rumale 0.18.2 → 0.18.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,3 +1,13 @@
+# 0.18.3
+- Fix API documentation on [KNeighborsRegressor](https://yoshoku.github.io/rumale/doc/Rumale/NearestNeighbors/KNeighborsRegressor.html)
+- Refector [rbf_kernel](https://yoshoku.github.io/rumale/doc/Rumale/PairwiseMetric.html#rbf_kernel-class_method) method.
+- Delete unneeded marshal dump and load methods. The deletion work is complete.
+  - [Tree](https://yoshoku.github.io/rumale/doc/Rumale/Tree.html),
+  [Ensemble](https://yoshoku.github.io/rumale/doc/Rumale/Ensemble.html),
+  [Optimizer](https://yoshoku.github.io/rumale/doc/Rumale/Optimizer.html),
+  [OneVsRestClassifier](https://yoshoku.github.io/rumale/doc/Rumale/Multiclass/OneVsRestClassifier.html),
+  [GridSearchCV](https://yoshoku.github.io/rumale/doc/Rumale/ModelSelection/GridSearchCV.html).
+
 # 0.18.2
 - Change file composition of naive bayes classifiers.
 - Add classifier class for [ComplementNaiveBayes](https://yoshoku.github.io/rumale/doc/Rumale/NaiveBayes/ComplementNB.html).

data/lib/rumale.rb

@@ -84,7 +84,7 @@ require 'rumale/decomposition/fast_ica'
 require 'rumale/manifold/tsne'
 require 'rumale/manifold/mds'
 require 'rumale/metric_learning/fisher_discriminant_analysis'
-require 'rumale/metric_learning/neighbourhood_component_analysis.rb'
+require 'rumale/metric_learning/neighbourhood_component_analysis'
 require 'rumale/neural_network/adam'
 require 'rumale/neural_network/base_mlp'
 require 'rumale/neural_network/mlp_regressor'

data/lib/rumale/ensemble/ada_boost_classifier.rb

@@ -171,27 +171,6 @@ module Rumale
         probs /= Numo::DFloat[sum_probs].transpose
         probs
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data about AdaBoostClassifier.
-      def marshal_dump
-        { params: @params,
-          estimators: @estimators,
-          classes: @classes,
-          feature_importances: @feature_importances,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @estimators = obj[:estimators]
-        @classes = obj[:classes]
-        @feature_importances = obj[:feature_importances]
-        @rng = obj[:rng]
-        nil
-      end
     end
   end
 end

data/lib/rumale/ensemble/ada_boost_regressor.rb

@@ -153,27 +153,6 @@ module Rumale
         sum_weight = @estimator_weights.sum
         predictions / sum_weight
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data about AdaBoostRegressor.
-      def marshal_dump
-        { params: @params,
-          estimators: @estimators,
-          estimator_weights: @estimator_weights,
-          feature_importances: @feature_importances,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @estimators = obj[:estimators]
-        @estimator_weights = obj[:estimator_weights]
-        @feature_importances = obj[:feature_importances]
-        @rng = obj[:rng]
-        nil
-      end
     end
   end
 end

data/lib/rumale/ensemble/extra_trees_classifier.rb

@@ -125,18 +125,6 @@ module Rumale
         super
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about ExtraTreesClassifier.
-      def marshal_dump
-        super
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        super
-      end
-
       private
 
       def plant_tree(rnd_seed)

data/lib/rumale/ensemble/extra_trees_regressor.rb

@@ -111,18 +111,6 @@ module Rumale
         super
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about ExtraTreesRegressor.
-      def marshal_dump
-        super
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        super
-      end
-
       private
 
       def plant_tree(rnd_seed)

data/lib/rumale/ensemble/gradient_boosting_classifier.rb

@@ -185,29 +185,6 @@ module Rumale
         Numo::Int32[*leaf_ids].transpose
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about GradientBoostingClassifier.
-      def marshal_dump
-        { params: @params,
-          estimators: @estimators,
-          classes: @classes,
-          base_predictions: @base_predictions,
-          feature_importances: @feature_importances,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @estimators = obj[:estimators]
-        @classes = obj[:classes]
-        @base_predictions = obj[:base_predictions]
-        @feature_importances = obj[:feature_importances]
-        @rng = obj[:rng]
-        nil
-      end
-
       private
 
       def partial_fit(x, y, init_pred)

data/lib/rumale/ensemble/gradient_boosting_regressor.rb

@@ -149,27 +149,6 @@ module Rumale
         Numo::Int32[*leaf_ids].transpose
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about GradientBoostingRegressor.
-      def marshal_dump
-        { params: @params,
-          estimators: @estimators,
-          base_predictions: @base_predictions,
-          feature_importances: @feature_importances,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @estimators = obj[:estimators]
-        @base_predictions = obj[:base_predictions]
-        @feature_importances = obj[:feature_importances]
-        @rng = obj[:rng]
-        nil
-      end
-
       private
 
       def partial_fit(x, y, init_pred)

data/lib/rumale/ensemble/random_forest_classifier.rb

@@ -162,27 +162,6 @@ module Rumale
         Numo::Int32[*Array.new(@params[:n_estimators]) { |n| @estimators[n].apply(x) }].transpose
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about RandomForestClassifier.
-      def marshal_dump
-        { params: @params,
-          estimators: @estimators,
-          classes: @classes,
-          feature_importances: @feature_importances,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @estimators = obj[:estimators]
-        @classes = obj[:classes]
-        @feature_importances = obj[:feature_importances]
-        @rng = obj[:rng]
-        nil
-      end
-
       private
 
       def plant_tree(rnd_seed)

data/lib/rumale/ensemble/random_forest_regressor.rb

@@ -139,25 +139,6 @@ module Rumale
         Numo::Int32[*Array.new(@params[:n_estimators]) { |n| @estimators[n].apply(x) }].transpose
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about RandomForestRegressor.
-      def marshal_dump
-        { params: @params,
-          estimators: @estimators,
-          feature_importances: @feature_importances,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @estimators = obj[:estimators]
-        @feature_importances = obj[:feature_importances]
-        @rng = obj[:rng]
-        nil
-      end
-
       private
 
       def plant_tree(rnd_seed)

data/lib/rumale/model_selection/grid_search_cv.rb

@@ -152,29 +152,6 @@ module Rumale
         @best_estimator.score(x, y)
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about GridSearchCV.
-      def marshal_dump
-        { params: @params,
-          cv_results: @cv_results,
-          best_score: @best_score,
-          best_params: @best_params,
-          best_index: @best_index,
-          best_estimator: @best_estimator }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @cv_results = obj[:cv_results]
-        @best_score = obj[:best_score]
-        @best_params = obj[:best_params]
-        @best_index = obj[:best_index]
-        @best_estimator = obj[:best_estimator]
-        nil
-      end
-
       private
 
       def valid_param_grid(grid)

data/lib/rumale/multiclass/one_vs_rest_classifier.rb

@@ -78,23 +78,6 @@ module Rumale
         decision_values = decision_function(x)
         Numo::Int32.asarray(Array.new(n_samples) { |n| @classes[decision_values[n, true].max_index] })
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data about OneVsRestClassifier.
-      def marshal_dump
-        { params: @params,
-          classes: @classes,
-          estimators: @estimators.map { |e| Marshal.dump(e) } }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @classes = obj[:classes]
-        @estimators = obj[:estimators].map { |e| Marshal.load(e) }
-        nil
-      end
     end
   end
 end

data/lib/rumale/nearest_neighbors/k_neighbors_regressor.rb

@@ -21,11 +21,11 @@ module Rumale
       # Return the prototypes for the nearest neighbor regressor.
       # If the metric is 'precomputed', that returns nil.
       # If the algorithm is 'vptree', that returns Rumale::NearestNeighbors::VPTree.
-      # @return [Numo::DFloat] (shape: [n_testing_samples, n_features])
+      # @return [Numo::DFloat] (shape: [n_training_samples, n_features])
       attr_reader :prototypes
 
       # Return the values of the prototypes
-      # @return [Numo::DFloat] (shape: [n_testing_samples, n_outputs])
+      # @return [Numo::DFloat] (shape: [n_training_samples, n_outputs])
       attr_reader :values
 
       # Create a new regressor with the nearest neighbor rule.
@@ -74,9 +74,9 @@ module Rumale
 
       # Predict values for samples.
       #
-      # @param x [Numo::DFloat] (shape: [n_training_samples, n_features]) The samples to predict the values.
+      # @param x [Numo::DFloat] (shape: [n_testing_samples, n_features]) The samples to predict the values.
       #   If the metric is 'precomputed', x must be a square distance matrix (shape: [n_testing_samples, n_training_samples]).
-      # @return [Numo::DFloat] (shape: [n_training_samples, n_outputs]) Predicted values per sample.
+      # @return [Numo::DFloat] (shape: [n_testing_samples, n_outputs]) Predicted values per sample.
       def predict(x)
         x = check_convert_sample_array(x)
         if @params[:metric] == 'precomputed' && x.shape[1] != @values.shape[0]

data/lib/rumale/optimizer/ada_grad.rb

@@ -34,21 +34,6 @@ module Rumale
         @moment += gradient**2
         weight - (@params[:learning_rate] / (@moment**0.5 + 1.0e-8)) * gradient
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data.
-      def marshal_dump
-        { params: @params,
-          moment: @moment }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @moment = obj[:moment]
-        nil
-      end
     end
   end
 end

data/lib/rumale/optimizer/adam.rb

@@ -48,25 +48,6 @@ module Rumale
 
         weight - @params[:learning_rate] * nm_fst_moment / (nm_sec_moment**0.5 + 1e-8)
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data.
-      def marshal_dump
-        { params: @params,
-          fst_moment: @fst_moment,
-          sec_moment: @sec_moment,
-          iter: @iter }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @fst_moment = obj[:fst_moment]
-        @sec_moment = obj[:sec_moment]
-        @iter = obj[:iter]
-        nil
-      end
     end
   end
 end

data/lib/rumale/optimizer/nadam.rb

@@ -57,27 +57,6 @@ module Rumale
 
         weight - (@params[:learning_rate] / (nm_sec_moment**0.5 + 1e-8)) * ((1 - decay1_curr) * nm_gradient + decay1_next * nm_fst_moment)
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data.
-      def marshal_dump
-        { params: @params,
-          fst_moment: @fst_moment,
-          sec_moment: @sec_moment,
-          decay1_prod: @decay1_prod,
-          iter: @iter }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @fst_moment = obj[:fst_moment]
-        @sec_moment = obj[:sec_moment]
-        @decay1_prod = obj[:decay1_prod]
-        @iter = obj[:iter]
-        nil
-      end
     end
   end
 end

data/lib/rumale/optimizer/rmsprop.rb

@@ -42,23 +42,6 @@ module Rumale
         @update = @params[:momentum] * @update - (@params[:learning_rate] / (@moment**0.5 + 1.0e-8)) * gradient
         weight + @update
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data.
-      def marshal_dump
-        { params: @params,
-          moment: @moment,
-          update: @update }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @moment = obj[:moment]
-        @update = obj[:update]
-        nil
-      end
     end
   end
 end

data/lib/rumale/optimizer/sgd.rb

@@ -38,23 +38,6 @@ module Rumale
         @update = @params[:momentum] * @update - current_learning_rate * gradient
         weight + @update
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data.
-      def marshal_dump
-        { params: @params,
-          iter: @iter,
-          update: @update }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @iter = obj[:iter]
-        @update = obj[:update]
-        nil
-      end
     end
   end
 end

data/lib/rumale/optimizer/yellow_fin.rb

@@ -96,43 +96,6 @@ module Rumale
         @curve_mean = @params[:decay] * @curve_mean + (1 - @params[:decay]) * grad_sqr
         @distance_mean = @params[:decay] * @distance_mean + (1 - @params[:decay]) * (@grad_norm_mean / @curve_mean)
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data.
-      def marshal_dump
-        { params: @params,
-          smth_learning_rate: @smth_learning_rate,
-          smth_momentum: @smth_momentum,
-          grad_norms: @grad_norms,
-          grad_norm_min: @grad_norm_min,
-          grad_norm_max: @grad_norm_max,
-          grad_mean_sqr: @grad_mean_sqr,
-          grad_mean: @grad_mean,
-          grad_var: @grad_var,
-          grad_norm_mean: @grad_norm_mean,
-          curve_mean: @curve_mean,
-          distance_mean: @distance_mean,
-          update: @update }
-      end
-
-      # Load marshal data.
-      # @return [nis]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @smth_learning_rate = obj[:smth_learning_rate]
-        @smth_momentum = obj[:smth_momentum]
-        @grad_norms = obj[:grad_norms]
-        @grad_norm_min = obj[:grad_norm_min]
-        @grad_norm_max = obj[:grad_norm_max]
-        @grad_mean_sqr = obj[:grad_mean_sqr]
-        @grad_mean = obj[:grad_mean]
-        @grad_var = obj[:grad_var]
-        @grad_norm_mean = obj[:grad_norm_mean]
-        @curve_mean = obj[:curve_mean]
-        @distance_mean = obj[:distance_mean]
-        @update = obj[:update]
-        nil
-      end
     end
   end
 end

data/lib/rumale/pairwise_metric.rb

@@ -61,12 +61,13 @@ module Rumale
       # @param gamma [Float] The parameter of rbf kernel, if nil it is 1 / n_features.
       # @return [Numo::DFloat] (shape: [n_samples_x, n_samples_x] or [n_samples_x, n_samples_y] if y is given)
       def rbf_kernel(x, y = nil, gamma = nil)
-        y = x if y.nil?
-        gamma ||= 1.0 / x.shape[1]
+        y_not_given = y.nil?
+        y = x if y_not_given
         x = Rumale::Validation.check_convert_sample_array(x)
-        y = Rumale::Validation.check_convert_sample_array(y)
+        y = Rumale::Validation.check_convert_sample_array(y) unless y_not_given
+        gamma ||= 1.0 / x.shape[1]
         Rumale::Validation.check_params_numeric(gamma: gamma)
-        Numo::NMath.exp(-gamma * squared_error(x, y).abs)
+        Numo::NMath.exp(-gamma * squared_error(x, y))
       end
 
       # Calculate the linear kernel between x and y.

data/lib/rumale/tree/decision_tree_classifier.rb

@@ -104,29 +104,6 @@ module Rumale
         Numo::DFloat[*(Array.new(x.shape[0]) { |n| predict_proba_at_node(@tree, x[n, true]) })]
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about DecisionTreeClassifier
-      def marshal_dump
-        { params: @params,
-          classes: @classes,
-          tree: @tree,
-          feature_importances: @feature_importances,
-          leaf_labels: @leaf_labels,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @classes = obj[:classes]
-        @tree = obj[:tree]
-        @feature_importances = obj[:feature_importances]
-        @leaf_labels = obj[:leaf_labels]
-        @rng = obj[:rng]
-        nil
-      end
-
       private
 
       def predict_proba_at_node(node, sample)

data/lib/rumale/tree/decision_tree_regressor.rb

@@ -90,27 +90,6 @@ module Rumale
         @leaf_values.shape[1].nil? ? @leaf_values[apply(x)].dup : @leaf_values[apply(x), true].dup
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about DecisionTreeRegressor
-      def marshal_dump
-        { params: @params,
-          tree: @tree,
-          feature_importances: @feature_importances,
-          leaf_values: @leaf_values,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @tree = obj[:tree]
-        @feature_importances = obj[:feature_importances]
-        @leaf_values = obj[:leaf_values]
-        @rng = obj[:rng]
-        nil
-      end
-
       private
 
       def stop_growing?(y)

data/lib/rumale/tree/extra_tree_classifier.rb

@@ -89,18 +89,6 @@ module Rumale
         super
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about ExtraTreeClassifier
-      def marshal_dump
-        super
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        super
-      end
-
       private
 
       def best_split(features, y, whole_impurity)

data/lib/rumale/tree/extra_tree_regressor.rb

@@ -76,18 +76,6 @@ module Rumale
         super
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about ExtraTreeRegressor
-      def marshal_dump
-        super
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        super
-      end
-
       private
 
       def best_split(features, y, whole_impurity)

data/lib/rumale/tree/gradient_tree_regressor.rb

@@ -118,27 +118,6 @@ module Rumale
         Numo::Int32[*(Array.new(x.shape[0]) { |n| apply_at_node(@tree, x[n, true]) })]
       end
 
-      # Dump marshal data.
-      # @return [Hash] The marshal data about DecisionTreeRegressor
-      def marshal_dump
-        { params: @params,
-          tree: @tree,
-          feature_importances: @feature_importances,
-          leaf_weights: @leaf_weights,
-          rng: @rng }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @params = obj[:params]
-        @tree = obj[:tree]
-        @feature_importances = obj[:feature_importances]
-        @leaf_weights = obj[:leaf_weights]
-        @rng = obj[:rng]
-        nil
-      end
-
       private
 
       def apply_at_node(node, sample)

data/lib/rumale/tree/node.rb

@@ -34,37 +34,6 @@ module Rumale
         @feature_id = feature_id
         @threshold = threshold
       end
-
-      # Dump marshal data.
-      # @return [Hash] The marshal data about Node
-      def marshal_dump
-        { depth: @depth,
-          impurity: @impurity,
-          n_samples: @n_samples,
-          probs: @probs,
-          leaf: @leaf,
-          leaf_id: @leaf_id,
-          left: @left,
-          right: @right,
-          feature_id: @feature_id,
-          threshold: @threshold }
-      end
-
-      # Load marshal data.
-      # @return [nil]
-      def marshal_load(obj)
-        @depth = obj[:depth]
-        @impurity = obj[:impurity]
-        @n_samples = obj[:n_samples]
-        @probs = obj[:probs]
-        @leaf = obj[:leaf]
-        @leaf_id = obj[:leaf_id]
-        @left = obj[:left]
-        @right = obj[:right]
-        @feature_id = obj[:feature_id]
-        @threshold = obj[:threshold]
-        nil
-      end
     end
   end
 end

data/lib/rumale/version.rb

@@ -3,5 +3,5 @@
 # Rumale is a machine learning library in Ruby.
 module Rumale
   # The version of Rumale you are using.
-  VERSION = '0.18.2'
+  VERSION = '0.18.3'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rumale
 version: !ruby/object:Gem::Version
-  version: 0.18.2
+  version: 0.18.3
 platform: ruby
 authors:
 - yoshoku
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-03-21 00:00:00.000000000 Z
+date: 2020-04-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray