rumale 0.22.0 → 0.22.5

data/lib/rumale/metric_learning/neighbourhood_component_analysis.rb

@@ -2,6 +2,8 @@
 
 require 'rumale/base/base_estimator'
 require 'rumale/base/transformer'
+require 'rumale/utils'
+require 'rumale/pairwise_metric'
 require 'lbfgsb'
 
 module Rumale
@@ -146,10 +148,11 @@ module Rumale
         mask_mat = y.expand_dims(1).eq(y)
         masked_prob_mat = prob_mat * mask_mat
         loss = n_samples - masked_prob_mat.sum
-        weighted_prob_mat = masked_prob_mat - prob_mat * masked_prob_mat.sum(1).expand_dims(1)
-        weighted_prob_mat += weighted_prob_mat.transpose
-        weighted_prob_mat[weighted_prob_mat.diag_indices] = -weighted_prob_mat.sum(0)
-        gradient = -2 * z.transpose.dot(weighted_prob_mat).dot(x)
+        sum_probs = masked_prob_mat.sum(1)
+        weight_mat = (sum_probs.expand_dims(1) * prob_mat - masked_prob_mat)
+        weight_mat += weight_mat.transpose
+        weight_mat = weight_mat.sum(0).diag - weight_mat
+        gradient = -2 * z.transpose.dot(weight_mat).dot(x)
         [loss, gradient.flatten.dup]
       end
 

data/lib/rumale/pairwise_metric.rb

@@ -123,7 +123,7 @@ module Rumale
       # @param gamma [Float] The parameter of polynomial kernel, if nil it is 1 / n_features.
       # @param coef [Integer] The parameter of polynomial kernel.
       # @return [Numo::DFloat] (shape: [n_samples_x, n_samples_x] or [n_samples_x, n_samples_y] if y is given)
-      def polynomial_kernel(x, y = nil, degree = 3, gamma = nil, coef = 1)
+      def polynomial_kernel(x, y = nil, degree = 3, gamma = nil, coef = 1) # rubocop:disable Metrics/ParameterLists
         y = x if y.nil?
         gamma ||= 1.0 / x.shape[1]
         x = Rumale::Validation.check_convert_sample_array(x)

data/lib/rumale/preprocessing/kernel_calculator.rb

@@ -0,0 +1,92 @@
+# frozen_string_literal: true
+
+require 'rumale/base/base_estimator'
+require 'rumale/base/transformer'
+require 'rumale/pairwise_metric'
+
+module Rumale
+  module Preprocessing
+    # KernelCalculator is a class that calculates the kernel matrix with training data.
+    #
+    # @example
+    #   transformer = Rumale::Preprocessing::KernelCalculator.new(kernel: 'rbf', gamma: 0.5)
+    #   regressor = Rumale::KernelMachine::KernelRidge.new
+    #   pipeline = Rumale::Pipeline::Pipeline.new(
+    #     steps: { trs: transfomer, est: regressor }
+    #   )
+    #   pipeline.fit(x_train, y_train)
+    #   results = pipeline.predict(x_test)
+    class KernelCalculator
+      include Base::BaseEstimator
+      include Base::Transformer
+
+      # Returns the training data for calculating kernel matrix.
+      # @return [Numo::DFloat] (shape: n_components, n_features)
+      attr_reader :components
+
+      # Create a new transformer that transforms feature vectors into a kernel matrix.
+      #
+      # @param kernel [String] The type of kernel function ('rbf', 'linear', 'poly', and 'sigmoid').
+      # @param gamma [Float] The gamma parameter in rbf/poly/sigmoid kernel function.
+      # @param degree [Integer] The degree parameter in polynomial kernel function.
+      # @param coef [Float] The coefficient in poly/sigmoid kernel function.
+      def initialize(kernel: 'rbf', gamma: 1, degree: 3, coef: 1)
+        check_params_string(kernel: kernel)
+        check_params_numeric(gamma: gamma, coef: coef, degree: degree)
+        @params = {}
+        @params[:kernel] = kernel
+        @params[:gamma] = gamma
+        @params[:degree] = degree
+        @params[:coef] = coef
+        @components = nil
+      end
+
+      # Fit the model with given training data.
+      #
+      # @overload fit(x) -> KernelCalculator
+      #   @param x [Numo::NArray] (shape: [n_samples, n_features]) The training data to be used for calculating kernel matrix.
+      # @return [KernelCalculator] The learned transformer itself.
+      def fit(x, _y = nil)
+        x = check_convert_sample_array(x)
+        @components = x.dup
+        self
+      end
+
+      # Fit the model with training data, and then transform them with the learned model.
+      #
+      # @overload fit_transform(x) -> Numo::DFloat
+      #   @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for calculating kernel matrix.
+      # @return [Numo::DFloat] (shape: [n_samples, n_samples]) The calculated kernel matrix.
+      def fit_transform(x, y = nil)
+        x = check_convert_sample_array(x)
+        fit(x, y).transform(x)
+      end
+
+      # Transform the given data with the learned model.
+      #
+      # @param x [Numo::DFloat] (shape: [n_samples, n_features]) The data to be used for calculating kernel matrix with the training data.
+      # @return [Numo::DFloat] (shape: [n_samples, n_components]) The calculated kernel matrix.
+      def transform(x)
+        x = check_convert_sample_array(x)
+        kernel_mat(x, @components)
+      end
+
+      private
+
+      def kernel_mat(x, y)
+        case @params[:kernel]
+        when 'rbf'
+          Rumale::PairwiseMetric.rbf_kernel(x, y, @params[:gamma])
+        when 'poly'
+          Rumale::PairwiseMetric.polynomial_kernel(x, y, @params[:degree], @params[:gamma], @params[:coef])
+        when 'sigmoid'
+          Rumale::PairwiseMetric.sigmoid_kernel(x, y, @params[:gamma], @params[:coef])
+        when 'linear'
+          Rumale::PairwiseMetric.linear_kernel(x, y)
+        else
+          raise ArgumentError, "Expect kernel parameter to be given 'rbf', 'linear', 'poly', or 'sigmoid'."
+        end
+      end
+    end
+  end
+end

data/lib/rumale/validation.rb

@@ -27,6 +27,7 @@ module Rumale
       y
     end
 
+    # @deprecated Use check_convert_sample_array instead of this method.
     # @!visibility private
     def check_sample_array(x)
       raise TypeError, 'Expect class of sample matrix to be Numo::DFloat' unless x.is_a?(Numo::DFloat)
@@ -35,6 +36,7 @@ module Rumale
       nil
     end
 
+    # @deprecated Use check_convert_label_array instead of this method.
     # @!visibility private
     def check_label_array(y)
       raise TypeError, 'Expect class of label vector to be Numo::Int32' unless y.is_a?(Numo::Int32)
@@ -43,6 +45,7 @@ module Rumale
       nil
     end
 
+    # @deprecated Use check_convert_tvalue_array instead of this method.
     # @!visibility private
     def check_tvalue_array(y)
       raise TypeError, 'Expect class of target value vector to be Numo::DFloat' unless y.is_a?(Numo::DFloat)
@@ -64,52 +67,61 @@ module Rumale
       nil
     end
 
+    # TODO: Better to replace with RBS in the future.
     # @!visibility private
     def check_params_type(type, params = {})
       params.each { |k, v| raise TypeError, "Expect class of #{k} to be #{type}" unless v.is_a?(type) }
       nil
     end
 
+    # TODO: Better to replace with RBS in the future.
     # @!visibility private
     def check_params_type_or_nil(type, params = {})
       params.each { |k, v| raise TypeError, "Expect class of #{k} to be #{type} or nil" unless v.is_a?(type) || v.is_a?(NilClass) }
       nil
     end
 
+    # TODO: Better to replace with RBS in the future.
     # @!visibility private
     def check_params_numeric(params = {})
       check_params_type(Numeric, params)
     end
 
+    # TODO: Better to replace with RBS in the future.
     # @!visibility private
     def check_params_numeric_or_nil(params = {})
       check_params_type_or_nil(Numeric, params)
     end
 
+    # @deprecated Use check_params_numeric instead of this method.
     # @!visibility private
     def check_params_float(params = {})
       check_params_type(Float, params)
     end
 
+    # @deprecated Use check_params_numeric instead of this method.
     # @!visibility private
     def check_params_integer(params = {})
       check_params_type(Integer, params)
     end
 
+    # TODO: Better to replace with RBS in the future.
     # @!visibility private
     def check_params_string(params = {})
       check_params_type(String, params)
     end
 
+    # TODO: Better to replace with RBS in the future.
     # @!visibility private
     def check_params_boolean(params = {})
       params.each { |k, v| raise TypeError, "Expect class of #{k} to be Boolean" unless v.is_a?(FalseClass) || v.is_a?(TrueClass) }
       nil
     end
 
+    # TODO: Better to replace with RBS in the future.
     # @!visibility private
     def check_params_positive(params = {})
-      params.reject { |_, v| v.nil? }.each { |k, v| raise ArgumentError, "Expect #{k} to be positive value" if v.negative? }
+      params.compact.each { |k, v| raise ArgumentError, "Expect #{k} to be positive value" if v.negative? }
       nil
     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 = '0.22.0'
+  VERSION = '0.22.5'
 end

data/rumale.gemspec

@@ -38,7 +38,7 @@ Gem::Specification.new do |spec|
 
   spec.metadata      = {
     'homepage_uri' => 'https://github.com/yoshoku/rumale',
-    'changelog_uri' => 'https://github.com/yoshoku/rumale/blob/master/CHANGELOG.md',
+    'changelog_uri' => 'https://github.com/yoshoku/rumale/blob/main/CHANGELOG.md',
     'source_code_uri' => 'https://github.com/yoshoku/rumale',
     'documentation_uri' => 'https://yoshoku.github.io/rumale/doc/',
     'bug_tracker_uri' => 'https://github.com/yoshoku/rumale/issues'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rumale
 version: !ruby/object:Gem::Version
-  version: 0.22.0
+  version: 0.22.5
 platform: ruby
 authors:
 - yoshoku
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2020-11-22 00:00:00.000000000 Z
+date: 2021-03-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
@@ -57,7 +57,9 @@ extensions:
 - ext/rumale/extconf.rb
 extra_rdoc_files: []
 files:
+- ".coveralls.yml"
 - ".github/workflows/build.yml"
+- ".github/workflows/coverage.yml"
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
@@ -104,6 +106,10 @@ files:
 - lib/rumale/ensemble/gradient_boosting_regressor.rb
 - lib/rumale/ensemble/random_forest_classifier.rb
 - lib/rumale/ensemble/random_forest_regressor.rb
+- lib/rumale/ensemble/stacking_classifier.rb
+- lib/rumale/ensemble/stacking_regressor.rb
+- lib/rumale/ensemble/voting_classifier.rb
+- lib/rumale/ensemble/voting_regressor.rb
 - lib/rumale/evaluation_measure/accuracy.rb
 - lib/rumale/evaluation_measure/adjusted_rand_score.rb
 - lib/rumale/evaluation_measure/calinski_harabasz_score.rb
@@ -133,18 +139,21 @@ files:
 - lib/rumale/kernel_machine/kernel_fda.rb
 - lib/rumale/kernel_machine/kernel_pca.rb
 - lib/rumale/kernel_machine/kernel_ridge.rb
+- lib/rumale/kernel_machine/kernel_ridge_classifier.rb
 - lib/rumale/kernel_machine/kernel_svc.rb
 - lib/rumale/linear_model/base_sgd.rb
 - lib/rumale/linear_model/elastic_net.rb
 - lib/rumale/linear_model/lasso.rb
 - lib/rumale/linear_model/linear_regression.rb
 - lib/rumale/linear_model/logistic_regression.rb
+- lib/rumale/linear_model/nnls.rb
 - lib/rumale/linear_model/ridge.rb
 - lib/rumale/linear_model/svc.rb
 - lib/rumale/linear_model/svr.rb
 - lib/rumale/manifold/mds.rb
 - lib/rumale/manifold/tsne.rb
 - lib/rumale/metric_learning/fisher_discriminant_analysis.rb
+- lib/rumale/metric_learning/mlkr.rb
 - lib/rumale/metric_learning/neighbourhood_component_analysis.rb
 - lib/rumale/model_selection/cross_validation.rb
 - lib/rumale/model_selection/function.rb
@@ -175,6 +184,7 @@ files:
 - lib/rumale/pipeline/pipeline.rb
 - lib/rumale/preprocessing/bin_discretizer.rb
 - lib/rumale/preprocessing/binarizer.rb
+- lib/rumale/preprocessing/kernel_calculator.rb
 - lib/rumale/preprocessing/l1_normalizer.rb
 - lib/rumale/preprocessing/l2_normalizer.rb
 - lib/rumale/preprocessing/label_binarizer.rb
@@ -204,7 +214,7 @@ licenses:
 - BSD-2-Clause
 metadata:
   homepage_uri: https://github.com/yoshoku/rumale
-  changelog_uri: https://github.com/yoshoku/rumale/blob/master/CHANGELOG.md
+  changelog_uri: https://github.com/yoshoku/rumale/blob/main/CHANGELOG.md
   source_code_uri: https://github.com/yoshoku/rumale
   documentation_uri: https://yoshoku.github.io/rumale/doc/
   bug_tracker_uri: https://github.com/yoshoku/rumale/issues
@@ -223,7 +233,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
+rubygems_version: 3.2.7
 signing_key:
 specification_version: 4
 summary: Rumale is a machine learning library in Ruby. Rumale provides machine learning