evosynth 0.1.0

data/lib/evosynth/operators/mutations/uniform_real_mutation.rb

@@ -0,0 +1,59 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+module EvoSynth
+	module Mutations
+
+		# GLEICHVERTEILTE-REELWERTIGE-MUTATION (Weicker page 131)
+		# TODO: needs rdoc
+
+		class UniformRealMutation
+
+			DEFAULT_PROBABILITY = 0.1
+			DEFAULT_STEP_SIZE = 0.1
+
+			def initialize(probability = DEFAULT_PROBABILITY, step_size = DEFAULT_STEP_SIZE)
+				@probability = probability
+				@step_size = step_size
+			end
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+				genome = mutated.genome
+
+				genome.size.times do |index|
+					genome[index] += @step_size - 2 * EvoSynth.rand * @step_size if EvoSynth.rand <= @probability
+				end
+
+				mutated
+			end
+
+			def to_s
+				"uniform real mutation <probability: #{@probability}>"
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/recombinations.rb

@@ -0,0 +1,48 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+module EvoSynth
+	module Recombinations
+
+		# Returns individual with the shorter genome
+
+		def Recombinations.individual_with_shorter_genome(individual_one, individual_two)
+			if individual_one.genome.size > individual_one.genome.size then
+				individual_two
+			else
+				individual_one
+			end
+		end
+
+	end
+end
+
+require 'evosynth/operators/recombinations/uniform_crossover'
+require 'evosynth/operators/recombinations/one_point_crossover'
+require 'evosynth/operators/recombinations/k_point_crossover'
+require 'evosynth/operators/recombinations/identity'
+require 'evosynth/operators/recombinations/partially_mapped_crossover'
+require 'evosynth/operators/recombinations/ordered_recombination'
+require 'evosynth/operators/recombinations/edge_recombination'
+require 'evosynth/operators/recombinations/arithmetic_crossover'

data/lib/evosynth/operators/recombinations/arithmetic_crossover.rb

@@ -0,0 +1,67 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+module EvoSynth
+	module Recombinations
+
+		# ARITHMETISCHER-CROSSOVER (Weicker page 83)
+		# 
+		# ATTENTION PLEASE! needs interpolation method to work:
+		#  interpolation_method.call(gene_one, gene_two, factor)
+
+		class ArithmeticCrossover
+
+			# TODO: add extrapolation and other useful stuff here!
+
+			INTERPOLATE_NUMBERS = lambda { |gene_one, gene_two, factor| factor * gene_one + (1.0 - factor) * gene_two }
+			INTERPOLATE_BOOLEANS = lambda { |gene_one, gene_two, factor| EvoSynth.rand < factor ? gene_one : gene_two }
+			EXTRAPOLATE_NUMBERS = lambda { |gene_one, gene_two, factor| EvoSynth.rand_bool ? gene_one + factor * gene_two : gene_two + factor * gene_one}
+
+			def initialize(interpolation_function)
+				@interpolation_function = interpolation_function
+			end
+
+			def recombine(individual_one, individual_two)
+				child_one = individual_one.deep_clone
+				child_two = individual_two.deep_clone
+
+				shorter = EvoSynth::Recombinations.individual_with_shorter_genome(individual_one, individual_two)
+				shorter.genome.each_with_index do |gene_one, index|
+					gene_two = individual_two.genome[index]
+
+					child_one.genome[index] = @interpolation_function.call(gene_one, gene_two, EvoSynth.rand)
+					child_two.genome[index] = @interpolation_function.call(gene_two, gene_one, EvoSynth.rand)
+				end
+
+				[child_one, child_two]
+			end
+
+			def to_s
+				"arithmetic crossover"
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/recombinations/edge_recombination.rb

@@ -0,0 +1,108 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+require 'set'
+
+
+module EvoSynth
+	module Recombinations
+
+		# KANTENREKOMBINATION (Weicker page 29)
+		#
+		# this can only recombine permutations (see partially mapped crossover).
+
+		class EdgeRecombination
+
+			def recombine(parent_one, parent_two)
+				child_one = recombine_to_one(parent_one, parent_two)
+				child_two = recombine_to_one(parent_two, parent_one)
+
+				[child_one, child_two]
+			end
+
+			def to_s
+				"edge recombination"
+			end
+
+			private
+
+			def recombine_to_one(parent_one, parent_two)
+				child = parent_one.deep_clone
+				child_genome = child.genome
+				adj_matrix = generate_adj_matrix(parent_one.genome)
+
+				start = EvoSynth.rand_bool ? parent_one.genome[0] : parent_two.genome[0]
+				child_genome[0] = start
+
+				child_genome.each_index do |index|
+					next if index == 0
+					child_genome[index] = find_next_gene(adj_matrix, start)
+					start = child_genome[index]
+				end
+
+				child
+			end
+
+			def find_next_gene(adj_matrix, start)
+				reachable = adj_matrix.delete(start)
+				next_gene, min = nil, nil
+				
+				reachable.each do |gene|
+					next unless adj_matrix.has_key?(gene)
+
+					neighbors = adj_matrix[gene]
+					adj_size = 1 if neighbors.include?(gene) ? neighbors.size - 1 : neighbors.size
+
+					if min.nil?
+						min = adj_size
+						next_gene = gene
+					elsif adj_size <= min
+						next if adj_size == min && EvoSynth.rand_bool # if equal let the fortune decide
+
+						min = adj_size
+						next_gene = gene
+					end
+				end
+
+				next_gene = EvoSynth.rand(adj_matrix.keys) if next_gene.nil?
+
+				next_gene
+			end
+
+			def generate_adj_matrix(genome)
+				adj_mat = {}
+				genome.each { |gene| adj_mat[gene] = Set.new }
+
+				genome.each_with_index do |gene, index|
+					right_neightbor = genome[(index + 1) % genome.size]
+					adj_mat[gene] << right_neightbor
+					adj_mat[right_neightbor] << gene
+				end
+
+				adj_mat
+			end
+		end
+
+	end
+end

data/lib/evosynth/operators/recombinations/identity.rb

@@ -0,0 +1,42 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+module EvoSynth
+	module Recombinations
+
+		class Identity
+
+			def recombine(individual_one, individual_two)
+				child_one = individual_one.deep_clone
+				child_two = individual_two.deep_clone
+				[child_one, child_two]
+			end
+
+			def to_s
+				"identity (just clones parents)"
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/recombinations/k_point_crossover.rb

@@ -0,0 +1,81 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+
+module EvoSynth
+	module Recombinations
+
+		# K-PUNKT-CROSSOVER (Weicker Page 130)
+
+		class KPointCrossover
+
+			attr_accessor :k
+
+			DEFAULT_K = 2
+
+			def initialize(k = DEFAULT_K)
+				@k = k
+			end
+
+			def recombine(individual_one, individual_two)
+				child_one = individual_one.deep_clone
+				child_two = individual_two.deep_clone
+
+				shorter = EvoSynth::Recombinations.individual_with_shorter_genome(individual_one, individual_two)
+				crossover_points = random_crossover_points(shorter.genome.size)
+
+				@k.times do |m|
+					begin
+						range = (crossover_points[m] + 1)..crossover_points[m + 1]
+					rescue ArgumentError
+						next
+					end
+
+					if m % 2 == 1
+						child_one.genome[range] = individual_two.genome[range]
+						child_two.genome[range] = individual_one.genome[range]
+					end
+				end
+
+				[child_one, child_two]
+			end
+
+			def to_s
+				"k-point crossover (k=#{@k})"
+			end
+
+			private
+
+			def random_crossover_points(genome_length)
+				points = []
+				@k.times { points << EvoSynth.rand(genome_length) }
+				points.sort!
+				points[0] = 0
+				points[@k-1] = genome_length
+				points
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/recombinations/one_point_crossover.rb

@@ -0,0 +1,56 @@
+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	Permission is hereby granted, free of charge, to any person
+#	obtaining a copy of this software and associated documentation
+#	files (the "Software"), to deal in the Software without
+#	restriction, including without limitation the rights to use,
+#	copy, modify, merge, publish, distribute, sublicense, and/or sell
+#	copies of the Software, and to permit persons to whom the
+#	Software is furnished to do so, subject to the following
+#	conditions:
+#
+#	The above copyright notice and this permission notice shall be
+#	included in all copies or substantial portions of the Software.
+#
+#	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#	OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#	HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#	WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#	FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#	OTHER DEALINGS IN THE SOFTWARE.
+
+module EvoSynth
+	module Recombinations
+
+		# EIN-PUNKT-CROSSOVER (Weicker Page 84)
+
+		class OnePointCrossover
+
+			def recombine(parent_one, parent_two)
+				child_one = parent_one.deep_clone
+				child_two = parent_two.deep_clone
+
+				shorter = EvoSynth::Recombinations.individual_with_shorter_genome(parent_one, parent_two)
+				crossover_point = EvoSynth.rand(shorter.genome.size)
+
+				first_range = 0..crossover_point
+				child_one.genome[first_range] =  parent_one.genome[first_range]
+				child_two.genome[first_range] =  parent_two.genome[first_range]
+
+				second_range = (crossover_point + 1)..(shorter.genome.size - 1)
+				child_one.genome[second_range] = parent_two.genome[second_range]
+				child_two.genome[second_range] = parent_one.genome[second_range]
+
+				[child_one, child_two]
+			end
+
+			def to_s
+				"one-point crossover"
+			end
+
+		end
+
+	end
+end