carmenere 0.1.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 7c713abdf23594300b13fe5ea26f28f668256315
+  data.tar.gz: a2fea35a639d442ce30e881292ebadc320525f8e
+SHA512:
+  metadata.gz: 63fb5e4e6e823df504690f770a9c3c7b0f84899b1d6faec790d06052517b0ba9b358c45d6bb6953d1ea698b1fcaad7029c6087cadb484cab3286ab6829b895eb
+  data.tar.gz: 47a6dfbc4b553adaaf09febfefedad64ca19f5d5de9a89206f80bf1062bf369a5610be5d48ef229e5a548da8442dfc0446e2ff00763f7664c1eba75ccefd559b

data/lib/carmenere/algorithm.rb

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+module Carmenere
+
+  class Algorithm
+
+    attr_reader :nodes
+
+    attr_reader :distance_matrix
+
+    def initialize k, nodes
+      @k = k
+      @nodes = Set.new(nodes).freeze
+      @clusters = Set.new(@nodes.map{ |n| Cluster.new([n]) })
+      @distance_matrix = @nodes.each.with_object({}) do |i, row|
+        row[i] = @nodes.each.with_object({}) do |j, col|
+          col[j] = i.distance(j) if i != j
+        end
+      end
+    end
+
+    # If a block is provided, it should yield each iteration of the clusters,
+    # otherwise, just returns the final state of the space.
+    def run
+      raise NotImplementedError.new
+    end
+
+  end
+
+end

data/lib/carmenere/cluster.rb

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+require 'set'
+
+module Carmenere
+
+  class Cluster < Set
+
+    # Minimum distance to other cluster
+    def distance other
+      self.reduce(nil) do |m, i|
+        other.reduce(m) do |m, j|
+          d = i.distance j
+          m = if m.nil? or m > d then d else m end
+        end
+      end
+    end
+
+    def to_s
+      "{" + self.reduce("") do |m, n|
+        m += ", " unless m.empty?
+        m += n.to_s
+      end + "}"
+    end
+
+    def inspect
+      self.to_s
+    end
+
+  end
+
+end

data/lib/carmenere/kmeans/algorithm.rb

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+require 'set'
+
+module Carmenere::KMeans
+
+  def self.centroids_eql? old_centroids, new_centroids
+    [old_centroids, new_centroids].each do |i|
+      unless i.is_a?(Set) and i.all?{ |j| j.is_a?(Carmenere::Node) }
+        raise TypeError.new("#{i.class} is not Set of Node")
+      end
+    end
+    old_centroids.count == new_centroids.count and old_centroids.all? do |i|
+      new_centroids.any? do |j|
+        i.attr_eql? j
+      end
+    end
+  end
+
+  class Algorithm < Carmenere::Algorithm
+
+    attr_reader :centroids
+
+    def initialize centroids, nodes, &mean
+      super centroids.count, nodes
+      @mean = mean
+      @centroids = centroids
+    end
+
+    def run
+      old_centroids = Set.new
+      centroids = Set.new @centroids
+      centroid_clusters = {nil => nil}
+      until Carmenere::KMeans::centroids_eql? old_centroids, centroids
+        old_centroids = centroids
+        node_centroids = @nodes.each.with_object({}) do |node, h|
+          h[node] = centroids.min_by do |c|
+            node.distance(c)
+          end
+        end
+        centroid_clusters = centroids.each.with_object({}) do |centroid, h|
+          nodes = node_centroids.lazy.select do |_, c|
+            c.attr_eql?(centroid)
+          end.map do |n, c|
+            n
+          end
+          h[centroid] = Carmenere::KMeans::Cluster.new nodes
+        end
+        yield centroid_clusters if block_given?
+        centroids = Set.new centroid_clusters.values.map do |cluster|
+          @mean.call(cluster)
+        end
+      end
+      centroid_clusters
+    end
+
+  end
+
+end

data/lib/carmenere/kmeans/cluster.rb

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+module Carmenere::KMeans
+
+  class Cluster < Carmenere::Cluster
+  end
+
+end

data/lib/carmenere/node.rb

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+module Carmenere
+
+  # Represents any node that can be used regardless of algorithm or cluster.
+  # The nodes attributes, problem domain-specific, are stored in
+  # Node#attributes.
+  class Node
+
+    include Comparable
+
+    attr_reader :name
+    attr_reader :attributes
+
+    def initialize name, attributes
+      @name = name
+      @cache = Hash.new
+      @attributes = attributes
+    end
+
+    def <=> node
+      @name <=> node.name
+    end
+
+    def hash
+      @name.hash
+    end
+
+    def to_s
+      @name
+    end
+
+    def inspect
+      @name
+    end
+    
+    def distance other
+      c = @cache[other]
+      if c
+        c
+      else
+        @cache[other] = other.cache[self] = yield
+      end
+    end
+
+    def attr_eql? other
+      return @attributes == other.attributes
+    end
+
+    protected
+
+    attr_reader :cache
+
+  end
+
+end

data/lib/carmenere/singlelinkage/algorithm.rb

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+module Carmenere::SingleLinkage
+
+  class Algorithm < Carmenere::Algorithm
+
+    attr_reader :nodes
+
+    attr_reader :distance_matrix
+
+    def initialize k, nodes
+      super k, nodes
+    end
+
+    # If step is true, then yields a copy of the array of clusters
+    def run
+      (nodes.size - @k).times do
+        a, b = self.closest_clusters
+        @clusters.delete a
+        @clusters.delete b
+        @clusters.add Cluster.new(a | b)
+        yield @clusters.to_a if block_given?
+      end
+      @clusters.to_a
+    end
+
+    def closest_clusters
+      @clusters.reduce(nil) do |m, i|
+        @clusters.reduce(m) do |m, j|
+          d = i.distance j
+          m = if i != j and (m.nil? or m[2] > d)
+            [i, j, d]
+          else
+            m
+          end
+        end
+      end
+    end
+
+  end
+
+end
+

data/lib/carmenere/singlelinkage/cluster.rb

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+module Carmenere::SingleLinkage
+
+  class Cluster < Carmenere::Cluster
+
+    # Minimum distance to other cluster
+    def distance other
+      self.reduce(nil) do |m, i|
+        other.reduce(m) do |m, j|
+          d = i.distance j
+          m = if m.nil? or m > d then d else m end
+        end
+      end
+    end
+
+    def to_s
+      "{" + self.reduce("") do |m, n|
+        m += ", " unless m.empty?
+        m += n.to_s
+      end + "}"
+    end
+
+    def inspect
+      self.to_s
+    end
+
+    def run
+      raise NotImplementedError.new
+    end
+
+  end
+
+end
+

data/lib/carmenere.rb

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+require 'carmenere/algorithm'
+require 'carmenere/cluster'
+require 'carmenere/node'
+require 'carmenere/kmeans/algorithm'
+require 'carmenere/kmeans/cluster'
+require 'carmenere/singlelinkage/algorithm'
+require 'carmenere/singlelinkage/cluster'

metadata

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+--- !ruby/object:Gem::Specification
+name: carmenere
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- Johnny Lee Othon
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-04-18 00:00:00.000000000 Z
+dependencies: []
+description: Cluster algorithms
+email: jleeothon@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/carmenere.rb
+- lib/carmenere/algorithm.rb
+- lib/carmenere/cluster.rb
+- lib/carmenere/kmeans/algorithm.rb
+- lib/carmenere/kmeans/cluster.rb
+- lib/carmenere/node.rb
+- lib/carmenere/singlelinkage/algorithm.rb
+- lib/carmenere/singlelinkage/cluster.rb
+homepage: https://github.com/jleeothon/carmenere
+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: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Single Linkage and K-means algorithms for clustering
+test_files: []