evosynth 0.1.0

data/lib/evosynth/core/randomizer.rb

@@ -0,0 +1,73 @@
+#	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
+
+	# Uniform distributed (between 0.0 and 1.0) pseudo-random number generator of EvoSynth,
+	# overwrite this function if you want to change the uniform distributed random number
+	# generator of EvoSynth.
+	# 
+	# This a fascade to Kernel.rand. For a complete documentation see the Ruby documentation of rand().
+
+	def EvoSynth.rand(*args)
+		Kernel.rand(*args)
+	end
+
+	# Returns a pseudo-random boolean value (true or false).
+
+	def EvoSynth.rand_bool
+		EvoSynth.rand(2) > 0
+	end
+
+	#	:call-seq:
+	#		EvoSynth.nrand				#=> pseudo-random normal distributed random number
+	#		EvoSynth.nrand(3.2)			#=> pseudo-random normal distributed random number around 3.2
+	#		EvoSynth.nrand(2.4, 1.5)	#=> pseudo-random normal distributed random number around 2.4 with sigma = 1.5
+	#
+	# Normal distributed pseudo-random number generator of EvoSynth. Uses the polar form of
+	# the Box-Mueller transformation to transform two Uniform distributed random numbers into
+	# one normal distributed random number (see: http://www.taygeta.com/random/gaussian.html=).
+
+	def EvoSynth.nrand(mu = 0.0, sigma = 1.0)
+		x1, x2, w, = 0.0, 0.0, 0.0, 0.0
+
+		begin
+			x1 = 2.0 * EvoSynth.rand - 1.0
+			x2 = 2.0 * EvoSynth.rand - 1.0
+			w = x1 ** 2.0 + x2 ** 2.0;
+		end while ( w >= 1.0 )
+
+		w = Math.sqrt( (-2.0 * Math.log( w ) ) / w )
+		mu + (x2 * w * sigma)
+	end
+
+	# Set the seed of the uniform distributed random number generator of EvoSynth.
+	#
+	# This a fascade to Kernel.srand, for a complete documentation see the Ruby documentation of srand().
+
+	def EvoSynth.srand(*args)
+		Kernel.srand(*args)
+	end
+
+end

data/lib/evosynth/decoder.rb

@@ -0,0 +1,33 @@
+#	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
+
+	# This module contains all genome decoders (genotype <-> phenotype conversion).
+	module Decoder
+	end
+end
+
+require 'evosynth/decoder/gray'
+require 'evosynth/decoder/binary_to_real'

data/lib/evosynth/decoder/binary_to_real.rb

@@ -0,0 +1,57 @@
+#	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 Decoder
+
+		#	:call-seq:
+		#		Decoder.binary_to_real([1,1,0,1]) -> Float (between -1.0 and 1.0)
+		#		Decoder.binary_to_real([1,1,0,1], 0.0) -> Float (between 0.0 and 1.0)
+		#		Decoder.binary_to_real([1,1,0,1], -5.12, 5.12) -> Float (between -5.12 and 5.12)
+		#
+		# This converts a given array of binary values (either 1/0 or true/false) into
+		# a Float in a given range.
+
+		def Decoder.binary_to_real(binary, min_bound = -1.0, max_bound = 1.0)
+			binary = binary.map do |bin|
+				case bin
+					when false then 0
+					when true then 1
+					else bin
+				end
+			end
+
+			max_bound, min_bound = min_bound, max_bound if min_bound > max_bound
+
+			range_size = max_bound.to_f - min_bound.to_f
+			integer = Integer("0b#{binary.join}")
+			max_integer = Integer("0b" + ("1" * binary.size))
+
+			float = integer * (range_size / max_integer) + min_bound;
+			float
+		end
+
+	end
+
+end

data/lib/evosynth/decoder/gray.rb

@@ -0,0 +1,54 @@
+#	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 Decoder
+
+		# Converts a binary gray code bitstring (either 1/0 or true/false) into a standard binary bitstring.
+
+		def Decoder.gray_to_binary(gray)
+			rev_stdbin = Array.new(gray.size)
+			gray.reverse!
+
+			rev_stdbin[gray.size - 1] = gray[gray.size - 1]
+			(gray.size - 2).downto(0) { |index| rev_stdbin[index] = rev_stdbin[index + 1] ^ gray[index] }
+
+			rev_stdbin.reverse
+		end
+
+		# Converts a standard binary bitstring (either 1/0 or true/false) into a gray code bitstring.
+
+		def Decoder.binary_to_gray(binary)
+			gray = Array.new(binary)
+
+			popped = gray.pop
+			gray.unshift(popped ^ popped)
+			gray.each_index { |index| gray[index] = binary[index] ^ gray[index]}
+
+			gray
+		end
+
+	end
+
+end

data/lib/evosynth/evolvers.rb

@@ -0,0 +1,41 @@
+#	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 'evosynth/evolvers/evolver'
+require 'evosynth/evolvers/elitism'
+
+require 'evosynth/evolvers/basic/hillclimber'
+require 'evosynth/evolvers/basic/population_hillclimber'
+require 'evosynth/evolvers/basic/genetic_algorithm'
+require 'evosynth/evolvers/basic/steady_state_ga'
+require 'evosynth/evolvers/basic/memetic_algorithm'
+
+require 'evosynth/evolvers/evolution_strategies/adaptive_es'
+require 'evosynth/evolvers/evolution_strategies/selfadaptive_es'
+require 'evosynth/evolvers/evolution_strategies/derandomized_es'
+
+require 'evosynth/evolvers/local_search/local_search'
+
+require 'evosynth/evolvers/coevolutionary/round_robin_coevolutionary'
+require 'evosynth/evolvers/coevolutionary/balanced_coevolutionary'

data/lib/evosynth/evolvers/basic/genetic_algorithm.rb

@@ -0,0 +1,92 @@
+#	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 Evolvers
+
+		# GENETISCHER-ALGORITHMUS (Weicker Page 85)
+
+		class GeneticAlgorithm
+			include EvoSynth::Evolvers::Evolver
+
+			DEFAULT_SELECTION = EvoSynth::Selections::FitnessProportionalSelection.new
+			DEFAULT_RECOMBINATION = EvoSynth::Recombinations::OnePointCrossover.new
+			DEFAULT_RECOMBINATION_PROBABILITY = 0.75
+			DEFAULT_CHILD_FACTOR = 0.5
+
+			def initialize(profile)
+				init_profile :population, 
+				    :evaluator,
+				    :mutation,
+				    :parent_selection			=> DEFAULT_SELECTION,
+				    :recombination				=> DEFAULT_RECOMBINATION,
+				    :recombination_probability	=> DEFAULT_RECOMBINATION_PROBABILITY,
+					:child_factor				=> DEFAULT_CHILD_FACTOR
+
+				use_profile profile
+
+				@population.each { |individual| @evaluator.calculate_and_set_initial_fitness(individual) }
+			end
+
+			def to_s
+				"basic genetic algoritm <mutation: #{@mutation}, parent selection: #{@parent_selection}, recombination: #{@recombination}>"
+			end
+
+			def best_solution
+				@population.best
+			end
+
+			def worst_solution
+				@population.worst
+			end
+
+			def return_result
+				@population
+			end
+
+			def next_generation
+				selected_pop = @parent_selection.select(@population, @population.size * @child_factor)
+				@population.clear
+
+				selected_pop.each_index do |index_one|
+					index_two = (index_one + 1) % selected_pop.size
+
+					if EvoSynth.rand < @recombination_probability
+						child_one, child_two = @recombination.recombine(selected_pop[index_one], selected_pop[index_two])
+					else
+						child_one = selected_pop[index_one]
+						child_two = selected_pop[index_two]
+					end
+
+					@population.add(@mutation.mutate(child_one))
+					@population.add(@mutation.mutate(child_two))
+				end
+
+				@population.each { |individual| @evaluator.calculate_and_set_fitness(individual) }
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/evolvers/basic/hillclimber.rb

@@ -0,0 +1,64 @@
+#	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 Evolvers
+
+		# BINÄRES-HILLCLIMBING (Weicker Page 49)
+
+		class Hillclimber
+			include EvoSynth::Evolvers::Evolver
+
+			def initialize(profile)
+				init_profile :individual, :mutation, :evaluator
+				use_profile profile
+
+				@evaluator.calculate_and_set_initial_fitness(@individual)
+			end
+
+			def to_s
+				"hillclimber <mutation: #{@mutation}, individual: #{@individual}>"
+			end
+
+			def best_solution
+				@individual
+			end
+
+			def worst_solution
+				@individual
+			end
+
+			def return_result
+				@individual
+			end
+
+			def next_generation
+				child = @mutation.mutate(@individual)
+				@evaluator.calculate_and_set_fitness(child)
+				@individual = child if child > @individual
+			end
+		end
+
+	end
+end

data/lib/evosynth/evolvers/basic/memetic_algorithm.rb

@@ -0,0 +1,111 @@
+#	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 Evolvers
+
+		# MEMETISCHER-ALGORITHMUS (Weicker Page 165)
+		# see also: http://en.wikipedia.org/wiki/Memetic_algorithm for later improvments
+
+		class MemeticAlgorithm
+			include EvoSynth::Evolvers::Evolver
+
+			DEFAULT_CHILD_FACTOR = 0.5
+			DEFAULT_RECOMBINATION_PROBABILITY = 1.0
+			DEFAULT_RECOMBINATION = EvoSynth::Recombinations::KPointCrossover.new(2)
+			DEFAULT_INDIVIDUAL_LEARNING_GOAL = ->(gen, best) { gen >= 10 }
+			DEFAULT_INDIVIDUAL_LEARNING_PROBABILITY = 0.75
+			DEFAULT_SELECTION = EvoSynth::Selections::FitnessProportionalSelection.new
+			DEFAULT_SUBEVOLVER_CREATOR = ->(profile) { EvoSynth::Evolvers::LocalSearch.new(profile) }
+
+			def initialize(profile)
+				init_profile :population,
+					:evaluator,
+				    :mutation,
+					:recombination						=> DEFAULT_RECOMBINATION,
+					:parent_selection					=> DEFAULT_SELECTION,
+					:enviromental_selection				=> DEFAULT_SELECTION,
+					:child_factor						=> DEFAULT_CHILD_FACTOR,
+					:recombination_probability			=> DEFAULT_RECOMBINATION_PROBABILITY,
+				    :subevolver_creator					=> DEFAULT_SUBEVOLVER_CREATOR,
+					:individual_learning_goal			=> DEFAULT_INDIVIDUAL_LEARNING_GOAL,
+					:individual_learning_probability	=> DEFAULT_INDIVIDUAL_LEARNING_PROBABILITY
+
+				use_profile profile
+
+				@population.each { |individual| @evaluator.calculate_and_set_initial_fitness(individual) }
+			end
+
+			def to_s
+				"memetic algoritm"
+			end
+
+			def best_solution
+				@population.best
+			end
+
+			def worst_solution
+				@population.worst
+			end
+
+			def return_result
+				@population
+			end
+
+			def next_generation
+				selected_population = @parent_selection.select(@population, @population.size * @child_factor)
+				child_population = EvoSynth::Population.new
+
+				selected_population.each_index do |index_one|
+					index_two = (index_one + 1) % selected_population.size
+
+					if EvoSynth.rand < @recombination_probability
+						child_one, child_two = @recombination.recombine(selected_population[index_one], selected_population[index_two])
+					else
+						child_one = selected_population[index_one]
+						child_two = selected_population[index_two]
+					end
+
+					child_population.add(@mutation.mutate(child_one))
+					child_population.add(@mutation.mutate(child_two))
+				end
+
+				child_population.map! do |child|
+					if EvoSynth.rand < @individual_learning_probability
+						@profile.individual = child
+						subevolver = @subevolver_creator.call(@profile)
+						subevolver.run_until &@individual_learning_goal
+					else
+						child
+					end
+				end
+
+				child_population.each { |individual| @evaluator.calculate_and_set_fitness(individual) }
+				@population = @enviromental_selection.select(child_population, @population.size)
+			end
+
+		end
+
+	end
+end