rumale 0.22.5 → 0.23.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/CHANGELOG.md +21 -0
- data/LICENSE.txt +1 -1
- data/README.md +34 -2
- data/ext/rumale/extconf.rb +1 -1
- data/ext/rumale/{tree.c → rumaleext.c} +51 -85
- data/ext/rumale/{tree.h → rumaleext.h} +5 -5
- data/lib/rumale/clustering/hdbscan.rb +28 -8
- data/lib/rumale/clustering/single_linkage.rb +23 -5
- data/lib/rumale/decomposition/fast_ica.rb +1 -1
- data/lib/rumale/ensemble/gradient_boosting_classifier.rb +2 -2
- data/lib/rumale/ensemble/gradient_boosting_regressor.rb +1 -1
- data/lib/rumale/ensemble/random_forest_classifier.rb +1 -1
- data/lib/rumale/ensemble/random_forest_regressor.rb +1 -1
- data/lib/rumale/evaluation_measure/roc_auc.rb +1 -2
- data/lib/rumale/kernel_approximation/nystroem.rb +1 -1
- data/lib/rumale/kernel_machine/kernel_svc.rb +1 -1
- data/lib/rumale/linear_model/linear_regression.rb +5 -3
- data/lib/rumale/linear_model/ridge.rb +3 -3
- data/lib/rumale/model_selection/grid_search_cv.rb +3 -3
- data/lib/rumale/naive_bayes/bernoulli_nb.rb +1 -1
- data/lib/rumale/naive_bayes/gaussian_nb.rb +1 -1
- data/lib/rumale/naive_bayes/multinomial_nb.rb +1 -1
- data/lib/rumale/nearest_neighbors/vp_tree.rb +2 -0
- data/lib/rumale/tree/base_decision_tree.rb +15 -10
- data/lib/rumale/tree/decision_tree_classifier.rb +14 -11
- data/lib/rumale/tree/decision_tree_regressor.rb +0 -1
- data/lib/rumale/tree/gradient_tree_regressor.rb +15 -11
- data/lib/rumale/version.rb +1 -1
- data/lib/rumale.rb +132 -133
- metadata +6 -17
- data/.coveralls.yml +0 -1
- data/.github/workflows/build.yml +0 -26
- data/.github/workflows/coverage.yml +0 -28
- data/.gitignore +0 -23
- data/.rspec +0 -3
- data/.rubocop.yml +0 -93
- data/.travis.yml +0 -17
- data/Gemfile +0 -17
- data/Rakefile +0 -14
- data/ext/rumale/rumale.c +0 -10
- data/ext/rumale/rumale.h +0 -8
- data/rumale.gemspec +0 -49
@@ -1,5 +1,7 @@
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# frozen_string_literal: true
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require 'lbfgsb'
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require 'rumale/linear_model/base_sgd'
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require 'rumale/base/regressor'
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@@ -58,7 +60,7 @@ module Rumale
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# @param tol [Float] The tolerance of loss for terminating optimization.
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# If solver is 'svd', this parameter is ignored.
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# @param solver [String] The algorithm to calculate weights. ('auto', 'sgd', 'svd' or 'lbfgs').
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# 'auto' chooses the 'svd' solver if Numo::Linalg is loaded. Otherwise, it chooses the '
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# 'auto' chooses the 'svd' solver if Numo::Linalg is loaded. Otherwise, it chooses the 'lbfgs' solver.
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# 'sgd' uses the stochastic gradient descent optimization.
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# 'svd' performs singular value decomposition of samples.
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# 'lbfgs' uses the L-BFGS method for optimization.
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@@ -82,9 +84,9 @@ module Rumale
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super()
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@params.merge!(method(:initialize).parameters.map { |_t, arg| [arg, binding.local_variable_get(arg)] }.to_h)
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@params[:solver] = if solver == 'auto'
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enable_linalg?(warning: false) ? 'svd' : '
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enable_linalg?(warning: false) ? 'svd' : 'lbfgs'
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else
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solver.match?(/^svd$|^sgd$|^lbfgs$/) ? solver : '
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solver.match?(/^svd$|^sgd$|^lbfgs$/) ? solver : 'lbfgs'
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end
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@params[:decay] ||= @params[:learning_rate]
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@params[:random_seed] ||= srand
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# @param tol [Float] The tolerance of loss for terminating optimization.
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# If solver is 'svd', this parameter is ignored.
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# @param solver [String] The algorithm to calculate weights. ('auto', 'sgd', 'svd', or 'lbfgs').
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# 'auto' chooses the 'svd' solver if Numo::Linalg is loaded. Otherwise, it chooses the '
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# 'auto' chooses the 'svd' solver if Numo::Linalg is loaded. Otherwise, it chooses the 'lbfgs' solver.
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# 'sgd' uses the stochastic gradient descent optimization.
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# 'svd' performs singular value decomposition of samples.
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# 'lbfgs' uses the L-BFGS method for optimization.
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@@ -87,9 +87,9 @@ module Rumale
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super()
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@params.merge!(method(:initialize).parameters.map { |_t, arg| [arg, binding.local_variable_get(arg)] }.to_h)
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@params[:solver] = if solver == 'auto'
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enable_linalg?(warning: false) ? 'svd' : '
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enable_linalg?(warning: false) ? 'svd' : 'lbfgs'
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else
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solver.match?(/^svd$|^sgd$|^lbfgs$/) ? solver : '
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solver.match?(/^svd$|^sgd$|^lbfgs$/) ? solver : 'lbfgs'
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end
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@params[:decay] ||= @params[:reg_param] * @params[:learning_rate]
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@params[:random_seed] ||= srand
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grid = [grid] if grid.is_a?(Hash)
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grid.each do |h|
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raise TypeError, 'Expect class of elements in param_grid to be Hash' unless h.is_a?(Hash)
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raise TypeError, 'Expect class of parameter values in param_grid to be Array' unless h.values.all?
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raise TypeError, 'Expect class of parameter values in param_grid to be Array' unless h.values.all?(Array)
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end
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grid
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end
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def param_combinations
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@param_combinations ||= @params[:param_grid].map do |prm|
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x =
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x[0].product(*x[1...x.size]).map
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x = prm.sort.to_h.map { |k, v| [k].product(v) }
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x[0].product(*x[1...x.size]).map(&:to_h)
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end
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end
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(Numo::DFloat[*bin_x] * Numo::NMath.log(@feature_probs[l, true])).sum(1)
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(Numo::DFloat[*not_bin_x] * Numo::NMath.log(1.0 - @feature_probs[l, true])).sum(1))
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end
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Numo::DFloat[*log_likelihoods].transpose
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Numo::DFloat[*log_likelihoods].transpose.dup
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end
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end
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end
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log_likelihoods = Array.new(n_classes) do |l|
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Math.log(@class_priors[l]) + (Numo::DFloat[*bin_x] * Numo::NMath.log(@feature_probs[l, true])).sum(1)
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end
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Numo::DFloat[*log_likelihoods].transpose
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Numo::DFloat[*log_likelihoods].transpose.dup
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end
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end
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end
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# This implementation, unlike the paper, does not perform random sampling with vantage point selection.
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# This class is used internally for k-nearest neighbor estimators.
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#
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# @deprecated This class will be removed in ver. 0.24.0. The author recommends to use the annoy-rb gem instead.
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#
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# *Reference*
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# - Yianilos, P N., "Data Structures and Algorithms for Nearest Neighbor Search in General Metric Spaces," Proc. SODA'93, pp. 311--321, 1993.
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class VPTree
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require 'rumale/base/base_estimator'
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require 'rumale/tree/node'
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require 'rumale/rumaleext'
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module Rumale
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# This module consists of the classes that implement tree models.
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# @return [Numo::Int32] (shape: [n_samples]) Leaf index for sample.
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def apply(x)
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x = check_convert_sample_array(x)
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Numo::Int32[*(Array.new(x.shape[0]) { |n|
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Numo::Int32[*(Array.new(x.shape[0]) { |n| partial_apply(@tree, x[n, true]) })]
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end
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private
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def
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def partial_apply(tree, sample)
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node = tree
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until node.leaf
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# :nocov:
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node = if node.right.nil?
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node.left
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elsif node.left.nil?
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node.right
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# :nocov:
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else
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sample[node.feature_id] <= node.threshold ? node.left : node.right
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end
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end
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node.leaf_id
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end
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def build_tree(x, y)
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# frozen_string_literal: true
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require 'rumale/rumale'
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require 'rumale/tree/base_decision_tree'
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require 'rumale/base/classifier'
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# @return [Numo::DFloat] (shape: [n_samples, n_classes]) Predicted probability of each class per sample.
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def predict_proba(x)
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x = check_convert_sample_array(x)
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Numo::DFloat[*(Array.new(x.shape[0]) { |n|
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Numo::DFloat[*(Array.new(x.shape[0]) { |n| partial_predict_proba(@tree, x[n, true]) })]
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end
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def partial_predict_proba(tree, sample)
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node = tree
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until node.leaf
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# :nocov:
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node = if node.right.nil?
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node.left
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elsif node.left.nil?
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node.right
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# :nocov:
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else
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sample[node.feature_id] <= node.threshold ? node.left : node.right
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end
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end
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node.probs
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end
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def stop_growing?(y)
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require 'rumale/rumale'
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require 'rumale/base/base_estimator'
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require 'rumale/base/regressor'
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require 'rumale/rumaleext'
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require 'rumale/tree/node'
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module Rumale
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# @return [Numo::Int32] (shape: [n_samples]) Leaf index for sample.
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def apply(x)
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x = check_convert_sample_array(x)
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Numo::Int32[*(Array.new(x.shape[0]) { |n|
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Numo::Int32[*(Array.new(x.shape[0]) { |n| partial_apply(@tree, x[n, true]) })]
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end
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def partial_apply(tree, sample)
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node = tree
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until node.leaf
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# :nocov:
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node = if node.right.nil?
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node.right
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# :nocov:
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else
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sample[node.feature_id] <= node.threshold ? node.left : node.right
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end
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end
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node.leaf_id
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end
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def build_tree(x, y, g, h)
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data/lib/rumale/version.rb
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require 'rumale/evaluation_measure/function'
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require_relative 'rumale/version'
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require_relative 'rumale/rumaleext'
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require_relative 'rumale/validation'
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require_relative 'rumale/values'
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require_relative 'rumale/utils'
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require_relative 'rumale/pairwise_metric'
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require_relative 'rumale/dataset'
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require_relative 'rumale/probabilistic_output'
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require_relative 'rumale/base/base_estimator'
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require_relative 'rumale/base/classifier'
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require_relative 'rumale/base/regressor'
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require_relative 'rumale/base/cluster_analyzer'
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require_relative 'rumale/base/transformer'
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require_relative 'rumale/base/splitter'
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require_relative 'rumale/base/evaluator'
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+
require_relative 'rumale/pipeline/pipeline'
|
21
|
+
require_relative 'rumale/pipeline/feature_union'
|
22
|
+
require_relative 'rumale/kernel_approximation/rbf'
|
23
|
+
require_relative 'rumale/kernel_approximation/nystroem'
|
24
|
+
require_relative 'rumale/linear_model/base_sgd'
|
25
|
+
require_relative 'rumale/linear_model/svc'
|
26
|
+
require_relative 'rumale/linear_model/svr'
|
27
|
+
require_relative 'rumale/linear_model/logistic_regression'
|
28
|
+
require_relative 'rumale/linear_model/linear_regression'
|
29
|
+
require_relative 'rumale/linear_model/ridge'
|
30
|
+
require_relative 'rumale/linear_model/lasso'
|
31
|
+
require_relative 'rumale/linear_model/elastic_net'
|
32
|
+
require_relative 'rumale/linear_model/nnls'
|
33
|
+
require_relative 'rumale/kernel_machine/kernel_svc'
|
34
|
+
require_relative 'rumale/kernel_machine/kernel_pca'
|
35
|
+
require_relative 'rumale/kernel_machine/kernel_fda'
|
36
|
+
require_relative 'rumale/kernel_machine/kernel_ridge'
|
37
|
+
require_relative 'rumale/kernel_machine/kernel_ridge_classifier'
|
38
|
+
require_relative 'rumale/multiclass/one_vs_rest_classifier'
|
39
|
+
require_relative 'rumale/nearest_neighbors/vp_tree'
|
40
|
+
require_relative 'rumale/nearest_neighbors/k_neighbors_classifier'
|
41
|
+
require_relative 'rumale/nearest_neighbors/k_neighbors_regressor'
|
42
|
+
require_relative 'rumale/naive_bayes/base_naive_bayes'
|
43
|
+
require_relative 'rumale/naive_bayes/bernoulli_nb'
|
44
|
+
require_relative 'rumale/naive_bayes/complement_nb'
|
45
|
+
require_relative 'rumale/naive_bayes/gaussian_nb'
|
46
|
+
require_relative 'rumale/naive_bayes/multinomial_nb'
|
47
|
+
require_relative 'rumale/naive_bayes/negation_nb'
|
48
|
+
require_relative 'rumale/tree/node'
|
49
|
+
require_relative 'rumale/tree/base_decision_tree'
|
50
|
+
require_relative 'rumale/tree/decision_tree_classifier'
|
51
|
+
require_relative 'rumale/tree/decision_tree_regressor'
|
52
|
+
require_relative 'rumale/tree/extra_tree_classifier'
|
53
|
+
require_relative 'rumale/tree/extra_tree_regressor'
|
54
|
+
require_relative 'rumale/tree/gradient_tree_regressor'
|
55
|
+
require_relative 'rumale/ensemble/ada_boost_classifier'
|
56
|
+
require_relative 'rumale/ensemble/ada_boost_regressor'
|
57
|
+
require_relative 'rumale/ensemble/gradient_boosting_classifier'
|
58
|
+
require_relative 'rumale/ensemble/gradient_boosting_regressor'
|
59
|
+
require_relative 'rumale/ensemble/random_forest_classifier'
|
60
|
+
require_relative 'rumale/ensemble/random_forest_regressor'
|
61
|
+
require_relative 'rumale/ensemble/extra_trees_classifier'
|
62
|
+
require_relative 'rumale/ensemble/extra_trees_regressor'
|
63
|
+
require_relative 'rumale/ensemble/stacking_classifier'
|
64
|
+
require_relative 'rumale/ensemble/stacking_regressor'
|
65
|
+
require_relative 'rumale/ensemble/voting_classifier'
|
66
|
+
require_relative 'rumale/ensemble/voting_regressor'
|
67
|
+
require_relative 'rumale/clustering/k_means'
|
68
|
+
require_relative 'rumale/clustering/mini_batch_k_means'
|
69
|
+
require_relative 'rumale/clustering/k_medoids'
|
70
|
+
require_relative 'rumale/clustering/gaussian_mixture'
|
71
|
+
require_relative 'rumale/clustering/dbscan'
|
72
|
+
require_relative 'rumale/clustering/hdbscan'
|
73
|
+
require_relative 'rumale/clustering/snn'
|
74
|
+
require_relative 'rumale/clustering/power_iteration'
|
75
|
+
require_relative 'rumale/clustering/spectral_clustering'
|
76
|
+
require_relative 'rumale/clustering/single_linkage'
|
77
|
+
require_relative 'rumale/decomposition/pca'
|
78
|
+
require_relative 'rumale/decomposition/nmf'
|
79
|
+
require_relative 'rumale/decomposition/factor_analysis'
|
80
|
+
require_relative 'rumale/decomposition/fast_ica'
|
81
|
+
require_relative 'rumale/manifold/tsne'
|
82
|
+
require_relative 'rumale/manifold/mds'
|
83
|
+
require_relative 'rumale/metric_learning/fisher_discriminant_analysis'
|
84
|
+
require_relative 'rumale/metric_learning/neighbourhood_component_analysis'
|
85
|
+
require_relative 'rumale/metric_learning/mlkr'
|
86
|
+
require_relative 'rumale/neural_network/adam'
|
87
|
+
require_relative 'rumale/neural_network/base_mlp'
|
88
|
+
require_relative 'rumale/neural_network/mlp_regressor'
|
89
|
+
require_relative 'rumale/neural_network/mlp_classifier'
|
90
|
+
require_relative 'rumale/feature_extraction/hash_vectorizer'
|
91
|
+
require_relative 'rumale/feature_extraction/feature_hasher'
|
92
|
+
require_relative 'rumale/feature_extraction/tfidf_transformer'
|
93
|
+
require_relative 'rumale/preprocessing/l2_normalizer'
|
94
|
+
require_relative 'rumale/preprocessing/l1_normalizer'
|
95
|
+
require_relative 'rumale/preprocessing/max_normalizer'
|
96
|
+
require_relative 'rumale/preprocessing/min_max_scaler'
|
97
|
+
require_relative 'rumale/preprocessing/max_abs_scaler'
|
98
|
+
require_relative 'rumale/preprocessing/standard_scaler'
|
99
|
+
require_relative 'rumale/preprocessing/bin_discretizer'
|
100
|
+
require_relative 'rumale/preprocessing/label_binarizer'
|
101
|
+
require_relative 'rumale/preprocessing/label_encoder'
|
102
|
+
require_relative 'rumale/preprocessing/one_hot_encoder'
|
103
|
+
require_relative 'rumale/preprocessing/ordinal_encoder'
|
104
|
+
require_relative 'rumale/preprocessing/binarizer'
|
105
|
+
require_relative 'rumale/preprocessing/polynomial_features'
|
106
|
+
require_relative 'rumale/preprocessing/kernel_calculator'
|
107
|
+
require_relative 'rumale/model_selection/k_fold'
|
108
|
+
require_relative 'rumale/model_selection/group_k_fold'
|
109
|
+
require_relative 'rumale/model_selection/stratified_k_fold'
|
110
|
+
require_relative 'rumale/model_selection/shuffle_split'
|
111
|
+
require_relative 'rumale/model_selection/group_shuffle_split'
|
112
|
+
require_relative 'rumale/model_selection/stratified_shuffle_split'
|
113
|
+
require_relative 'rumale/model_selection/time_series_split'
|
114
|
+
require_relative 'rumale/model_selection/cross_validation'
|
115
|
+
require_relative 'rumale/model_selection/grid_search_cv'
|
116
|
+
require_relative 'rumale/model_selection/function'
|
117
|
+
require_relative 'rumale/evaluation_measure/accuracy'
|
118
|
+
require_relative 'rumale/evaluation_measure/precision'
|
119
|
+
require_relative 'rumale/evaluation_measure/recall'
|
120
|
+
require_relative 'rumale/evaluation_measure/f_score'
|
121
|
+
require_relative 'rumale/evaluation_measure/roc_auc'
|
122
|
+
require_relative 'rumale/evaluation_measure/log_loss'
|
123
|
+
require_relative 'rumale/evaluation_measure/r2_score'
|
124
|
+
require_relative 'rumale/evaluation_measure/explained_variance_score'
|
125
|
+
require_relative 'rumale/evaluation_measure/mean_squared_error'
|
126
|
+
require_relative 'rumale/evaluation_measure/mean_squared_log_error'
|
127
|
+
require_relative 'rumale/evaluation_measure/mean_absolute_error'
|
128
|
+
require_relative 'rumale/evaluation_measure/median_absolute_error'
|
129
|
+
require_relative 'rumale/evaluation_measure/adjusted_rand_score'
|
130
|
+
require_relative 'rumale/evaluation_measure/purity'
|
131
|
+
require_relative 'rumale/evaluation_measure/mutual_information'
|
132
|
+
require_relative 'rumale/evaluation_measure/normalized_mutual_information'
|
133
|
+
require_relative 'rumale/evaluation_measure/silhouette_score'
|
134
|
+
require_relative 'rumale/evaluation_measure/davies_bouldin_score'
|
135
|
+
require_relative 'rumale/evaluation_measure/calinski_harabasz_score'
|
136
|
+
require_relative 'rumale/evaluation_measure/function'
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rumale
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.23.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- yoshoku
|
8
8
|
autorequire:
|
9
9
|
bindir: exe
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2022-05-17 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: numo-narray
|
@@ -57,24 +57,13 @@ extensions:
|
|
57
57
|
- ext/rumale/extconf.rb
|
58
58
|
extra_rdoc_files: []
|
59
59
|
files:
|
60
|
-
- ".coveralls.yml"
|
61
|
-
- ".github/workflows/build.yml"
|
62
|
-
- ".github/workflows/coverage.yml"
|
63
|
-
- ".gitignore"
|
64
|
-
- ".rspec"
|
65
|
-
- ".rubocop.yml"
|
66
|
-
- ".travis.yml"
|
67
60
|
- CHANGELOG.md
|
68
61
|
- CODE_OF_CONDUCT.md
|
69
|
-
- Gemfile
|
70
62
|
- LICENSE.txt
|
71
63
|
- README.md
|
72
|
-
- Rakefile
|
73
64
|
- ext/rumale/extconf.rb
|
74
|
-
- ext/rumale/
|
75
|
-
- ext/rumale/
|
76
|
-
- ext/rumale/tree.c
|
77
|
-
- ext/rumale/tree.h
|
65
|
+
- ext/rumale/rumaleext.c
|
66
|
+
- ext/rumale/rumaleext.h
|
78
67
|
- lib/rumale.rb
|
79
68
|
- lib/rumale/base/base_estimator.rb
|
80
69
|
- lib/rumale/base/classifier.rb
|
@@ -208,7 +197,6 @@ files:
|
|
208
197
|
- lib/rumale/validation.rb
|
209
198
|
- lib/rumale/values.rb
|
210
199
|
- lib/rumale/version.rb
|
211
|
-
- rumale.gemspec
|
212
200
|
homepage: https://github.com/yoshoku/rumale
|
213
201
|
licenses:
|
214
202
|
- BSD-2-Clause
|
@@ -218,6 +206,7 @@ metadata:
|
|
218
206
|
source_code_uri: https://github.com/yoshoku/rumale
|
219
207
|
documentation_uri: https://yoshoku.github.io/rumale/doc/
|
220
208
|
bug_tracker_uri: https://github.com/yoshoku/rumale/issues
|
209
|
+
rubygems_mfa_required: 'true'
|
221
210
|
post_install_message:
|
222
211
|
rdoc_options: []
|
223
212
|
require_paths:
|
@@ -233,7 +222,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
233
222
|
- !ruby/object:Gem::Version
|
234
223
|
version: '0'
|
235
224
|
requirements: []
|
236
|
-
rubygems_version: 3.2.
|
225
|
+
rubygems_version: 3.2.33
|
237
226
|
signing_key:
|
238
227
|
specification_version: 4
|
239
228
|
summary: Rumale is a machine learning library in Ruby. Rumale provides machine learning
|
data/.coveralls.yml
DELETED
@@ -1 +0,0 @@
|
|
1
|
-
service_name: github-ci
|