som 0.0.1
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- data/.document +5 -0
- data/.gitignore +21 -0
- data/LICENSE +20 -0
- data/README.rdoc +24 -0
- data/Rakefile +45 -0
- data/VERSION +1 -0
- data/examples/example.rb +10 -0
- data/lib/som/node.rb +42 -0
- data/lib/som.rb +107 -0
- data/som.gemspec +60 -0
- data/spec/node_spec.rb +75 -0
- data/spec/som_spec.rb +82 -0
- data/spec/spec.opts +1 -0
- data/spec/spec_helper.rb +9 -0
- metadata +81 -0
data/.document
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data/.gitignore
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data/LICENSE
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Copyright (c) 2009 reddavis
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.rdoc
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= SOM - Self Organising Map
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A pure Ruby implementation of the Self Organising Map machine learning Algorithm.
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== Install
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gem sources -a -http://gemcutter.org
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sudo gem install som
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== How To Use
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require 'rubygems'
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require 'som'
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a = SOM.new(:number_of_nodes => 4, :dimensions => 3)
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a.train(data)
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# Returns the index of the data you gave it
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a.inspect
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#=> [[1, 0...], [99, 84...], [11, 23...], [2, 6...]]
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== Copyright
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Copyright (c) 2009 Red Davis. See LICENSE for details.
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data/Rakefile
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require 'rubygems'
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require 'rake'
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begin
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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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gem.name = "som"
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gem.summary = %Q{A Self Organising Map}
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gem.description = %Q{A Self Organising Map}
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gem.email = "reddavis@gmail.com"
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gem.homepage = "http://github.com/reddavis/som"
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gem.authors = ["reddavis"]
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gem.add_development_dependency "rspec", ">= 1.2.9"
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# gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
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end
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Jeweler::GemcutterTasks.new
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rescue LoadError
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puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
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end
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require 'spec/rake/spectask'
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Spec::Rake::SpecTask.new(:spec) do |spec|
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spec.libs << 'lib' << 'spec'
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spec.spec_files = FileList['spec/**/*_spec.rb']
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end
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Spec::Rake::SpecTask.new(:rcov) do |spec|
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spec.libs << 'lib' << 'spec'
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spec.pattern = 'spec/**/*_spec.rb'
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spec.rcov = true
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end
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task :spec => :check_dependencies
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task :default => :spec
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require 'rake/rdoctask'
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Rake::RDocTask.new do |rdoc|
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version = File.exist?('VERSION') ? File.read('VERSION') : ""
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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "som #{version}"
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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data/VERSION
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0.0.1
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data/examples/example.rb
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require File.expand_path(File.dirname(__FILE__) + '/../lib/som')
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data = Array.new(100) {Array.new(3) {rand}}
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a = SOM.new(:number_of_nodes => 4, :dimensions => 3)
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a.train(data)
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# Returns the index of the data you gave it
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puts a.inspect.inspect
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data/lib/som/node.rb
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class Node
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attr_reader :bucket
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def initialize(number_of_weights)
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create_weights(number_of_weights)
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@bucket = []
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end
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def weights
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@weights ||= []
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end
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def update_weight(learning_rate, inputs, neighborhood_function=1)
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weights.each_with_index do |weight, index|
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@weights[index] += learning_rate * neighborhood_function * (inputs[index] - weight)
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end
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end
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# A bucket is a place to put the data that is closest to it
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def <<(data)
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@bucket << data
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end
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# Euclidean Distance
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def distance_from(data_points)
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distance = 0
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data_points.each_with_index do |point, index|
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distance += (point - weights[index]) ** 2
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end
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Math.sqrt(distance)
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end
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private
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def create_weights(number_of_weights)
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number_of_weights.times do
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weights << (rand > 0.5 ? -rand : rand)
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end
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end
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end
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data/lib/som.rb
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require File.expand_path(File.dirname(__FILE__) + '/som/node')
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class SOM
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def initialize(options={})
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@number_of_nodes = options[:nodes] || 5
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@dimensions = options[:dimensions]
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@learning_rate = options[:learning_rate] || 0.5
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@radius = options[:radius] || @number_of_nodes / 2
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@iteration_count = 0
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@max_iterations = options[:max_iterations] || 500
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# TODO: Allow a lambda so we can use different neighborhood functions
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@neighborhood_function = options[:neighborhood_function] || 1
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create_nodes
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end
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def nodes
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@nodes ||= []
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end
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def train(data)
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while train_it!(data)
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end
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# Place the data in the nodes buckets so we can see how
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# The data has been clustered
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place_data_into_buckets(data)
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end
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# Returns an array of buckets containing the index of the data given
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def inspect
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nodes.map {|x| x.bucket.map {|x| x[0]}}
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end
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# Return data from node that is closest to data
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# You are returned a bucket which contains arrays that look like:
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# [index, [data]]
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# The index is the original index of that that was pumped into the classifier
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# during the training process
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def classify(data)
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closest_node = find_closest_node(data)
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closest_node.bucket
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end
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private
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def train_it!(data)
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return false if @iteration_count >= @max_iterations
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data.each do |input|
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# Update closest node
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closest_node = find_closest_node(input)
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closest_node.update_weight(@learning_rate, input)
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# Update nodes that closer than the radius
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other_nodes = nodes - [closest_node]
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other_nodes.each do |node|
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next if @radius > node.distance_from(closest_node.weights)
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node.update_weight(@learning_rate, input, neighborhood_function)
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end
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end
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decrease_radius!
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decrease_learning_rate!
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increase_iteration_count!
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end
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def place_data_into_buckets(data)
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data.each_with_index do |input, index|
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closest_node = find_closest_node(input)
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closest_node << [index, input]
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end
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end
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def decrease_radius!
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@radius = 0.5 * @radius * @iteration_count / @max_iterations
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end
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def decrease_learning_rate!
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@learning_rate = 0.5 * @learning_rate * @iteration_count / @max_iterations
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end
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def increase_iteration_count!
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@iteration_count += 1
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end
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def neighborhood_function
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0.5 * @neighborhood_function * @iteration_count / @max_iterations
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end
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def find_closest_node(data)
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closest_node = [nodes[0], nodes[0].distance_from(data)]
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nodes[1..-1].each do |node|
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distance = node.distance_from(data)
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if distance < closest_node[1]
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closest_node = [node, distance]
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end
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end
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closest_node[0]
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end
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def create_nodes
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@number_of_nodes.times { nodes << Node.new(@dimensions) }
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end
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end
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data/som.gemspec
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = %q{som}
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s.version = "0.0.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["reddavis"]
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s.date = %q{2009-11-26}
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s.description = %q{A Self Organising Map}
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s.email = %q{reddavis@gmail.com}
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s.extra_rdoc_files = [
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"LICENSE",
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"README.rdoc"
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]
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s.files = [
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".document",
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".gitignore",
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"LICENSE",
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"README.rdoc",
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"Rakefile",
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"VERSION",
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"examples/example.rb",
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"lib/som.rb",
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"lib/som/node.rb",
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"som.gemspec",
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"spec/node_spec.rb",
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"spec/som_spec.rb",
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"spec/spec.opts",
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"spec/spec_helper.rb"
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]
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s.homepage = %q{http://github.com/reddavis/som}
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s.rdoc_options = ["--charset=UTF-8"]
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s.require_paths = ["lib"]
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s.rubygems_version = %q{1.3.5}
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s.summary = %q{A Self Organising Map}
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s.test_files = [
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"spec/node_spec.rb",
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"spec/som_spec.rb",
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"spec/spec_helper.rb",
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"examples/example.rb"
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]
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if s.respond_to? :specification_version then
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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s.specification_version = 3
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
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s.add_development_dependency(%q<rspec>, [">= 1.2.9"])
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else
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s.add_dependency(%q<rspec>, [">= 1.2.9"])
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end
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else
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s.add_dependency(%q<rspec>, [">= 1.2.9"])
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end
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end
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data/spec/node_spec.rb
ADDED
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require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
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describe "Node" do
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describe "Initialization" do
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before do
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@a = Node.new(5)
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end
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it "should have 5 weights" do
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@a.weights.size.should == 5
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end
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end
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describe "Distance Calculation" do
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before do
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@a = Node.new(2)
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@b = Node.new(2)
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end
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it "should return 0" do
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@a.weights[0] = @b.weights[0]
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@a.weights[1] = @b.weights[1]
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@a.distance_from(@b.weights).should == 0
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end
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it "should return 1" do
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@b.weights[0] = 0.0
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@b.weights[1] = 0.0
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@a.weights[0] = 1.0
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@a.weights[1] = 0.0
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@a.distance_from(@b.weights).should == 1
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end
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end
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describe "Update Weight" do
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describe "Closest" do
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before do
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@a = Node.new(2)
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@data = [1,2]
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end
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it "should change the weight" do
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before = @a.weights.clone
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@a.update_weight(0.5, @data)
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@a.weights.should_not == before
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48
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end
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49
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end
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50
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|
51
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describe "Neighbor" do
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52
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before do
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53
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@a = Node.new(2)
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@data = [1,2]
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55
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+
end
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56
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+
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57
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it "should change the weight" do
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58
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before = @a.weights.clone
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@a.update_weight(0.5, @data, 0.23)
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@a.weights.should_not == before
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end
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62
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end
|
63
|
+
end
|
64
|
+
|
65
|
+
describe "Bucket" do
|
66
|
+
before do
|
67
|
+
@a = Node.new(2)
|
68
|
+
end
|
69
|
+
|
70
|
+
it "should put data into the nodes bucket" do
|
71
|
+
@a << 'some_data'
|
72
|
+
@a.bucket.size.should == 1
|
73
|
+
end
|
74
|
+
end
|
75
|
+
end
|
data/spec/som_spec.rb
ADDED
@@ -0,0 +1,82 @@
|
|
1
|
+
require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
|
2
|
+
|
3
|
+
describe "Som" do
|
4
|
+
describe "Initialization" do
|
5
|
+
before do
|
6
|
+
@a = SOM.new(:nodes => 10, :dimensions => 5)
|
7
|
+
end
|
8
|
+
|
9
|
+
it "should have 10 nodes" do
|
10
|
+
@a.nodes.size.should == 10
|
11
|
+
end
|
12
|
+
end
|
13
|
+
|
14
|
+
describe "Training" do
|
15
|
+
before do
|
16
|
+
@a = SOM.new(:nodes => 1, :dimensions => 2)
|
17
|
+
@data = [[2,3]]
|
18
|
+
end
|
19
|
+
|
20
|
+
it "should change the weight of the best matching node" do
|
21
|
+
before = @a.nodes.map {|x| x.weights.clone}
|
22
|
+
@a.train(@data)
|
23
|
+
after = @a.nodes.map {|x| x.weights}
|
24
|
+
|
25
|
+
before.should_not == after
|
26
|
+
end
|
27
|
+
|
28
|
+
it "should will the nodes bucket with the data" do
|
29
|
+
@a.train(@data)
|
30
|
+
@a.nodes[0].bucket.should_not be_empty
|
31
|
+
end
|
32
|
+
|
33
|
+
it "should preserve data indexes" do
|
34
|
+
data = [[0,0], [0,0.5], [2,4], [6,5]]
|
35
|
+
@a.train(data)
|
36
|
+
|
37
|
+
index_returned = @a.nodes[0].bucket[0][0]
|
38
|
+
data_returned = @a.nodes[0].bucket[0][1]
|
39
|
+
|
40
|
+
data[index_returned].should == data_returned
|
41
|
+
end
|
42
|
+
end
|
43
|
+
|
44
|
+
describe "Inspect" do
|
45
|
+
before do
|
46
|
+
@a = SOM.new(:nodes => 1, :dimensions => 2)
|
47
|
+
@data = [[2,3]]
|
48
|
+
end
|
49
|
+
|
50
|
+
it "should show the clusters of data indexes" do
|
51
|
+
@a.train(@data)
|
52
|
+
@a.inspect.should be_an(Array)
|
53
|
+
@a.inspect.size.should == 1
|
54
|
+
end
|
55
|
+
end
|
56
|
+
|
57
|
+
describe "Clustering" do
|
58
|
+
before do
|
59
|
+
@a = SOM.new(:nodes => 2, :dimensions => 2)
|
60
|
+
end
|
61
|
+
|
62
|
+
it "should belong to 2 seperate nodes" do
|
63
|
+
data = [[0,0], [999,999]]
|
64
|
+
@a.train(data)
|
65
|
+
@a.inspect[0].should_not be_empty
|
66
|
+
@a.inspect[1].should_not be_empty
|
67
|
+
end
|
68
|
+
end
|
69
|
+
|
70
|
+
describe "Classify" do
|
71
|
+
before do
|
72
|
+
@a = SOM.new(:nodes => 2, :dimensions => 2)
|
73
|
+
end
|
74
|
+
|
75
|
+
it "should belong to 2 seperate nodes" do
|
76
|
+
data = [[0,0], [999,999]]
|
77
|
+
@a.train(data)
|
78
|
+
@a.classify([1,1]).should be_an(Array)
|
79
|
+
@a.classify([1,1]).size.should == 1
|
80
|
+
end
|
81
|
+
end
|
82
|
+
end
|
data/spec/spec.opts
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
--color
|
data/spec/spec_helper.rb
ADDED
metadata
ADDED
@@ -0,0 +1,81 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: som
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- reddavis
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
|
12
|
+
date: 2009-11-26 00:00:00 +00:00
|
13
|
+
default_executable:
|
14
|
+
dependencies:
|
15
|
+
- !ruby/object:Gem::Dependency
|
16
|
+
name: rspec
|
17
|
+
type: :development
|
18
|
+
version_requirement:
|
19
|
+
version_requirements: !ruby/object:Gem::Requirement
|
20
|
+
requirements:
|
21
|
+
- - ">="
|
22
|
+
- !ruby/object:Gem::Version
|
23
|
+
version: 1.2.9
|
24
|
+
version:
|
25
|
+
description: A Self Organising Map
|
26
|
+
email: reddavis@gmail.com
|
27
|
+
executables: []
|
28
|
+
|
29
|
+
extensions: []
|
30
|
+
|
31
|
+
extra_rdoc_files:
|
32
|
+
- LICENSE
|
33
|
+
- README.rdoc
|
34
|
+
files:
|
35
|
+
- .document
|
36
|
+
- .gitignore
|
37
|
+
- LICENSE
|
38
|
+
- README.rdoc
|
39
|
+
- Rakefile
|
40
|
+
- VERSION
|
41
|
+
- examples/example.rb
|
42
|
+
- lib/som.rb
|
43
|
+
- lib/som/node.rb
|
44
|
+
- som.gemspec
|
45
|
+
- spec/node_spec.rb
|
46
|
+
- spec/som_spec.rb
|
47
|
+
- spec/spec.opts
|
48
|
+
- spec/spec_helper.rb
|
49
|
+
has_rdoc: true
|
50
|
+
homepage: http://github.com/reddavis/som
|
51
|
+
licenses: []
|
52
|
+
|
53
|
+
post_install_message:
|
54
|
+
rdoc_options:
|
55
|
+
- --charset=UTF-8
|
56
|
+
require_paths:
|
57
|
+
- lib
|
58
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
59
|
+
requirements:
|
60
|
+
- - ">="
|
61
|
+
- !ruby/object:Gem::Version
|
62
|
+
version: "0"
|
63
|
+
version:
|
64
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: "0"
|
69
|
+
version:
|
70
|
+
requirements: []
|
71
|
+
|
72
|
+
rubyforge_project:
|
73
|
+
rubygems_version: 1.3.5
|
74
|
+
signing_key:
|
75
|
+
specification_version: 3
|
76
|
+
summary: A Self Organising Map
|
77
|
+
test_files:
|
78
|
+
- spec/node_spec.rb
|
79
|
+
- spec/som_spec.rb
|
80
|
+
- spec/spec_helper.rb
|
81
|
+
- examples/example.rb
|