rumale 0.18.6 → 0.19.3

data/lib/rumale/kernel_approximation/nystroem.rb

@@ -69,7 +69,7 @@ module Rumale
         n_components = [1, [@params[:n_components], n_samples].min].max
 
         # random sampling.
-        @component_indices = Numo::Int32.cast([*0...n_samples].shuffle(random: sub_rng)[0...n_components])
+        @component_indices = Numo::Int32.cast(Array(0...n_samples).shuffle(random: sub_rng)[0...n_components])
         @components = x[@component_indices, true]
 
         # calculate normalizing factor.

data/lib/rumale/kernel_machine/kernel_ridge.rb

@@ -30,6 +30,7 @@ module Rumale
       def initialize(reg_param: 1.0)
         raise TypeError, 'Expect class of reg_param to be Float or Numo::DFloat' unless reg_param.is_a?(Float) || reg_param.is_a?(Numo::DFloat)
         raise ArgumentError, 'Expect reg_param array to be 1-D arrray' if reg_param.is_a?(Numo::DFloat) && reg_param.shape.size != 1
+
         @params = {}
         @params[:reg_param] = reg_param
         @weight_vec = nil
@@ -55,6 +56,7 @@ module Rumale
           @weight_vec = Numo::Linalg.solve(reg_kernel_mat, y, driver: 'sym')
         else
           raise ArgumentError, 'Expect y and reg_param to have the same number of elements.' unless y.shape[1] == @params[:reg_param].shape[0]
+
           n_outputs = y.shape[1]
           @weight_vec = Numo::DFloat.zeros(n_samples, n_outputs)
           n_outputs.times do |n|

data/lib/rumale/kernel_machine/kernel_svc.rb

@@ -172,7 +172,7 @@ module Rumale
         # Start optimization.
         @params[:max_iter].times do |t|
           # random sampling
-          rand_ids = [*0...n_training_samples].shuffle(random: sub_rng) if rand_ids.empty?
+          rand_ids = Array(0...n_training_samples).shuffle(random: sub_rng) if rand_ids.empty?
           target_id = rand_ids.shift
           # update the weight vector
           func = (weight_vec * bin_y).dot(x[target_id, true].transpose).to_f

data/lib/rumale/linear_model/base_linear_model.rb

@@ -8,6 +8,7 @@ module Rumale
     # @note
     #   In version 0.17.0, a new linear model abstract class called BaseSGD is introduced.
     #   BaseLienarModel is deprecated and will be removed in the future.
+    # @deprecated Use BaseSGD class instead. This class will be deleted in version 0.20.0.
     #
     # BaseLinearModel is an abstract class for implementation of linear estimator
     # with mini-batch stochastic gradient descent optimization.
@@ -55,7 +56,7 @@ module Rumale
         samples = @params[:fit_bias] ? expand_feature(x) : x
         # Initialize some variables.
         n_samples, n_features = samples.shape
-        rand_ids = [*0...n_samples].shuffle(random: @rng.dup)
+        rand_ids = Array(0...n_samples).shuffle(random: @rng.dup)
         weight = Numo::DFloat.zeros(n_features)
         optimizer = @params[:optimizer].dup
         # Optimization.
@@ -68,6 +69,7 @@ module Rumale
           # Update weight.
           loss_gradient = calc_loss_gradient(sub_samples, sub_targets, weight)
           next if loss_gradient.ne(0.0).count.zero?
+
           weight = calc_new_weight(optimizer, sub_samples, weight, loss_gradient)
         end
         split_weight(weight)

data/lib/rumale/linear_model/base_sgd.rb

@@ -209,7 +209,7 @@ module Rumale
         l1_penalty = LinearModel::Penalty::L1Penalty.new(reg_param: l1_reg_param) if apply_l1_penalty?
         # Optimization.
         @params[:max_iter].times do |t|
-          sample_ids = [*0...n_samples]
+          sample_ids = Array(0...n_samples)
           sample_ids.shuffle!(random: sub_rng)
           until (subset_ids = sample_ids.shift(@params[:batch_size])).empty?
             # sampling

data/lib/rumale/linear_model/linear_regression.rb

@@ -162,6 +162,7 @@ module Rumale
       def load_linalg?
         return false if defined?(Numo::Linalg).nil?
         return false if Numo::Linalg::VERSION < '0.1.4'
+
         true
       end
     end

data/lib/rumale/linear_model/ridge.rb

@@ -164,6 +164,7 @@ module Rumale
       def load_linalg?
         return false if defined?(Numo::Linalg).nil?
         return false if Numo::Linalg::VERSION < '0.1.4'
+
         true
       end
     end

data/lib/rumale/manifold/mds.rb

@@ -83,6 +83,7 @@ module Rumale
       def fit(x, _not_used = nil)
         x = check_convert_sample_array(x)
         raise ArgumentError, 'Expect the input distance matrix to be square.' if @params[:metric] == 'precomputed' && x.shape[0] != x.shape[1]
+
         # initialize some varibales.
         n_samples = x.shape[0]
         hi_distance_mat = @params[:metric] == 'precomputed' ? x : Rumale::PairwiseMetric.euclidean_distance(x)
@@ -142,6 +143,7 @@ module Rumale
       def terminate?(old_stress, new_stress)
         return false if @params[:tol].nil?
         return false if old_stress.nil?
+
         (old_stress - new_stress).abs <= @params[:tol]
       end
 

data/lib/rumale/manifold/tsne.rb

@@ -89,6 +89,7 @@ module Rumale
       def fit(x, _not_used = nil)
         x = check_convert_sample_array(x)
         raise ArgumentError, 'Expect the input distance matrix to be square.' if @params[:metric] == 'precomputed' && x.shape[0] != x.shape[1]
+
         # initialize some varibales.
         @n_iter = 0
         distance_mat = @params[:metric] == 'precomputed' ? x**2 : Rumale::PairwiseMetric.squared_error(x)
@@ -99,6 +100,7 @@ module Rumale
         one_vec = Numo::DFloat.ones(x.shape[0]).expand_dims(1)
         @params[:max_iter].times do |t|
           break if terminate?(hi_prob_mat, lo_prob_mat)
+
           a = hi_prob_mat * lo_prob_mat
           b = lo_prob_mat * lo_prob_mat
           y = (b.dot(one_vec) * y + (a - b).dot(y)) / a.dot(one_vec)
@@ -170,6 +172,7 @@ module Rumale
           entropy, probs = gaussian_distributed_probability_vector(sample_id, distance_vec, beta)
           diff_entropy = entropy - init_entropy
           break if diff_entropy.abs <= 1e-5
+
           if diff_entropy.positive?
             betamin = beta
             if betamax == Float::MAX
@@ -211,6 +214,7 @@ module Rumale
 
       def terminate?(p, q)
         return false if @params[:tol].nil?
+
         cost(p, q) <= @params[:tol]
       end
     end

data/lib/rumale/metric_learning/neighbourhood_component_analysis.rb

@@ -2,13 +2,15 @@
 
 require 'rumale/base/base_estimator'
 require 'rumale/base/transformer'
-require 'mopti/scaled_conjugate_gradient'
 
 module Rumale
   module MetricLearning
     # NeighbourhoodComponentAnalysis is a class that implements Neighbourhood Component Analysis.
     #
     # @example
+    #   require 'mopti'
+    #   require 'rumale'
+    #
     #   transformer = Rumale::MetricLearning::NeighbourhoodComponentAnalysis.new
     #   transformer.fit(training_samples, traininig_labels)
     #   low_samples = transformer.transform(testing_samples)
@@ -63,6 +65,8 @@ module Rumale
       # @param y [Numo::Int32] (shape: [n_samples]) The labels to be used for fitting the model.
       # @return [NeighbourhoodComponentAnalysis] The learned classifier itself.
       def fit(x, y)
+        raise 'NeighbourhoodComponentAnalysis#fit requires Mopti but that is not loaded.' unless enable_mopti?
+
         x = check_convert_sample_array(x)
         y = check_convert_label_array(y)
         check_sample_label_size(x, y)
@@ -98,6 +102,14 @@ module Rumale
 
       private
 
+      def enable_mopti?
+        if defined?(Mopti).nil?
+          warn('NeighbourhoodComponentAnalysis#fit requires Mopti but that is not loaded. You should intall and load mopti gem in advance.')
+          return false
+        end
+        true
+      end
+
       def init_components(x, n_features, n_components)
         if @params[:init] == 'pca'
           pca = Rumale::Decomposition::PCA.new(n_components: n_components, solver: 'evd')
@@ -126,6 +138,7 @@ module Rumale
           res = prm
           puts "[NeighbourhoodComponentAnalysis] The value of objective function after #{res[:n_iter]} epochs: #{x.shape[0] - res[:fnc]}" if @params[:verbose]
           break if (fold - res[:fnc]).abs <= @params[:tol] && (dold - res[:jcb]).abs <= @params[:tol]
+
           fold = res[:fnc]
           dold = res[:jcb]
         end

data/lib/rumale/model_selection/cross_validation.rb

@@ -69,10 +69,11 @@ module Rumale
       #     the return_train_score is false.
       def perform(x, y)
         x = check_convert_sample_array(x)
-        if @estimator.is_a?(Rumale::Base::Classifier)
+        case @estimator
+        when Rumale::Base::Classifier
           y = check_convert_label_array(y)
           check_sample_label_size(x, y)
-        elsif @estimator.is_a?(Rumale::Base::Regressor)
+        when Rumale::Base::Regressor
           y = check_convert_tvalue_array(y)
           check_sample_tvalue_size(x, y)
         else

data/lib/rumale/model_selection/grid_search_cv.rb

@@ -156,6 +156,7 @@ module Rumale
 
       def valid_param_grid(grid)
         raise TypeError, 'Expect class of param_grid to be Hash or Array' unless grid.is_a?(Hash) || grid.is_a?(Array)
+
         grid = [grid] if grid.is_a?(Hash)
         grid.each do |h|
           raise TypeError, 'Expect class of elements in param_grid to be Hash' unless h.is_a?(Hash)

data/lib/rumale/model_selection/k_fold.rb

@@ -62,7 +62,7 @@ module Rumale
         end
         sub_rng = @rng.dup
         # Splits dataset ids to each fold.
-        dataset_ids = [*0...n_samples]
+        dataset_ids = Array(0...n_samples)
         dataset_ids.shuffle!(random: sub_rng) if @shuffle
         fold_sets = Array.new(@n_splits) do |n|
           n_fold_samples = n_samples / @n_splits

data/lib/rumale/model_selection/shuffle_split.rb

@@ -74,7 +74,7 @@ module Rumale
         end
         sub_rng = @rng.dup
         # Returns array consisting of the training and testing ids for each fold.
-        dataset_ids = [*0...n_samples]
+        dataset_ids = Array(0...n_samples)
         Array.new(@n_splits) do
           test_ids = dataset_ids.sample(n_test_samples, random: sub_rng)
           train_ids = if @train_size.nil?

data/lib/rumale/multiclass/one_vs_rest_classifier.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
-require 'rumale/base/base_estimator.rb'
-require 'rumale/base/classifier.rb'
+require 'rumale/base/base_estimator'
+require 'rumale/base/classifier'
 
 module Rumale
   # This module consists of the classes that implement multi-class classification strategy.

data/lib/rumale/nearest_neighbors/k_neighbors_classifier.rb

@@ -67,6 +67,7 @@ module Rumale
         y = check_convert_label_array(y)
         check_sample_label_size(x, y)
         raise ArgumentError, 'Expect the input distance matrix to be square.' if @params[:metric] == 'precomputed' && x.shape[0] != x.shape[1]
+
         @prototypes = if @params[:metric] == 'euclidean'
                         if @params[:algorithm] == 'vptree'
                           VPTree.new(x)

data/lib/rumale/nearest_neighbors/k_neighbors_regressor.rb

@@ -61,6 +61,7 @@ module Rumale
         y = check_convert_tvalue_array(y)
         check_sample_tvalue_size(x, y)
         raise ArgumentError, 'Expect the input distance matrix to be square.' if @params[:metric] == 'precomputed' && x.shape[0] != x.shape[1]
+
         @prototypes = if @params[:metric] == 'euclidean'
                         if @params[:algorithm] == 'vptree'
                           VPTree.new(x)
@@ -82,6 +83,7 @@ module Rumale
         if @params[:metric] == 'precomputed' && x.shape[1] != @values.shape[0]
           raise ArgumentError, 'Expect the size input matrix to be n_testing_samples-by-n_training_samples.'
         end
+
         # Initialize some variables.
         n_samples = x.shape[0]
         n_prototypes, n_outputs = @values.shape

data/lib/rumale/nearest_neighbors/vp_tree.rb

@@ -30,7 +30,7 @@ module Rumale
         @params = {}
         @params[:min_samples_leaf] = min_samples_leaf
         @data = x
-        @tree = build_tree(Numo::Int32.cast([*0...@data.shape[0]]))
+        @tree = build_tree(Numo::Int32.cast(Array(0...@data.shape[0])))
       end
 
       # Search k-nearest neighbors of given query point.

data/lib/rumale/neural_network/adam.rb

@@ -32,7 +32,7 @@ module Rumale
         end
 
         # @!visibility private
-        # Calculate the updated weight with Nadam adaptive learning rate.
+        # Calculate the updated weight with Adam adaptive learning rate.
         #
         # @param weight [Numo::DFloat] (shape: [n_features]) The weight to be updated.
         # @param gradient [Numo::DFloat] (shape: [n_features]) The gradient for updating the weight.

data/lib/rumale/neural_network/base_mlp.rb

@@ -222,7 +222,7 @@ module Rumale
         n_samples = x.shape[0]
 
         @params[:max_iter].times do |t|
-          sample_ids = [*0...n_samples]
+          sample_ids = Array(0...n_samples)
           sample_ids.shuffle!(random: srng)
           until (subset_ids = sample_ids.shift(@params[:batch_size])).empty?
             # random sampling
@@ -233,6 +233,7 @@ module Rumale
             # calc loss function
             loss, dout = loss_func.call(out, sub_y)
             break if loss < @params[:tol]
+
             # backward
             backward.call(dout)
           end

data/lib/rumale/optimizer/ada_grad.rb

@@ -7,6 +7,8 @@ module Rumale
   module Optimizer
     # AdaGrad is a class that implements AdaGrad optimizer.
     #
+    # @deprecated AdaGrad will be deleted in version 0.20.0.
+    #
     # *Reference*
     # - Duchi, J., Hazan, E., and Singer, Y., "Adaptive Subgradient Methods for Online Learning and Stochastic Optimization," J. Machine Learning Research, vol. 12, pp. 2121--2159, 2011.
     class AdaGrad
@@ -17,6 +19,7 @@ module Rumale
       #
       # @param learning_rate [Float] The initial value of learning rate.
       def initialize(learning_rate: 0.01)
+        warn 'warning: AdaGrad is deprecated. This class will be deleted in version 0.20.0.'
         check_params_numeric(learning_rate: learning_rate)
         check_params_positive(learning_rate: learning_rate)
         @params = {}

data/lib/rumale/optimizer/adam.rb

@@ -7,6 +7,8 @@ module Rumale
   module Optimizer
     # Adam is a class that implements Adam optimizer.
     #
+    # @deprecated Adam will be deleted in version 0.20.0.
+    #
     # *Reference*
     # - Kingma, D P., and Ba, J., "Adam: A Method for Stochastic Optimization," Proc. ICLR'15, 2015.
     class Adam
@@ -19,6 +21,7 @@ module Rumale
       # @param decay1 [Float] The smoothing parameter for the first moment.
       # @param decay2 [Float] The smoothing parameter for the second moment.
       def initialize(learning_rate: 0.001, decay1: 0.9, decay2: 0.999)
+        warn 'warning: Adam is deprecated. This class will be deleted in version 0.20.0.'
         check_params_numeric(learning_rate: learning_rate, decay1: decay1, decay2: decay2)
         check_params_positive(learning_rate: learning_rate, decay1: decay1, decay2: decay2)
         @params = {}

data/lib/rumale/optimizer/nadam.rb

@@ -5,9 +5,13 @@ require 'rumale/base/base_estimator'
 
 module Rumale
   # This module consists of the classes that implement optimizers adaptively tuning hyperparameters.
+  #
+  # @deprecated Optimizer module will be deleted in version 0.20.0.
   module Optimizer
     # Nadam is a class that implements Nadam optimizer.
     #
+    # @deprecated Nadam will be deleted in version 0.20.0.
+    #
     # *Reference*
     # - Dozat, T., "Incorporating Nesterov Momentum into Adam," Tech. Repo. Stanford University, 2015.
     class Nadam
@@ -20,6 +24,7 @@ module Rumale
       # @param decay1 [Float] The smoothing parameter for the first moment.
       # @param decay2 [Float] The smoothing parameter for the second moment.
       def initialize(learning_rate: 0.01, decay1: 0.9, decay2: 0.999)
+        warn 'warning: Nadam is deprecated. This class will be deleted in version 0.20.0.'
         check_params_numeric(learning_rate: learning_rate, decay1: decay1, decay2: decay2)
         check_params_positive(learning_rate: learning_rate, decay1: decay1, decay2: decay2)
         @params = {}

data/lib/rumale/optimizer/rmsprop.rb

@@ -7,6 +7,8 @@ module Rumale
   module Optimizer
     # RMSProp is a class that implements RMSProp optimizer.
     #
+    # @deprecated RMSProp will be deleted in version 0.20.0.
+    #
     # *Reference*
     # - Sutskever, I., Martens, J., Dahl, G., and Hinton, G., "On the importance of initialization and momentum in deep learning," Proc. ICML' 13, pp. 1139--1147, 2013.
     # - Hinton, G., Srivastava, N., and Swersky, K., "Lecture 6e rmsprop," Neural Networks for Machine Learning, 2012.
@@ -20,6 +22,7 @@ module Rumale
       # @param momentum [Float] The initial value of momentum.
       # @param decay [Float] The smooting parameter.
       def initialize(learning_rate: 0.01, momentum: 0.9, decay: 0.9)
+        warn 'warning: RMSProp is deprecated. This class will be deleted in version 0.20.0.'
         check_params_numeric(learning_rate: learning_rate, momentum: momentum, decay: decay)
         check_params_positive(learning_rate: learning_rate, momentum: momentum, decay: decay)
         @params = {}

data/lib/rumale/optimizer/sgd.rb

@@ -6,6 +6,8 @@ require 'rumale/base/base_estimator'
 module Rumale
   module Optimizer
     # SGD is a class that implements SGD optimizer.
+    #
+    # @deprecated SGD will be deleted in version 0.20.0.
     class SGD
       include Base::BaseEstimator
       include Validation
@@ -16,6 +18,7 @@ module Rumale
       # @param momentum [Float] The initial value of momentum.
       # @param decay [Float] The smooting parameter.
       def initialize(learning_rate: 0.01, momentum: 0.0, decay: 0.0)
+        warn 'warning: SGD is deprecated. This class will be deleted in version 0.20.0.'
         check_params_numeric(learning_rate: learning_rate, momentum: momentum, decay: decay)
         check_params_positive(learning_rate: learning_rate, momentum: momentum, decay: decay)
         @params = {}

data/lib/rumale/optimizer/yellow_fin.rb

@@ -7,6 +7,8 @@ module Rumale
   module Optimizer
     # YellowFin is a class that implements YellowFin optimizer.
     #
+    # @deprecated YellowFin will be deleted in version 0.20.0.
+    #
     # *Reference*
     # - Zhang, J., and Mitliagkas, I., "YellowFin and the Art of Momentum Tuning," CoRR abs/1706.03471, 2017.
     class YellowFin
@@ -20,6 +22,7 @@ module Rumale
       # @param decay [Float] The smooting parameter.
       # @param window_width [Integer] The sliding window width for searching curvature range.
       def initialize(learning_rate: 0.01, momentum: 0.9, decay: 0.999, window_width: 20)
+        warn 'warning: YellowFin is deprecated. This class will be deleted in version 0.20.0.'
         check_params_numeric(learning_rate: learning_rate, momentum: momentum, decay: decay, window_width: window_width)
         check_params_positive(learning_rate: learning_rate, momentum: momentum, decay: decay, window_width: window_width)
         @params = {}

data/lib/rumale/pipeline/pipeline.rb

@@ -119,6 +119,7 @@ module Rumale
         @steps.keys.reverse_each do |name|
           transformer = @steps[name]
           next if transformer.nil?
+
           itrans_z = transformer.inverse_transform(itrans_z)
         end
         itrans_z
@@ -140,6 +141,7 @@ module Rumale
         steps.keys[0...-1].each do |name|
           transformer = steps[name]
           next if transformer.nil? || %i[fit transform].all? { |m| transformer.class.method_defined?(m) }
+
           raise TypeError,
                 'Class of intermediate step in pipeline should be implemented fit and transform methods: ' \
                 "#{name} => #{transformer.class}"
@@ -158,6 +160,7 @@ module Rumale
         @steps.keys[0...-1].each do |name|
           transformer = @steps[name]
           next if transformer.nil?
+
           transformer.fit(trans_x, y) if fit
           trans_x = transformer.transform(trans_x)
         end

data/lib/rumale/polynomial_model/base_factorization_machine.rb

@@ -5,9 +5,13 @@ require 'rumale/optimizer/nadam'
 
 module Rumale
   # This module consists of the classes that implement polynomial models.
+  #
+  # @deprecated PolynomialModel module will be deleted in version 0.20.0.
   module PolynomialModel
     # BaseFactorizationMachine is an abstract class for implementation of Factorization Machine-based estimators.
     # This class is used internally.
+    #
+    # @deprecated BaseFactorizationMachine will be deleted in version 0.20.0.
     class BaseFactorizationMachine
       include Base::BaseEstimator
 
@@ -65,7 +69,7 @@ module Rumale
         factor_optimizers = Array.new(@params[:n_factors]) { @params[:optimizer].dup }
         # Start optimization.
         @params[:max_iter].times do |t|
-          sample_ids = [*0...n_samples]
+          sample_ids = Array(0...n_samples)
           sample_ids.shuffle!(random: sub_rng)
           until (subset_ids = sample_ids.shift(@params[:batch_size])).empty?
             # Sampling.
@@ -75,6 +79,7 @@ module Rumale
             # Calculate gradients for loss function.
             loss_grad = loss_gradient(sub_x, ex_sub_x, sub_y, factor_mat, weight_vec)
             next if loss_grad.ne(0.0).count.zero?
+
             # Update each parameter.
             weight_vec = weight_optimizer.call(weight_vec, weight_gradient(loss_grad, ex_sub_x, weight_vec))
             @params[:n_factors].times do |n|