kmeans-clusterer 0.4.0

checksums.yaml

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+SHA512:
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data/lib/kmeans-clusterer.rb

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+require 'narray'
+
+class KMeansClusterer
+
+  # Euclidean distance function. Requires instances of NArray as args
+  Distance = -> (a, b) { NMath.sqrt ((a - b)**2).sum(0) }
+  CalculateCentroid = -> (a) { a.mean(1) }
+
+  class Point
+    attr_reader :data
+    attr_accessor :cluster, :label
+
+    def initialize data, label = nil
+      @data = NArray.to_na data
+      @label = label
+    end
+
+    def [] index
+      @data[index]
+    end
+
+    def to_a
+      @data.to_a
+    end
+
+    def to_s
+      to_a.to_s
+    end
+
+    def dimension
+      @data.length
+    end
+  end
+
+
+  class Cluster
+    attr_reader :centroid, :points
+    attr_accessor :label
+
+    def initialize centroid, label = nil
+      @centroid = centroid
+      @label = label
+      @points = []
+    end
+
+    def recenter
+      if @points.empty?
+        0
+      else
+        old_centroid = @centroid
+        @centroid = calculate_centroid_from_points
+        Distance.call @centroid.data, old_centroid.data
+      end
+    end
+
+    def << point
+      point.cluster = self
+      @points << point
+    end
+
+    def reset_points
+      @points = []
+    end
+
+    def sorted_points
+      distances = Distance.call points_narray, centroid.data
+      @points.sort_by.with_index {|c, i| distances[i] }
+    end
+
+    def sum_of_squares_error
+      if @points.empty?
+        0
+      else
+        distances = Distance.call points_narray, centroid.data
+        (distances**2).sum
+      end
+    end
+
+    def sum_of_distances
+      return 0 if @points.empty?
+      Distance.call(points_narray, centroid.data).sum
+    end
+
+    def dissimilarity point
+      distances = Distance.call points_narray, point.data
+      distances.sum / distances.length.to_f
+    end
+
+    private
+      def calculate_centroid_from_points
+        data = CalculateCentroid.call points_narray
+        Point.new data
+      end
+
+      def points_narray
+        NArray.to_na @points.map(&:data)
+      end
+  end
+
+
+  def self.run k, data, opts = {}
+    raise(ArgumentError, "k cannot be greater than the number of points") if k > data.length
+
+    data = if opts[:scale_data]
+      scale_data data
+    else
+      data.map {|row| NArray.to_na(row).to_f}
+    end
+
+    runcount = opts[:runs] || 10
+    errors = []
+
+    runs = runcount.times.map do |i|
+      km = new(k, data, opts).run
+      error = km.error
+      if opts[:log]
+        puts "[#{i + 1}] #{km.iterations} iter\t#{km.runtime.round(2)}s\t#{error.round(2)} err"
+      end
+      errors << error
+      km
+    end
+
+    runs.sort_by.with_index {|run, i| errors[i] }.first
+  end
+
+  # see scikit-learn scale and _mean_and_std methods
+  def self.scale_data data
+    nadata = NArray.to_na(data).to_f
+    mean = nadata.mean(1)
+    std = nadata.rmsdev(1)
+    std[std.eq(0)] = 1.0 # so we don't divide by 0
+    nadata = (nadata - mean) / std
+    # convert back to an array, containing NArrays for each row
+    data.length.times.map {|i| nadata[true, i] }
+  end
+
+
+  attr_reader :k, :points, :clusters, :iterations, :runtime
+
+
+  def initialize k, data, opts = {}
+    @k = k
+    @init = opts[:init] || :kmpp
+    labels = opts[:labels] || []
+
+    @points = data.map.with_index do |instance, i|
+      Point.new instance, labels[i]
+    end
+
+    init_clusters
+  end
+
+  def run 
+    start_time = Time.now
+    @iterations, @runtime = 0, 0
+
+    loop do
+      @iterations +=1
+
+      centroids = get_cluster_centroids
+
+      @points.each do |point|
+        distances = Distance.call(centroids, point.data)
+        cluster = @clusters.sort_by.with_index {|c, i| distances[i] }.first
+        cluster << point
+      end
+
+      moves = clusters.map(&:recenter)
+
+      break if moves.max < 0.001 # i.e., no movement
+      break if @iterations >= 300
+
+      clusters.each(&:reset_points)
+    end
+
+    @runtime =  Time.now - start_time
+    self
+  end
+
+  def error
+    @clusters.map(&:sum_of_squares_error).reduce(:+)
+  end
+
+  def closest_cluster point = origin
+    sorted_clusters(point).first
+  end
+
+  def sorted_clusters point = origin
+    point = Point.new(point) unless point.is_a?(Point)
+    centroids = get_cluster_centroids
+    distances = Distance.call(centroids, point.data)
+    @clusters.sort_by.with_index {|c, i| distances[i] }
+  end
+
+  def origin
+    Point.new Array.new(@points[0].dimension, 0)
+  end
+
+  def silhouette_score
+    return 1.0 if @clusters.length < 2
+    
+    scores = @points.map do |point|
+      acluster, bcluster = sorted_clusters(point).slice(0,2)
+      a = acluster.dissimilarity(point)
+      b = bcluster.dissimilarity(point)
+      (b - a) / [a,b].max
+    end
+
+    scores.reduce(:+) / scores.length # mean score for all points
+  end
+
+  private
+    def init_clusters
+      case @init
+      when :random
+        random_cluster_init
+      when Array
+        custom_cluster_init
+      else
+        kmpp_cluster_init
+      end
+    end
+
+    # k-means++
+    def kmpp_cluster_init
+      @clusters = []
+      pick = rand(@points.length)
+      centroid = Point.new @points[pick].data.to_a
+      @clusters << Cluster.new(centroid, 1)
+
+      while @clusters.length < @k
+        centroids = get_cluster_centroids
+
+        d2 = @points.map do |point|
+          dists = Distance.call centroids, point.data
+          dists.min**2 # closest cluster distance, squared
+        end
+
+        d2 = NArray.to_na d2
+        probs = d2 / d2.sum
+        cumprobs = probs.cumsum
+        r = rand
+        # pick = cumprobs.to_a.index {|prob| r < prob }
+        pick = (cumprobs >= r).where[0]
+        centroid = Point.new @points[pick].data.to_a
+        cluster = Cluster.new(centroid, @clusters.length + 1)
+        @clusters << cluster
+      end
+    end
+
+    def custom_cluster_init
+      @clusters = @init.map.with_index do |instance, i|
+        point = Point.new NArray.to_na(instance).to_f
+        Cluster.new point, i+1
+      end
+    end
+
+    def random_cluster_init
+      @clusters = pick_k_random_points.map.with_index {|centroid, i| Cluster.new centroid, i+1 }
+    end
+
+    def pick_k_random_points
+      pick_k_random_indexes.map {|i| Point.new @points[i].data.to_a }
+    end
+
+    def pick_k_random_indexes
+      @points.length.times.to_a.shuffle.slice(0, @k)
+    end
+
+    def get_cluster_centroids
+      NArray.to_na @clusters.map {|c| c.centroid.data }
+    end
+end
+
+class KMediansClusterer < KMeansClusterer
+  Distance = -> (a, b) { (a - b).abs.sum(0) }
+  CalculateCentroid = -> (a) { a.rot90.median(0) }
+
+  def error
+    @clusters.map(&:sum_of_distances).reduce(:+)
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: kmeans-clusterer
+version: !ruby/object:Gem::Version
+  version: 0.4.0
+platform: ruby
+authors:
+- Geoff Buesing
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-01-29 00:00:00.000000000 Z
+dependencies: []
+description: k-means/k-medians clustering. Uses NArray for fast calculations.
+email: gbuesing@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/kmeans-clusterer.rb
+homepage: https://github.com/gbuesing/kmeans-clusterer
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.5
+signing_key: 
+specification_version: 4
+summary: k-means/k-medians clustering
+test_files: []