som 0.0.1

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data/.document ADDED
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+ README.rdoc
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+ lib/**/*.rb
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+ bin/*
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+ features/**/*.feature
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+ LICENSE
data/.gitignore ADDED
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+ ## MAC OS
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+ .DS_Store
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+
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+ ## TEXTMATE
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+ *.tmproj
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+ tmtags
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+
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+ ## EMACS
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+ *~
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+ \#*
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+ .\#*
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+
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+ ## VIM
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+ *.swp
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+
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+ ## PROJECT::GENERAL
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+ coverage
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+ rdoc
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+ pkg
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+
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+ ## PROJECT::SPECIFIC
data/LICENSE ADDED
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+ Copyright (c) 2009 reddavis
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+
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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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+
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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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+
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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.
data/README.rdoc ADDED
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+ = SOM - Self Organising Map
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+
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+ A pure Ruby implementation of the Self Organising Map machine learning Algorithm.
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+
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+ == Install
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+
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+ gem sources -a -http://gemcutter.org
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+ sudo gem install som
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+
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+ == How To Use
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+
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+ require 'rubygems'
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+ require 'som'
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+
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+ a = SOM.new(:number_of_nodes => 4, :dimensions => 3)
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+ a.train(data)
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+
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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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+
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+ == Copyright
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+
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+ Copyright (c) 2009 Red Davis. See LICENSE for details.
data/Rakefile ADDED
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+ require 'rubygems'
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+ require 'rake'
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+
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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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+
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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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+
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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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+
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+ task :spec => :check_dependencies
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+
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+ task :default => :spec
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+
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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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+
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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
data/VERSION ADDED
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+ 0.0.1
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+ require File.expand_path(File.dirname(__FILE__) + '/../lib/som')
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+
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+ data = Array.new(100) {Array.new(3) {rand}}
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+
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+ a = SOM.new(:number_of_nodes => 4, :dimensions => 3)
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+
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+ a.train(data)
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+
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+ # Returns the index of the data you gave it
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+ puts a.inspect.inspect
data/lib/som/node.rb ADDED
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+ class Node
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+
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+ attr_reader :bucket
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+
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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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+
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+ def weights
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+ @weights ||= []
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+ end
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+
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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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+
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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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+
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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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+
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+ private
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+
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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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+
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+ end
data/lib/som.rb ADDED
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+ require File.expand_path(File.dirname(__FILE__) + '/som/node')
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+
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+ class SOM
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+
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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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+
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+ def nodes
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+ @nodes ||= []
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+ end
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+
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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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+
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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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+
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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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+
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+ private
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+
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+ def train_it!(data)
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+ return false if @iteration_count >= @max_iterations
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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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+ def increase_iteration_count!
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+ @iteration_count += 1
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+ end
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+
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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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+
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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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+
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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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+
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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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+
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+ end
data/som.gemspec ADDED
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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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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+
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+ @a.weights[0] = 1.0
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+ @a.weights[1] = 0.0
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+
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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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+
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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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+
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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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+ end
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+ end
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+
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+ describe "Neighbor" 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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+
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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, 0.23)
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+ @a.weights.should_not == before
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+ end
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+ end
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+ end
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+
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+ describe "Bucket" do
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+ before do
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+ @a = Node.new(2)
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+ end
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+
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+ it "should put data into the nodes bucket" do
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+ @a << 'some_data'
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+ @a.bucket.size.should == 1
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+ end
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+ end
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+ end
data/spec/som_spec.rb ADDED
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+ require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
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+
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+ describe "Som" do
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+ describe "Initialization" do
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+ before do
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+ @a = SOM.new(:nodes => 10, :dimensions => 5)
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+ end
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+
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+ it "should have 10 nodes" do
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+ @a.nodes.size.should == 10
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+ end
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+ end
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+
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+ describe "Training" do
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+ before do
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+ @a = SOM.new(:nodes => 1, :dimensions => 2)
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+ @data = [[2,3]]
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+ end
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+
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+ it "should change the weight of the best matching node" do
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+ before = @a.nodes.map {|x| x.weights.clone}
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+ @a.train(@data)
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+ after = @a.nodes.map {|x| x.weights}
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+
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+ before.should_not == after
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+ end
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+
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+ it "should will the nodes bucket with the data" do
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+ @a.train(@data)
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+ @a.nodes[0].bucket.should_not be_empty
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+ end
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+
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+ it "should preserve data indexes" do
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+ data = [[0,0], [0,0.5], [2,4], [6,5]]
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+ @a.train(data)
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+
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+ index_returned = @a.nodes[0].bucket[0][0]
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+ data_returned = @a.nodes[0].bucket[0][1]
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+
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+ data[index_returned].should == data_returned
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+ end
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+ end
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+
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+ describe "Inspect" do
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+ before do
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+ @a = SOM.new(:nodes => 1, :dimensions => 2)
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+ @data = [[2,3]]
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+ end
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+
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+ it "should show the clusters of data indexes" do
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+ @a.train(@data)
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+ @a.inspect.should be_an(Array)
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+ @a.inspect.size.should == 1
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+ end
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+ end
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+
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+ describe "Clustering" do
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+ before do
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+ @a = SOM.new(:nodes => 2, :dimensions => 2)
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+ end
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+
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+ it "should belong to 2 seperate nodes" do
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+ data = [[0,0], [999,999]]
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+ @a.train(data)
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+ @a.inspect[0].should_not be_empty
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+ @a.inspect[1].should_not be_empty
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+ end
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+ end
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+
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+ describe "Classify" do
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+ before do
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+ @a = SOM.new(:nodes => 2, :dimensions => 2)
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+ end
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+
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+ it "should belong to 2 seperate nodes" do
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+ data = [[0,0], [999,999]]
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+ @a.train(data)
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+ @a.classify([1,1]).should be_an(Array)
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+ @a.classify([1,1]).size.should == 1
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+ end
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+ end
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+ end
data/spec/spec.opts ADDED
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+ --color
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ require 'som'
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+ require 'spec'
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+ require 'spec/autorun'
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+
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+ Spec::Runner.configure do |config|
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+
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: som
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+ version: !ruby/object:Gem::Version
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+ version: 0.0.1
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+ platform: ruby
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+ authors:
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+ - reddavis
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+
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+ date: 2009-11-26 00:00:00 +00:00
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+ default_executable:
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: rspec
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+ type: :development
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+ version_requirement:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 1.2.9
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+ version:
25
+ description: A Self Organising Map
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+ email: reddavis@gmail.com
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+ executables: []
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+
29
+ extensions: []
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+
31
+ extra_rdoc_files:
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+ - LICENSE
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+ - README.rdoc
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+ 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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+ has_rdoc: true
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+ homepage: http://github.com/reddavis/som
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+ licenses: []
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+
53
+ post_install_message:
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+ rdoc_options:
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+ - --charset=UTF-8
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+ require_paths:
57
+ - lib
58
+ required_ruby_version: !ruby/object:Gem::Requirement
59
+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
63
+ version:
64
+ required_rubygems_version: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: "0"
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+ version:
70
+ requirements: []
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+
72
+ rubyforge_project:
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+ rubygems_version: 1.3.5
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+ signing_key:
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+ specification_version: 3
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+ summary: A Self Organising Map
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+ 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