src/ttc-ga-clustering.rb

   1 require '/home/neil/programming/ruby/programming-collective/intelligence/k-means-clustering'
   2
   3 def read_genome_file(filename)
   4   genomes = []
   5   IO.foreach(filename) { |line| genomes << line.chomp.split('').collect {|i| i.to_i} }
   6   genomes
   7 end
   8
   9 def find_centroid_sets(rows, k = 10, n = 10)
  10   centroid_set = []
  11   1.upto(n) do
  12     centroid_set << (k_means_cluster(rows, k, :domain => :discrete) {|x, y| hamming_distance x, y})
  13   end
  14   centroid_set
  15 end
  16
  17 def order_centroids_by_cluster_size(centroids, rows)
  18   clusters = clusters_of_centroids(centroids, rows) {|x, y| hamming_distance x, y}
  19   cluster_sizes = clusters.collect {|c| c.length}
  20   sized_centroids = centroid.zip(cluster_sizes)
  21   sorted_sized_centroids = (sized_centroids.sort_by {|t| t[1]}).reverse
  22 end
  23
  24 def best_centroids(centroid_set)
  25   centroid_set.collect {|tc| tc[0][0]}
  26 end
  27