lda-ruby 0.4.0-x86_64-linux

data/lib/lda-ruby/backends/pure_ruby.rb

@@ -0,0 +1,613 @@
+# frozen_string_literal: true
+
+module Lda
+  module Backends
+    class PureRuby < Base
+      MIN_PROBABILITY = 1e-12
+
+      def initialize(random_seed: nil)
+        super(random_seed: random_seed)
+        @beta_probabilities = nil
+        @beta_log = nil
+        @gamma = nil
+        @phi = nil
+        @topic_weights_kernel = nil
+        @topic_term_accumulator_kernel = nil
+        @document_inference_kernel = nil
+        @corpus_iteration_kernel = nil
+        @topic_term_finalizer_kernel = nil
+        @gamma_shift_kernel = nil
+        @topic_document_probability_kernel = nil
+        @topic_term_seed_kernel = nil
+        @trusted_kernel_outputs = false
+      end
+
+      attr_writer :topic_weights_kernel,
+                  :topic_term_accumulator_kernel,
+                  :document_inference_kernel,
+                  :corpus_iteration_kernel,
+                  :topic_term_finalizer_kernel,
+                  :gamma_shift_kernel,
+                  :topic_document_probability_kernel,
+                  :topic_term_seed_kernel,
+                  :trusted_kernel_outputs
+
+      def name
+        "pure_ruby"
+      end
+
+      def corpus=(corpus)
+        super
+        @beta_probabilities = nil
+        @beta_log = nil
+        @gamma = nil
+        @phi = nil
+        true
+      end
+
+      def em(start)
+        return nil if @corpus.nil? || @corpus.num_docs.zero?
+
+        topics = Integer(num_topics)
+        raise ArgumentError, "num_topics must be greater than zero" if topics <= 0
+
+        terms = max_term_index + 1
+        raise ArgumentError, "corpus must contain terms" if terms <= 0
+
+        document_words = @corpus.documents.map { |document| document.words.map(&:to_i) }
+        document_counts = @corpus.documents.map { |document| document.counts.map(&:to_f) }
+
+        @beta_probabilities =
+          if start.to_s.strip.casecmp("seeded").zero? || start.to_s.strip.casecmp("deterministic").zero?
+            seeded_topic_term_probabilities(topics, terms, document_words, document_counts)
+          else
+            initial_topic_term_probabilities(topics, terms)
+          end
+
+        document_totals = document_counts.map { |counts| counts.sum.to_f }
+        document_lengths = document_words.map(&:length)
+
+        previous_gamma = nil
+
+        Integer(em_max_iter).times do
+          if @trusted_kernel_outputs && @corpus_iteration_kernel
+            current_gamma, current_phi, topic_term_counts = infer_corpus_iteration(
+              nil,
+              document_words,
+              document_counts,
+              document_totals,
+              document_lengths,
+              topics,
+              terms
+            )
+          else
+            topic_term_counts = Array.new(topics) { Array.new(terms, MIN_PROBABILITY) }
+            current_gamma, current_phi, topic_term_counts = infer_corpus_iteration(
+              topic_term_counts,
+              document_words,
+              document_counts,
+              document_totals,
+              document_lengths,
+              topics,
+              terms
+            )
+          end
+
+          @beta_probabilities, @beta_log = finalize_topic_term_counts(topic_term_counts)
+          @gamma = current_gamma
+          @phi = current_phi
+
+          break if previous_gamma && average_gamma_shift(previous_gamma, current_gamma) <= Float(em_convergence)
+
+          previous_gamma = current_gamma
+        end
+
+        nil
+      end
+
+      def beta
+        @beta_log || []
+      end
+
+      def gamma
+        @gamma || []
+      end
+
+      def compute_phi
+        clone_matrix(@phi || [])
+      end
+
+      def model
+        [Integer(num_topics), max_term_index + 1, Float(init_alpha)]
+      end
+
+      def topic_document_probability(phi_matrix, document_counts)
+        kernel_output = nil
+        if @topic_document_probability_kernel
+          kernel_output = @topic_document_probability_kernel.call(
+            phi_matrix,
+            document_counts,
+            Integer(num_topics),
+            MIN_PROBABILITY
+          )
+        end
+
+        if valid_topic_document_probability_output?(kernel_output, document_counts.size, Integer(num_topics))
+          if @trusted_kernel_outputs
+            kernel_output
+          else
+            kernel_output.map { |row| row.map(&:to_f) }
+          end
+        else
+          default_topic_document_probability(phi_matrix, document_counts)
+        end
+      rescue StandardError
+        default_topic_document_probability(phi_matrix, document_counts)
+      end
+
+      private
+
+      def max_term_index
+        return -1 if @corpus.nil? || @corpus.documents.empty?
+
+        @corpus.documents
+          .flat_map(&:words)
+          .max || -1
+      end
+
+      def initial_topic_term_probabilities(topics, terms)
+        Array.new(topics) do
+          weights = Array.new(terms) { @random.rand + MIN_PROBABILITY }
+          normalize!(weights)
+        end
+      end
+
+      def seeded_topic_term_probabilities(topics, terms, document_words, document_counts)
+        kernel_output = nil
+        if @topic_term_seed_kernel
+          kernel_output = @topic_term_seed_kernel.call(
+            document_words,
+            document_counts,
+            Integer(topics),
+            Integer(terms),
+            MIN_PROBABILITY
+          )
+        end
+
+        if valid_seeded_topic_term_probabilities?(kernel_output, topics, terms)
+          if @trusted_kernel_outputs
+            kernel_output
+          else
+            kernel_output.map { |weights| normalize!(weights.map(&:to_f)) }
+          end
+        else
+          default_seeded_topic_term_probabilities(topics, terms, document_words, document_counts)
+        end
+      rescue StandardError
+        default_seeded_topic_term_probabilities(topics, terms, document_words, document_counts)
+      end
+
+      def valid_seeded_topic_term_probabilities?(matrix, expected_topics, expected_terms)
+        return false unless matrix.is_a?(Array)
+        return false unless matrix.size == expected_topics
+
+        matrix.each do |row|
+          return false unless row.is_a?(Array)
+          return false unless row.size == expected_terms
+          row.each do |value|
+            return false unless value.is_a?(Numeric)
+            return false unless value.finite?
+          end
+        end
+
+        true
+      end
+
+      def default_seeded_topic_term_probabilities(topics, terms, document_words, document_counts)
+        topic_term_counts = Array.new(topics) { Array.new(terms, MIN_PROBABILITY) }
+
+        document_words.each_with_index do |words, document_index|
+          topic_index = document_index % topics
+          counts = document_counts[document_index] || []
+
+          words.each_with_index do |word_index, word_offset|
+            next if word_index >= terms
+
+            topic_term_counts[topic_index][word_index] += counts[word_offset].to_f
+          end
+        end
+
+        topic_term_counts.map { |weights| normalize!(weights) }
+      end
+
+      def topic_weights_for_word(word_index, gamma_d)
+        kernel_weights = nil
+        if @topic_weights_kernel
+          kernel_weights = @topic_weights_kernel.call(@beta_probabilities, gamma_d, Integer(word_index), MIN_PROBABILITY)
+        end
+
+        weights =
+          if valid_topic_weights?(kernel_weights, gamma_d.length)
+            kernel_weights.map(&:to_f)
+          else
+            default_topic_weights_for_word(word_index, gamma_d)
+          end
+
+        normalize!(weights)
+      rescue StandardError
+        normalize!(default_topic_weights_for_word(word_index, gamma_d))
+      end
+
+      def valid_topic_weights?(weights, expected_size)
+        weights.is_a?(Array) && weights.size == expected_size
+      end
+
+      def default_topic_weights_for_word(word_index, gamma_d)
+        topics = gamma_d.length
+
+        Array.new(topics) do |topic_index|
+          @beta_probabilities[topic_index][word_index] * [gamma_d[topic_index], MIN_PROBABILITY].max
+        end
+      end
+
+      def infer_document(gamma_initial, phi_initial, words, counts)
+        kernel_output = nil
+
+        if @document_inference_kernel
+          kernel_output = @document_inference_kernel.call(
+            @beta_probabilities,
+            gamma_initial,
+            words.map(&:to_i),
+            counts.map(&:to_f),
+            Integer(max_iter),
+            Float(convergence),
+            MIN_PROBABILITY,
+            Float(init_alpha)
+          )
+        end
+
+        if valid_document_inference_output?(kernel_output, gamma_initial.length, phi_initial.length)
+          if @trusted_kernel_outputs
+            [kernel_output[0], kernel_output[1]]
+          else
+            gamma_out = kernel_output[0].map(&:to_f)
+            phi_out = kernel_output[1].map { |row| normalize!(row.map(&:to_f)) }
+            [gamma_out, phi_out]
+          end
+        else
+          default_infer_document(gamma_initial, phi_initial, words, counts)
+        end
+      rescue StandardError
+        default_infer_document(gamma_initial, phi_initial, words, counts)
+      end
+
+      def valid_document_inference_output?(output, expected_topics, expected_length)
+        return false unless output.is_a?(Array)
+        return false unless output.size == 2
+
+        gamma_out = output[0]
+        phi_out = output[1]
+
+        return false unless gamma_out.is_a?(Array) && gamma_out.size == expected_topics
+        return false unless phi_out.is_a?(Array) && phi_out.size == expected_length
+
+        phi_out.all? { |row| row.is_a?(Array) && row.size == expected_topics }
+      end
+
+      def default_infer_document(gamma_initial, phi_initial, words, counts)
+        topics = gamma_initial.length
+        gamma_d = gamma_initial.dup
+        phi_d = phi_initial
+
+        Integer(max_iter).times do
+          gamma_next = Array.new(topics, Float(init_alpha))
+
+          words.each_with_index do |word_index, word_offset|
+            topic_weights = topic_weights_for_word(word_index, gamma_d)
+            phi_d[word_offset] = topic_weights
+
+            count = counts[word_offset].to_f
+            topics.times do |topic_index|
+              gamma_next[topic_index] += count * topic_weights[topic_index]
+            end
+          end
+
+          gamma_shift = max_absolute_distance(gamma_d, gamma_next)
+          gamma_d = gamma_next
+          break if gamma_shift <= Float(convergence)
+        end
+
+        [gamma_d, phi_d]
+      end
+
+      def infer_corpus_iteration(
+        topic_term_counts_initial,
+        document_words,
+        document_counts,
+        document_totals,
+        document_lengths,
+        topics,
+        terms
+      )
+        topic_term_counts_fallback =
+          topic_term_counts_initial || Array.new(topics) { Array.new(terms, MIN_PROBABILITY) }
+        kernel_output = nil
+
+        if @corpus_iteration_kernel
+          kernel_output = @corpus_iteration_kernel.call(
+            @beta_probabilities,
+            document_words,
+            document_counts,
+            Integer(max_iter),
+            Float(convergence),
+            MIN_PROBABILITY,
+            Float(init_alpha)
+          )
+        end
+
+        if valid_corpus_iteration_output?(kernel_output, document_words.size, document_lengths, topics, terms)
+          if @trusted_kernel_outputs
+            [kernel_output[0], kernel_output[1], kernel_output[2]]
+          else
+            current_gamma = kernel_output[0].map { |row| row.map(&:to_f) }
+            current_phi = kernel_output[1].map do |doc_phi|
+              doc_phi.map { |row| normalize!(row.map(&:to_f)) }
+            end
+            topic_term_counts = kernel_output[2].map { |row| row.map(&:to_f) }
+
+            [current_gamma, current_phi, topic_term_counts]
+          end
+        else
+          default_infer_corpus_iteration(
+            topic_term_counts_fallback,
+            document_words,
+            document_counts,
+            document_totals,
+            topics
+          )
+        end
+      rescue StandardError
+        default_infer_corpus_iteration(
+          topic_term_counts_fallback,
+          document_words,
+          document_counts,
+          document_totals,
+          topics
+        )
+      end
+
+      def valid_corpus_iteration_output?(output, expected_docs, expected_lengths, expected_topics, expected_terms)
+        return false unless output.is_a?(Array)
+        return false unless output.size == 3
+
+        gamma_matrix = output[0]
+        phi_tensor = output[1]
+        topic_term_counts = output[2]
+
+        return false unless gamma_matrix.is_a?(Array) && gamma_matrix.size == expected_docs
+        return false unless phi_tensor.is_a?(Array) && phi_tensor.size == expected_docs
+        return false unless topic_term_counts.is_a?(Array) && topic_term_counts.size == expected_topics
+
+        gamma_matrix.each do |row|
+          return false unless row.is_a?(Array) && row.size == expected_topics
+        end
+
+        phi_tensor.each_with_index do |doc_phi, index|
+          return false unless doc_phi.is_a?(Array) && doc_phi.size == expected_lengths[index]
+          doc_phi.each do |row|
+            return false unless row.is_a?(Array) && row.size == expected_topics
+          end
+        end
+
+        topic_term_counts.each do |row|
+          return false unless row.is_a?(Array) && row.size == expected_terms
+        end
+
+        true
+      end
+
+      def default_infer_corpus_iteration(
+        topic_term_counts_initial,
+        document_words,
+        document_counts,
+        document_totals,
+        topics
+      )
+        topic_term_counts = topic_term_counts_initial
+        current_gamma = Array.new(document_words.size) { Array.new(topics, Float(init_alpha)) }
+        current_phi = Array.new(document_words.size)
+
+        document_words.each_with_index do |words, document_index|
+          counts = document_counts[document_index]
+          total = document_totals[document_index].to_f
+
+          gamma_d = Array.new(topics, Float(init_alpha) + (total / topics))
+          phi_d = Array.new(words.length) { Array.new(topics, 1.0 / topics) }
+
+          gamma_d, phi_d = infer_document(gamma_d, phi_d, words, counts)
+
+          current_gamma[document_index] = gamma_d
+          current_phi[document_index] = phi_d
+          topic_term_counts = accumulate_topic_term_counts(topic_term_counts, phi_d, words, counts)
+        end
+
+        [current_gamma, current_phi, topic_term_counts]
+      end
+
+      def accumulate_topic_term_counts(topic_term_counts, phi_d, words, counts)
+        kernel_counts = nil
+        if @topic_term_accumulator_kernel
+          kernel_counts = @topic_term_accumulator_kernel.call(
+            topic_term_counts,
+            phi_d,
+            words.map(&:to_i),
+            counts.map(&:to_f)
+          )
+        end
+
+        if valid_topic_term_counts?(kernel_counts, topic_term_counts)
+          kernel_counts
+        else
+          default_accumulate_topic_term_counts(topic_term_counts, phi_d, words, counts)
+        end
+      rescue StandardError
+        default_accumulate_topic_term_counts(topic_term_counts, phi_d, words, counts)
+      end
+
+      def valid_topic_term_counts?(candidate, reference)
+        return false unless candidate.is_a?(Array)
+        return false unless candidate.size == reference.size
+
+        candidate.each_with_index do |row, index|
+          return false unless row.is_a?(Array)
+          return false unless row.size == reference[index].size
+        end
+
+        true
+      end
+
+      def default_accumulate_topic_term_counts(topic_term_counts, phi_d, words, counts)
+        topics = topic_term_counts.size
+
+        words.each_with_index do |word_index, word_offset|
+          count = counts[word_offset].to_f
+          next if count.zero?
+
+          topics.times do |topic_index|
+            topic_term_counts[topic_index][word_index] += count * phi_d[word_offset][topic_index]
+          end
+        end
+
+        topic_term_counts
+      end
+
+      def finalize_topic_term_counts(topic_term_counts)
+        kernel_output = nil
+        if @topic_term_finalizer_kernel
+          kernel_output = @topic_term_finalizer_kernel.call(topic_term_counts, MIN_PROBABILITY)
+        end
+
+        if valid_topic_term_finalization_output?(kernel_output, topic_term_counts)
+          if @trusted_kernel_outputs
+            [kernel_output[0], kernel_output[1]]
+          else
+            beta_probabilities = kernel_output[0].map { |row| row.map(&:to_f) }
+            beta_log = kernel_output[1].map { |row| row.map(&:to_f) }
+            [beta_probabilities, beta_log]
+          end
+        else
+          default_finalize_topic_term_counts(topic_term_counts)
+        end
+      rescue StandardError
+        default_finalize_topic_term_counts(topic_term_counts)
+      end
+
+      def valid_topic_term_finalization_output?(output, topic_term_counts)
+        return false unless output.is_a?(Array)
+        return false unless output.size == 2
+
+        beta_probabilities = output[0]
+        beta_log = output[1]
+        return false unless beta_probabilities.is_a?(Array) && beta_log.is_a?(Array)
+        return false unless beta_probabilities.size == topic_term_counts.size
+        return false unless beta_log.size == topic_term_counts.size
+
+        beta_probabilities.each_with_index do |row, index|
+          return false unless row.is_a?(Array)
+          return false unless row.size == topic_term_counts[index].size
+        end
+
+        beta_log.each_with_index do |row, index|
+          return false unless row.is_a?(Array)
+          return false unless row.size == topic_term_counts[index].size
+        end
+
+        true
+      end
+
+      def default_finalize_topic_term_counts(topic_term_counts)
+        beta_probabilities = topic_term_counts.map { |weights| normalize!(weights) }
+        beta_log = beta_probabilities.map do |topic_weights|
+          topic_weights.map { |probability| Math.log([probability, MIN_PROBABILITY].max) }
+        end
+
+        [beta_probabilities, beta_log]
+      end
+
+      def valid_topic_document_probability_output?(output, expected_docs, expected_topics)
+        return false unless output.is_a?(Array)
+        return false unless output.size == expected_docs
+
+        output.each do |row|
+          return false unless row.is_a?(Array)
+          return false unless row.size == expected_topics
+          row.each do |value|
+            return false unless value.is_a?(Numeric)
+            return false unless value.finite?
+          end
+        end
+
+        true
+      end
+
+      def default_topic_document_probability(phi_matrix, document_counts)
+        topics = Integer(num_topics)
+        output = []
+
+        document_counts.each_with_index do |counts, doc_index|
+          tops = Array.new(topics, 0.0)
+          ttl = counts.inject(0.0) { |sum, value| sum + value.to_f }
+          doc_phi = phi_matrix[doc_index] || []
+
+          doc_phi.each_with_index do |word_dist, word_idx|
+            count = counts[word_idx].to_f
+            next if count.zero?
+
+            topics.times do |topic_idx|
+              top_prob = word_dist[topic_idx].to_f
+              tops[topic_idx] += Math.log([top_prob, MIN_PROBABILITY].max) * count
+            end
+          end
+
+          tops = tops.map { |value| value / ttl } if ttl.positive?
+          output << tops
+        end
+
+        output
+      end
+
+      def max_absolute_distance(left, right)
+        left.zip(right).map { |a, b| (a - b).abs }.max.to_f
+      end
+
+      def average_gamma_shift(previous_gamma, current_gamma)
+        kernel_shift = nil
+        if @gamma_shift_kernel
+          kernel_shift = @gamma_shift_kernel.call(previous_gamma, current_gamma)
+        end
+
+        if kernel_shift.is_a?(Numeric) && kernel_shift.finite? && kernel_shift >= 0.0
+          kernel_shift.to_f
+        else
+          default_average_gamma_shift(previous_gamma, current_gamma)
+        end
+      rescue StandardError
+        default_average_gamma_shift(previous_gamma, current_gamma)
+      end
+
+      def default_average_gamma_shift(previous_gamma, current_gamma)
+        deltas = []
+
+        previous_gamma.each_with_index do |previous_row, row_index|
+          previous_row.each_with_index do |previous_value, col_index|
+            deltas << (previous_value - current_gamma[row_index][col_index]).abs
+          end
+        end
+
+        return 0.0 if deltas.empty?
+
+        deltas.sum / deltas.size.to_f
+      end
+    end
+  end
+end