/neural_network/mlp_regressor.rb +0 -90
- data/lib/rumale/pairwise_metric.rb +0 -152
- data/lib/rumale/pipeline/feature_union.rb +0 -69
- data/lib/rumale/pipeline/pipeline.rb +0 -175
- data/lib/rumale/preprocessing/bin_discretizer.rb +0 -93
- data/lib/rumale/preprocessing/binarizer.rb +0 -60
- data/lib/rumale/preprocessing/kernel_calculator.rb +0 -92
- data/lib/rumale/preprocessing/l1_normalizer.rb +0 -62
- data/lib/rumale/preprocessing/l2_normalizer.rb +0 -63
- data/lib/rumale/preprocessing/label_binarizer.rb +0 -89
- data/lib/rumale/preprocessing/label_encoder.rb +0 -79
- data/lib/rumale/preprocessing/max_abs_scaler.rb +0 -61
- data/lib/rumale/preprocessing/max_normalizer.rb +0 -62
- data/lib/rumale/preprocessing/min_max_scaler.rb +0 -76
- data/lib/rumale/preprocessing/one_hot_encoder.rb +0 -100
- data/lib/rumale/preprocessing/ordinal_encoder.rb +0 -109
- data/lib/rumale/preprocessing/polynomial_features.rb +0 -109
- data/lib/rumale/preprocessing/standard_scaler.rb +0 -71
- data/lib/rumale/probabilistic_output.rb +0 -114
- data/lib/rumale/tree/base_decision_tree.rb +0 -150
- data/lib/rumale/tree/decision_tree_classifier.rb +0 -150
- data/lib/rumale/tree/decision_tree_regressor.rb +0 -116
- data/lib/rumale/tree/extra_tree_classifier.rb +0 -107
- data/lib/rumale/tree/extra_tree_regressor.rb +0 -94
- data/lib/rumale/tree/gradient_tree_regressor.rb +0 -202
- data/lib/rumale/tree/node.rb +0 -39
- data/lib/rumale/utils.rb +0 -42
- data/lib/rumale/validation.rb +0 -128
- data/lib/rumale/values.rb +0 -13
data/lib/rumale/dataset.rb
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# frozen_string_literal: true
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require 'csv'
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require 'rumale/validation'
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require 'rumale/utils'
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require 'rumale/preprocessing/min_max_scaler'
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module Rumale
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# Module for loading and saving a dataset file.
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module Dataset
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class << self
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# Load a dataset with the libsvm file format into Numo::NArray.
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#
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# @param filename [String] A path to a dataset file.
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# @param n_features [Integer/Nil] The number of features of data to load.
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# If nil is given, it will be detected automatically from given file.
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# @param zero_based [Boolean] Whether the column index starts from 0 (true) or 1 (false).
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# @param dtype [Numo::NArray] Data type of Numo::NArray for features to be loaded.
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#
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# @return [Array<Numo::NArray>]
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# Returns array containing the (n_samples x n_features) matrix for feature vectors
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# and (n_samples) vector for labels or target values.
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def load_libsvm_file(filename, n_features: nil, zero_based: false, dtype: Numo::DFloat)
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ftvecs = []
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labels = []
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n_features_detected = 0
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CSV.foreach(filename, col_sep: "\s", headers: false) do |line|
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label, ftvec, max_idx = parse_libsvm_line(line, zero_based)
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labels.push(label)
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ftvecs.push(ftvec)
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n_features_detected = max_idx if n_features_detected < max_idx
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end
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n_features ||= n_features_detected
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n_features = [n_features, n_features_detected].max
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[convert_to_matrix(ftvecs, n_features, dtype), Numo::NArray.asarray(labels)]
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end
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# Dump the dataset with the libsvm file format.
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#
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# @param data [Numo::NArray] (shape: [n_samples, n_features]) matrix consisting of feature vectors.
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# @param labels [Numo::NArray] (shape: [n_samples]) matrix consisting of labels or target values.
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# @param filename [String] A path to the output libsvm file.
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# @param zero_based [Boolean] Whether the column index starts from 0 (true) or 1 (false).
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def dump_libsvm_file(data, labels, filename, zero_based: false)
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n_samples = [data.shape[0], labels.shape[0]].min
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single_label = labels.shape[1].nil?
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label_type = detect_dtype(labels)
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value_type = detect_dtype(data)
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File.open(filename, 'w') do |file|
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n_samples.times do |n|
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label = single_label ? labels[n] : labels[n, true].to_a
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file.puts(dump_libsvm_line(label, data[n, true],
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label_type, value_type, zero_based))
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end
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end
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end
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# Generate a two-dimensional data set consisting of an inner circle and an outer circle.
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#
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# @param n_samples [Integer] The number of samples.
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# @param shuffle [Boolean] The flag indicating whether to shuffle the dataset
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# @param noise [Float] The standard deviaion of gaussian noise added to the data.
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# If nil is given, no noise is added.
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# @param factor [Float] The scale factor between inner and outer circles. The interval of factor is (0, 1).
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# @param random_seed [Integer] The seed value using to initialize the random generator.
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def make_circles(n_samples, shuffle: true, noise: nil, factor: 0.8, random_seed: nil)
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Rumale::Validation.check_params_numeric(n_samples: n_samples, factor: factor)
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Rumale::Validation.check_params_boolean(shuffle: shuffle)
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Rumale::Validation.check_params_numeric_or_nil(noise: noise, random_seed: random_seed)
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raise ArgumentError, 'The number of samples must be more than 2.' if n_samples <= 1
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raise RangeError, 'The interval of factor is (0, 1).' if factor <= 0 || factor >= 1
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# initialize some variables.
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rs = random_seed
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rs ||= srand
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rng = Random.new(rs)
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n_samples_out = n_samples.fdiv(2).to_i
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n_samples_in = n_samples - n_samples_out
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# make two circles.
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linsp_out = Numo::DFloat.linspace(0, 2 * Math::PI, n_samples_out)
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linsp_in = Numo::DFloat.linspace(0, 2 * Math::PI, n_samples_in)
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circle_out = Numo::DFloat[Numo::NMath.cos(linsp_out), Numo::NMath.sin(linsp_out)].transpose
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circle_in = Numo::DFloat[Numo::NMath.cos(linsp_in), Numo::NMath.sin(linsp_in)].transpose
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x = Numo::DFloat.vstack([circle_out, factor * circle_in])
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y = Numo::Int32.hstack([Numo::Int32.zeros(n_samples_out), Numo::Int32.ones(n_samples_in)])
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# shuffle data indices.
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if shuffle
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rand_ids = Array(0...n_samples).shuffle(random: rng.dup)
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x = x[rand_ids, true].dup
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y = y[rand_ids].dup
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end
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# add gaussian noise.
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x += Rumale::Utils.rand_normal(x.shape, rng.dup, 0.0, noise) unless noise.nil?
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[x, y]
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end
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# Generate a two-dimensional data set consisting of two half circles shifted.
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#
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# @param n_samples [Integer] The number of samples.
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# @param shuffle [Boolean] The flag indicating whether to shuffle the dataset
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# @param noise [Float] The standard deviaion of gaussian noise added to the data.
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# If nil is given, no noise is added.
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# @param random_seed [Integer] The seed value using to initialize the random generator.
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def make_moons(n_samples, shuffle: true, noise: nil, random_seed: nil)
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Rumale::Validation.check_params_numeric(n_samples: n_samples)
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Rumale::Validation.check_params_boolean(shuffle: shuffle)
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Rumale::Validation.check_params_numeric_or_nil(noise: noise, random_seed: random_seed)
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raise ArgumentError, 'The number of samples must be more than 2.' if n_samples <= 1
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# initialize some variables.
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rs = random_seed
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rs ||= srand
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rng = Random.new(rs)
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n_samples_out = n_samples.fdiv(2).to_i
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n_samples_in = n_samples - n_samples_out
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# make two half circles.
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linsp_out = Numo::DFloat.linspace(0, Math::PI, n_samples_out)
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linsp_in = Numo::DFloat.linspace(0, Math::PI, n_samples_in)
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circle_out = Numo::DFloat[Numo::NMath.cos(linsp_out), Numo::NMath.sin(linsp_out)].transpose
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circle_in = Numo::DFloat[1 - Numo::NMath.cos(linsp_in), 1 - Numo::NMath.sin(linsp_in) - 0.5].transpose
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x = Numo::DFloat.vstack([circle_out, circle_in])
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y = Numo::Int32.hstack([Numo::Int32.zeros(n_samples_out), Numo::Int32.ones(n_samples_in)])
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# shuffle data indices.
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if shuffle
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rand_ids = Array(0...n_samples).shuffle(random: rng.dup)
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x = x[rand_ids, true].dup
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y = y[rand_ids].dup
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end
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# add gaussian noise.
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x += Rumale::Utils.rand_normal(x.shape, rng.dup, 0.0, noise) unless noise.nil?
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[x, y]
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end
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# Generate Gaussian blobs.
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#
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# @param n_samples [Integer] The total number of samples.
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# @param n_features [Integer] The number of features.
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# If "centers" parameter is given as a Numo::DFloat array, this parameter is ignored.
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# @param centers [Integer/Numo::DFloat/Nil] The number of cluster centroids or the fixed cluster centroids.
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# If nil is given, the number of cluster centroids is set to 3.
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# @param cluster_std [Float] The standard deviation of the clusters.
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# @param center_box [Array] The bounding box for each cluster centroids.
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# If "centers" parameter is given as a Numo::DFloat array, this parameter is ignored.
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# @param shuffle [Boolean] The flag indicating whether to shuffle the dataset
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# @param random_seed [Integer] The seed value using to initialize the random generator.
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def make_blobs(n_samples = 1000, n_features = 2,
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centers: nil, cluster_std: 1.0, center_box: [-10, 10], shuffle: true, random_seed: nil)
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Rumale::Validation.check_params_numeric(n_samples: n_samples, n_features: n_features, cluster_std: cluster_std)
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Rumale::Validation.check_params_type(Array, center_box: center_box)
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Rumale::Validation.check_params_boolean(shuffle: shuffle)
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Rumale::Validation.check_params_numeric_or_nil(random_seed: random_seed)
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# initialize rng.
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rs = random_seed
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rs ||= srand
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rng = Random.new(rs)
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# initialize centers.
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if centers.is_a?(Numo::DFloat)
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n_centers = centers.shape[0]
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n_features = centers.shape[1]
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else
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n_centers = centers.is_a?(Integer) ? centers : 3
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center_min = center_box.first
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center_max = center_box.last
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centers = Rumale::Utils.rand_uniform([n_centers, n_features], rng)
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normalizer = Rumale::Preprocessing::MinMaxScaler.new(feature_range: [center_min, center_max])
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centers = normalizer.fit_transform(centers)
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end
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# generate blobs.
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sz_cluster = [n_samples / n_centers] * n_centers
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(n_samples % n_centers).times { |n| sz_cluster[n] += 1 }
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dtype.asarray(mat)
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end
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type
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def dump_libsvm_line(label, ftvec, label_type, value_type, zero_based)
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format(label_type_str, label)
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end
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# frozen_string_literal: true
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require 'rumale/base/base_estimator'
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require 'rumale/base/transformer'
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require 'rumale/utils'
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module Rumale
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module Decomposition
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# FactorAnalysis is a class that implements fator analysis with EM algorithm.
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#
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# @example
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# require 'numo/linalg/autoloader'
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# decomposer = Rumale::Decomposition::FactorAnalysis.new(n_components: 2)
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# representaion = decomposer.fit_transform(samples)
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#
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# *Reference*
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# - Barber, D., "Bayesian Reasoning and Machine Learning," Cambridge University Press, 2012.
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class FactorAnalysis
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include Base::BaseEstimator
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include Base::Transformer
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# Returns the mean vector.
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# @return [Numo::DFloat] (shape: [n_features])
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attr_reader :mean
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# Returns the estimated noise variance for each feature.
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# @return [Numo::DFloat] (shape: [n_features])
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attr_reader :noise_variance
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# Returns the components with maximum variance.
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# @return [Numo::DFloat] (shape: [n_components, n_features])
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attr_reader :components
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# Returns the log likelihood at each iteration.
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# @return [Numo::DFloat] (shape: [n_iter])
|
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attr_reader :loglike
|
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# Return the number of iterations run for optimization
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# @return [Integer]
|
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attr_reader :n_iter
|
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|
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|
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# Create a new transformer with factor analysis.
|
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#
|
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# @param n_components [Integer] The number of components (dimensionality of latent space).
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# @param max_iter [Integer] The maximum number of iterations.
|
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|
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# @param tol [Float/Nil] The tolerance of termination criterion for EM algorithm.
|
47
|
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# If nil is given, iterate EM steps up to the maximum number of iterations.
|
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|
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def initialize(n_components: 2, max_iter: 100, tol: 1e-8)
|
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|
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check_params_numeric(n_components: n_components, max_iter: max_iter)
|
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|
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check_params_numeric_or_nil(tol: tol)
|
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|
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check_params_positive(n_components: n_components, max_iter: max_iter)
|
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|
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@params = {}
|
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|
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@params[:n_components] = n_components
|
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|
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@params[:max_iter] = max_iter
|
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|
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@params[:tol] = tol
|
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|
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@mean = nil
|
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|
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@noise_variance = nil
|
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|
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@components = nil
|
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|
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@loglike = nil
|
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|
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@n_iter = nil
|
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|
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end
|
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|
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|
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|
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# Fit the model with given training data.
|
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|
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#
|
65
|
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# @overload fit(x) -> FactorAnalysis
|
66
|
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# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for fitting the model.
|
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|
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# @return [FactorAnalysis] The learned transformer itself.
|
68
|
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def fit(x, _y = nil)
|
69
|
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raise 'FactorAnalysis#fit requires Numo::Linalg but that is not loaded.' unless enable_linalg?
|
70
|
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|
71
|
-
# initialize some variables.
|
72
|
-
n_samples, n_features = x.shape
|
73
|
-
@mean = x.mean(0)
|
74
|
-
centered_x = x - @mean
|
75
|
-
cov_mat = centered_x.transpose.dot(centered_x) / n_samples
|
76
|
-
sample_vars = x.var(0)
|
77
|
-
sqrt_n_samples = Math.sqrt(n_samples)
|
78
|
-
@noise_variance = Numo::DFloat.ones(n_features)
|
79
|
-
|
80
|
-
# run optimization.
|
81
|
-
old_loglike = 0.0
|
82
|
-
@n_iter = 0
|
83
|
-
@loglike = [] unless @params[:tol].nil?
|
84
|
-
@params[:max_iter].times do |t|
|
85
|
-
@n_iter = t + 1
|
86
|
-
sqrt_noise_variance = Numo::NMath.sqrt(@noise_variance)
|
87
|
-
scaled_x = centered_x / (sqrt_noise_variance * sqrt_n_samples + 1e-12)
|
88
|
-
s, u = truncate_svd(scaled_x, @params[:n_components])
|
89
|
-
scaler = Numo::NMath.sqrt(Numo::DFloat.maximum(s**2 - 1.0, 0.0))
|
90
|
-
@components = (sqrt_noise_variance.diag.dot(u) * scaler).transpose.dup
|
91
|
-
@noise_variance = Numo::DFloat.maximum(sample_vars - @components.transpose.dot(@components).diagonal, 1e-12)
|
92
|
-
next if @params[:tol].nil?
|
93
|
-
|
94
|
-
new_loglike = log_likelihood(cov_mat, @components, @noise_variance)
|
95
|
-
@loglike.push(new_loglike)
|
96
|
-
break if (old_loglike - new_loglike).abs <= @params[:tol]
|
97
|
-
|
98
|
-
old_loglike = new_loglike
|
99
|
-
end
|
100
|
-
|
101
|
-
@loglike = Numo::DFloat.cast(@loglike) unless @params[:tol].nil?
|
102
|
-
@components = @components[0, true].dup if @params[:n_components] == 1
|
103
|
-
self
|
104
|
-
end
|
105
|
-
|
106
|
-
# Fit the model with training data, and then transform them with the learned model.
|
107
|
-
#
|
108
|
-
# @overload fit_transform(x) -> Numo::DFloat
|
109
|
-
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for fitting the model.
|
110
|
-
# @return [Numo::DFloat] (shape: [n_samples, n_components]) The transformed data
|
111
|
-
def fit_transform(x, _y = nil)
|
112
|
-
x = check_convert_sample_array(x)
|
113
|
-
raise 'FactorAnalysis#fit_transform requires Numo::Linalg but that is not loaded.' unless enable_linalg?
|
114
|
-
|
115
|
-
fit(x).transform(x)
|
116
|
-
end
|
117
|
-
|
118
|
-
# Transform the given data with the learned model.
|
119
|
-
#
|
120
|
-
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The data to be transformed with the learned model.
|
121
|
-
# @return [Numo::DFloat] (shape: [n_samples, n_components]) The transformed data.
|
122
|
-
def transform(x)
|
123
|
-
x = check_convert_sample_array(x)
|
124
|
-
raise 'FactorAnalysis#transform requires Numo::Linalg but that is not loaded.' unless enable_linalg?
|
125
|
-
|
126
|
-
factors = @params[:n_components] == 1 ? @components.expand_dims(0) : @components
|
127
|
-
centered_x = x - @mean
|
128
|
-
beta = Numo::Linalg.inv(Numo::DFloat.eye(factors.shape[0]) + (factors / @noise_variance).dot(factors.transpose))
|
129
|
-
z = centered_x.dot((beta.dot(factors) / @noise_variance).transpose)
|
130
|
-
@params[:n_components] == 1 ? z[true, 0].dup : z
|
131
|
-
end
|
132
|
-
|
133
|
-
private
|
134
|
-
|
135
|
-
def log_likelihood(cov_mat, factors, noise_vars)
|
136
|
-
n_samples = noise_vars.size
|
137
|
-
fact_cov_mat = factors.transpose.dot(factors) + noise_vars.diag
|
138
|
-
n_samples.fdiv(2) * Math.log(Numo::Linalg.det(fact_cov_mat)) + Numo::Linalg.inv(fact_cov_mat).dot(cov_mat).trace
|
139
|
-
end
|
140
|
-
|
141
|
-
def truncate_svd(x, k)
|
142
|
-
m = x.shape[1]
|
143
|
-
eig_vals, eig_vecs = Numo::Linalg.eigh(x.transpose.dot(x), vals_range: (m - k)...m)
|
144
|
-
s = Numo::NMath.sqrt(eig_vals.reverse.dup)
|
145
|
-
u = eig_vecs.reverse(1).dup
|
146
|
-
[s, u]
|
147
|
-
end
|
148
|
-
end
|
149
|
-
end
|
150
|
-
end
|
@@ -1,188 +0,0 @@
|
|
1
|
-
# frozen_string_literal: true
|
2
|
-
|
3
|
-
require 'rumale/base/base_estimator'
|
4
|
-
require 'rumale/base/transformer'
|
5
|
-
|
6
|
-
module Rumale
|
7
|
-
module Decomposition
|
8
|
-
# FastICA is a class that implments Fast Independent Component Analaysis.
|
9
|
-
#
|
10
|
-
# @example
|
11
|
-
# require 'numo/linalg/autoloader'
|
12
|
-
#
|
13
|
-
# transformer = Rumale::Decomposition::FastICA.new(n_components: 2, random_seed: 1)
|
14
|
-
# source_data = transformer.fit_transform(observed_data)
|
15
|
-
#
|
16
|
-
# *Reference*
|
17
|
-
# - Hyvarinen, A., "Fast and Robust Fixed-Point Algorithms for Independent Component Analysis," IEEE Trans. Neural Networks, Vol. 10 (3), pp. 626--634, 1999.
|
18
|
-
# - Hyvarinen, A., and Oja, E., "Independent Component Analysis: Algorithms and Applications," Neural Networks, Vol. 13 (4-5), pp. 411--430, 2000.
|
19
|
-
class FastICA
|
20
|
-
include Base::BaseEstimator
|
21
|
-
include Base::Transformer
|
22
|
-
|
23
|
-
# Returns the unmixing matrix.
|
24
|
-
# @return [Numo::DFloat] (shape: [n_components, n_features])
|
25
|
-
attr_reader :components
|
26
|
-
|
27
|
-
# Returns the mixing matrix.
|
28
|
-
# @return [Numo::DFloat] (shape: [n_features, n_components])
|
29
|
-
attr_reader :mixing
|
30
|
-
|
31
|
-
# Returns the number of iterations when converged.
|
32
|
-
# @return [Integer]
|
33
|
-
attr_reader :n_iter
|
34
|
-
|
35
|
-
# Return the random generator.
|
36
|
-
# @return [Random]
|
37
|
-
attr_reader :rng
|
38
|
-
|
39
|
-
# Create a new transformer with FastICA.
|
40
|
-
#
|
41
|
-
# @param n_components [Integer] The number of independent components.
|
42
|
-
# @param whiten [Boolean] The flag indicating whether to perform whitening.
|
43
|
-
# @param fun [String] The type of contrast function ('logcosh', 'exp', or 'cube').
|
44
|
-
# @param alpha [Float] The parameter of contrast function for 'logcosh' and 'exp'.
|
45
|
-
# If fun = 'cube', this parameter is ignored.
|
46
|
-
# @param max_iter [Integer] The maximum number of iterations.
|
47
|
-
# @param tol [Float] The tolerance of termination criterion.
|
48
|
-
# @param random_seed [Integer] The seed value using to initialize the random generator.
|
49
|
-
def initialize(n_components: 2, whiten: true, fun: 'logcosh', alpha: 1.0, max_iter: 200, tol: 1e-4, random_seed: nil)
|
50
|
-
check_params_numeric(n_components: n_components, max_iter: max_iter, alpha: alpha, tol: tol)
|
51
|
-
check_params_boolean(whiten: whiten)
|
52
|
-
check_params_string(fun: fun)
|
53
|
-
check_params_numeric_or_nil(random_seed: random_seed)
|
54
|
-
check_params_positive(n_components: n_components, max_iter: max_iter, tol: tol)
|
55
|
-
@params = {}
|
56
|
-
@params[:n_components] = n_components
|
57
|
-
@params[:whiten] = whiten
|
58
|
-
@params[:fun] = fun
|
59
|
-
@params[:alpha] = alpha
|
60
|
-
@params[:max_iter] = max_iter
|
61
|
-
@params[:tol] = tol
|
62
|
-
@params[:random_seed] = random_seed
|
63
|
-
@params[:random_seed] ||= srand
|
64
|
-
@components = nil
|
65
|
-
@mixing = nil
|
66
|
-
@n_iter = nil
|
67
|
-
@mean = nil
|
68
|
-
@rng = Random.new(@params[:random_seed])
|
69
|
-
end
|
70
|
-
|
71
|
-
# Fit the model with given training data.
|
72
|
-
#
|
73
|
-
# @overload fit(x) -> FastICA
|
74
|
-
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for fitting the model.
|
75
|
-
# @return [FastICA] The learned transformer itself.
|
76
|
-
def fit(x, _y = nil)
|
77
|
-
x = check_convert_sample_array(x)
|
78
|
-
raise 'FastICA#fit requires Numo::Linalg but that is not loaded.' unless enable_linalg?
|
79
|
-
|
80
|
-
@mean, whiten_mat = whitening(x, @params[:n_components]) if @params[:whiten]
|
81
|
-
wx = @params[:whiten] ? (x - @mean).dot(whiten_mat.transpose) : x
|
82
|
-
unmixing, @n_iter = ica(wx, @params[:fun], @params[:max_iter], @params[:tol], @rng.dup)
|
83
|
-
@components = @params[:whiten] ? unmixing.dot(whiten_mat) : unmixing
|
84
|
-
@mixing = Numo::Linalg.pinv(@components).dup
|
85
|
-
if @params[:n_components] == 1
|
86
|
-
@components = @components.flatten.dup
|
87
|
-
@mixing = @mixing.flatten.dup
|
88
|
-
end
|
89
|
-
self
|
90
|
-
end
|
91
|
-
|
92
|
-
# Fit the model with training data, and then transform them with the learned model.
|
93
|
-
#
|
94
|
-
# @overload fit_transform(x) -> Numo::DFloat
|
95
|
-
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for fitting the model.
|
96
|
-
# @return [Numo::DFloat] (shape: [n_samples, n_components]) The transformed data
|
97
|
-
def fit_transform(x, _y = nil)
|
98
|
-
x = check_convert_sample_array(x)
|
99
|
-
raise 'FastICA#fit_transform requires Numo::Linalg but that is not loaded.' unless enable_linalg?
|
100
|
-
|
101
|
-
fit(x).transform(x)
|
102
|
-
end
|
103
|
-
|
104
|
-
# Transform the given data with the learned model.
|
105
|
-
#
|
106
|
-
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The data to be transformed with the learned model.
|
107
|
-
# @return [Numo::DFloat] (shape: [n_samples, n_components]) The transformed data.
|
108
|
-
def transform(x)
|
109
|
-
x = check_convert_sample_array(x)
|
110
|
-
cx = @params[:whiten] ? (x - @mean) : x
|
111
|
-
cx.dot(@components.transpose)
|
112
|
-
end
|
113
|
-
|
114
|
-
# Inverse transform the given transformed data with the learned model.
|
115
|
-
#
|
116
|
-
# @param z [Numo::DFloat] (shape: [n_samples, n_components]) The source data reconstructed to the mixed data.
|
117
|
-
# @return [Numo::DFloat] (shape: [n_samples, n_featuress]) The mixed data.
|
118
|
-
def inverse_transform(z)
|
119
|
-
z = check_convert_sample_array(z)
|
120
|
-
m = @mixing.shape[1].nil? ? @mixing.expand_dims(0).transpose : @mixing
|
121
|
-
x = z.dot(m.transpose)
|
122
|
-
x += @mean if @params[:whiten]
|
123
|
-
x
|
124
|
-
end
|
125
|
-
|
126
|
-
private
|
127
|
-
|
128
|
-
def whitening(x, n_components)
|
129
|
-
n_samples, n_features = x.shape
|
130
|
-
mean_vec = x.mean(0)
|
131
|
-
centered_x = x - mean_vec
|
132
|
-
covar_mat = centered_x.transpose.dot(centered_x) / n_samples
|
133
|
-
eig_vals, eig_vecs = Numo::Linalg.eigh(covar_mat, vals_range: (n_features - n_components)...n_features)
|
134
|
-
[mean_vec, (eig_vecs.reverse(1).dup * (1 / Numo::NMath.sqrt(eig_vals.reverse.dup))).transpose.dup]
|
135
|
-
end
|
136
|
-
|
137
|
-
def ica(x, fun, max_iter, tol, sub_rng)
|
138
|
-
n_samples, n_components = x.shape
|
139
|
-
w = decorrelation(Rumale::Utils.rand_normal([n_components, n_components], sub_rng))
|
140
|
-
n_iters = 0
|
141
|
-
max_iter.times do |t|
|
142
|
-
n_iters = t + 1
|
143
|
-
gx, ggx = gradient(x.dot(w.transpose), fun)
|
144
|
-
new_w = decorrelation(gx.transpose.dot(x) / n_samples - w * ggx / n_samples)
|
145
|
-
err = (new_w - w).abs.max
|
146
|
-
w = new_w
|
147
|
-
break if err <= tol
|
148
|
-
end
|
149
|
-
[w, n_iters]
|
150
|
-
end
|
151
|
-
|
152
|
-
def decorrelation(w)
|
153
|
-
eig_vals, eig_vecs = Numo::Linalg.eigh(w.dot(w.transpose))
|
154
|
-
decorr_mat = (eig_vecs * (1 / Numo::NMath.sqrt(eig_vals))).dot(eig_vecs.transpose)
|
155
|
-
decorr_mat.dot(w)
|
156
|
-
end
|
157
|
-
|
158
|
-
def gradient(x, func)
|
159
|
-
case func
|
160
|
-
when 'exp'
|
161
|
-
grad_exp(x, @params[:alpha])
|
162
|
-
when 'cube'
|
163
|
-
grad_cube(x)
|
164
|
-
else
|
165
|
-
grad_logcosh(x, @params[:alpha])
|
166
|
-
end
|
167
|
-
end
|
168
|
-
|
169
|
-
def grad_logcosh(x, alpha)
|
170
|
-
gx = Numo::NMath.tanh(alpha * x)
|
171
|
-
ggx = (alpha * (1 - gx**2)).sum(0)
|
172
|
-
[gx, ggx]
|
173
|
-
end
|
174
|
-
|
175
|
-
def grad_exp(x, alpha)
|
176
|
-
squared_x = x**2
|
177
|
-
exp_x = Numo::NMath.exp(-0.5 * alpha * squared_x)
|
178
|
-
gx = exp_x * x
|
179
|
-
ggx = (exp_x * (1 - alpha * squared_x)).sum(0)
|
180
|
-
[gx, ggx]
|
181
|
-
end
|
182
|
-
|
183
|
-
def grad_cube(x)
|
184
|
-
[x**3, (3 * x**2).sum(0)]
|
185
|
-
end
|
186
|
-
end
|
187
|
-
end
|
188
|
-
end
|