rumale-manifold 2.0.2 → 2.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2022-2024 Atsushi Tatsuma
+Copyright (c) 2022-2026 Atsushi Tatsuma
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

data/lib/rumale/manifold/classical_mds.rb

@@ -0,0 +1,84 @@
+# frozen_string_literal: true
+
+require 'rumale/base/estimator'
+require 'rumale/base/transformer'
+require 'rumale/utils'
+require 'rumale/validation'
+require 'rumale/pairwise_metric'
+
+module Rumale
+  module Manifold
+    # ClassicalMDS is a class that implements classical multi-dimensional scaling.
+    #
+    # @example
+    #   require 'rumale/manifold/classical_mds'
+    #
+    #   mds = Rumale::Manifold::ClassicalMDS.new(n_components: 2)
+    #   representations = mds.fit_transform(data)
+    #
+    class ClassicalMDS < Rumale::Base::Estimator
+      include Rumale::Base::Transformer
+
+      # Return the data in representation space.
+      # @return [Numo::DFloat] (shape: [n_samples, n_components])
+      attr_reader :embedding
+
+      # Create a new transformer with Classical MDS.
+      #
+      # @param n_components [Integer] The number of dimensions on representation space.
+      # @param metric [String] The metric to calculate the distances in original space.
+      #   If metric is 'euclidean', Euclidean distance is calculated for distance in original space.
+      #   If metric is 'precomputed', the fit and fit_transform methods expect to be given a distance matrix.
+      def initialize(n_components: 2, metric: 'euclidean')
+        super()
+        @params = {
+          n_components: n_components,
+          metric: metric
+        }
+      end
+
+      # Fit the model with given training data.
+      #
+      # @overload fit(x) -> ClassicalMDS
+      #   @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for fitting the model.
+      #     If the metric is 'precomputed', x must be a square distance matrix (shape: [n_samples, n_samples]).
+      #   @return [ClassicalMDS] The learned transformer itself.
+      def fit(x, _not_used = nil)
+        raise 'ClassicalMDS#fit requires Numo::Linalg but that is not loaded' unless enable_linalg?(warning: false)
+
+        x = ::Rumale::Validation.check_convert_sample_array(x)
+        if @params[:metric] == 'precomputed' && x.shape[0] != x.shape[1]
+          raise ArgumentError, 'Expect the input distance matrix to be square.'
+        end
+
+        n_samples = x.shape[0]
+        distance_mat = @params[:metric] == 'precomputed' ? x : ::Rumale::PairwiseMetric.euclidean_distance(x)
+
+        centering_mat = Numo::DFloat.eye(n_samples) - Numo::DFloat.new(n_samples, n_samples).fill(1.fdiv(n_samples))
+        kernel_mat = -0.5 * centering_mat.dot(distance_mat * distance_mat).dot(centering_mat)
+        eig_vals, eig_vecs = Numo::Linalg.eigh(kernel_mat, vals_range: (n_samples - @params[:n_components])...n_samples)
+        eig_vals = eig_vals.reverse
+        eig_vecs = eig_vecs.reverse(1)
+        @embedding = eig_vecs.dot(Numo::NMath.sqrt(eig_vals.abs).diag)
+
+        @embedding = @embedding.flatten.dup if @params[:n_components] == 1
+
+        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 fitting the model.
+      #     If the metric is 'precomputed', x must be a square distance matrix (shape: [n_samples, n_samples]).
+      #   @return [Numo::DFloat] (shape: [n_samples, n_components]) The transformed data
+      def fit_transform(x, _not_used = nil)
+        raise 'ClassicalMDS#fit_transform requires Numo::Linalg but that is not loaded' unless enable_linalg?(warning: false)
+
+        x = ::Rumale::Validation.check_convert_sample_array(x)
+        fit(x)
+        @embedding.dup
+      end
+    end
+  end
+end

data/lib/rumale/manifold/version.rb

@@ -5,6 +5,6 @@ module Rumale
   # Module for data embedding algorithms.
   module Manifold
     # @!visibility private
-    VERSION = '2.0.2'
+    VERSION = '2.1.0'
   end
 end

data/lib/rumale/manifold.rb

@@ -6,6 +6,7 @@ require_relative 'manifold/laplacian_eigenmaps'
 require_relative 'manifold/locally_linear_embedding'
 require_relative 'manifold/hessian_eigenmaps'
 require_relative 'manifold/local_tangent_space_alignment'
+require_relative 'manifold/classical_mds'
 require_relative 'manifold/mds'
 require_relative 'manifold/tsne'
 require_relative 'manifold/version'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rumale-manifold
 version: !ruby/object:Gem::Version
-  version: 2.0.2
+  version: 2.1.0
 platform: ruby
 authors:
 - yoshoku
@@ -13,44 +13,50 @@ dependencies:
   name: numo-narray-alt
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.10
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: 0.11.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.9.10
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: 0.11.0
 - !ruby/object:Gem::Dependency
   name: rumale-core
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.2
+        version: 2.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.2
+        version: 2.1.0
 - !ruby/object:Gem::Dependency
   name: rumale-decomposition
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.2
+        version: 2.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.2
+        version: 2.1.0
 description: |
   Rumale::Manifold provides data embedding algorithms,
   such as Multi-dimensional Scaling, Locally Linear Embedding, Laplacian Eigenmaps, Hessian Eigenmaps,
@@ -65,6 +71,7 @@ files:
 - LICENSE.txt
 - README.md
 - lib/rumale/manifold.rb
+- lib/rumale/manifold/classical_mds.rb
 - lib/rumale/manifold/hessian_eigenmaps.rb
 - lib/rumale/manifold/laplacian_eigenmaps.rb
 - lib/rumale/manifold/local_tangent_space_alignment.rb
@@ -94,7 +101,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.6.9
+rubygems_version: 4.0.3
 specification_version: 4
 summary: Rumale::Manifold provides data embedding algorithms with Rumale interface.
 test_files: []