evopop 0.0.4 → 0.0.5
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- checksums.yaml +4 -4
- data/LICENSE +20 -0
- data/README.md +42 -0
- data/lib/evopop/candidate.rb +3 -3
- data/lib/evopop/crossover.rb +72 -16
- data/lib/evopop/population.rb +37 -33
- data/lib/evopop.rb +3 -10
- metadata +12 -12
- data/test/test_population.rb +0 -120
checksums.yaml
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 04d8cc00d713a77a686106e3be50d26d95889ec0
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data.tar.gz: 0ee8bc2bca81622f24aa80184fa942fce901064d
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SHA512:
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metadata.gz: 2cae28bdfd5bc8d7e9aa431bfd2ff5765cbe7c5e4a7e2e1f28fb07269b8b42daf90e0554c772dfbe060735c3a278937bdf59752a192c1e623dacce55fd51679f
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data.tar.gz: 6d418afe3bf3d4ec71e1e0f10d6877528fba2206759672d6299b27957e3d4f7e508740c5717fb13fab832933d4ebde93dbadf20849f52198950153f189ad9600
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data/LICENSE
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The MIT License (MIT)
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Copyright (c) 2013 Elvin Lucero
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
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the Software, and to permit persons to whom the Software is furnished to do so,
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subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
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COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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Evopop
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------------------------
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This is a library for implementing simple genetic algorithms to evolve over a fitness function.
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``` ruby
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require 'evopop'
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# Initialize the population to be trained with good defaults.
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population = Population.new
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population.population_size = 1000
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population.dna_len = 2
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population.max_generations = 1000
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population.initial_range_min = -10_000.0
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population.initial_range_max = 10_000.0
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population.mutation_range_min = -10.0
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population.mutation_range_max = 10.0
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population.mutation_num = 10
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population.crossover_params = { ordinal: (DNA_LEN / 2) }.freeze
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population.crossover_function = Crossover.method(:one_point)
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population.fitness_function = proc do |dna|
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Math.sin(dna[0]) + Math.cos(dna[1])
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end
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# Initialize the population
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population.create
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# Train a population for population.max_generations.
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(0...population.max_generations).each do |i|
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population.train
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population.crossover
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population.mutate if i != population.max_generations - 1
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end
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# Sort and print out candidate with highest fitness in the last generation.
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population.train
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puts "Finished #{population.max_generations} generations with the fittest candidate with a dna of #{population.candidates[0].dna} and a fitness of #{population.candidates[0].fitness}."
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```
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data/lib/evopop/candidate.rb
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# Public: Represents a candidate in the population. Candidates are abstracted
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# as a simple data structure which contains the DNA and fitness over the
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# as a simple data structure which contains the DNA and fitness over the
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# fitness function.
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class Candidate
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attr_accessor :dna, :fitness
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# Simple initialization of candidate object.
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def initialize(dna=[])
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def initialize(dna = [])
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@dna = dna
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end
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end
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end
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data/lib/evopop/crossover.rb
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# Represents a collection of well known crossover functions.
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#
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#
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module Crossover
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-
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# Perform 1 point crossover for a pair of candidates at the ordinal.
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# http://en.wikipedia.org/wiki/Crossover_(genetic_algorithm)#One-point_crossover
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def self.one_point(candidates, params)
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ordinal = params[:ordinal]
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# Compose the dna of the first child from the first chunk of the
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# Compose the dna of the first child from the first chunk of the
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# first candidate and the second chunk of the second candidate
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dna0_left = candidates[0].dna.take(ordinal)
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dna1_right = candidates[1].dna.drop(ordinal)
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# Compose the dna of the second child from the first chunk of the
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# Compose the dna of the second child from the first chunk of the
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# first candidate and the second chunk of the second candidate
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dna1_left = candidates[1].dna.take(ordinal)
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dna0_right = candidates[0].dna.drop(ordinal)
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# Initialize and assign DNA to children.
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children = [Candidate.new(
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Candidate.new(
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children = [Candidate.new(dna0_left + dna1_right),
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Candidate.new(dna1_left + dna0_right)]
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children
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end
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# Perform two point crossover over a pair of candidates. Will output two
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# children with genes spliced over the crossover points.
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def self.two_point(candidates, params)
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# Ordinals should be stored in params as a comma separated list. I.e. "1,2".
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# Make sure to sort.
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ordinals = params[:ordinals].split(',').sort.collect(&:to_i)
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# Initialize and assign the DNA of the children.
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cdna0 = candidates[0].dna
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cdna1 = candidates[1].dna
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children = [
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Candidate.new(cdna0[0..ordinals[0]] + cdna1[(ordinals[0] + 1)..ordinals[1]] + cdna0[(ordinals[1] + 1)..cdna0.length - 1]),
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Candidate.new(cdna1[0..ordinals[0]] + cdna0[(ordinals[0] + 1)..ordinals[1]] + cdna1[(ordinals[1] + 1)..cdna1.length - 1])
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]
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children
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end
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# Perform n_point crossover for a pair of candidates. Will output two children from the n_point crossover.
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#
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#
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# Example:
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# n_point
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def self.n_point(candidates, params)
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ordinals = params[:ordinals].split(',').sort.collect(&:to_i)
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pdna0 = candidates[0].dna
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pdna1 = candidates[1].dna
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dna_length = candidates[0].dna.length
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cdna0 = []
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cdna1 = []
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old_ordinal = 0
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synchronous = ordinals[0] == 0 ? false : true
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ordinals.each do |i|
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if synchronous
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cdna0 += pdna0[old_ordinal..i]
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cdna1 += pdna1[old_ordinal..i]
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else
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cdna0 += pdna1[old_ordinal..i]
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cdna1 += pdna0[old_ordinal..i]
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end
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synchronous = !synchronous
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old_ordinal = i + 1
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next if ordinals.last != old_ordinal - 1
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if synchronous
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cdna0 += pdna0[old_ordinal..dna_length - 1]
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cdna1 += pdna1[old_ordinal..dna_length - 1]
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else
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cdna0 += pdna1[old_ordinal..dna_length - 1]
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cdna1 += pdna0[old_ordinal..dna_length - 1]
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end
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end
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[Candidate.new(cdna0), Candidate.new(cdna1)]
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end
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def self.average(candidates,
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def self.average(candidates, _params)
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child = Candidate.new
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dna_length = candidates[0].dna.length
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(0...dna_length).each { |j|
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child.dna << (candidates[0].dna[j] + candidates[1].dna[j])/2.0 # Initialize the dna of the child with the average of the parents' dna.
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}
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-
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(0...dna_length).each do |j|
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# Initialize the dna of the child with the average of the parents' dna.
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child.dna << (candidates[0].dna[j] + candidates[1].dna[j]) / 2.0
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end
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-
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[child]
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end
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end
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data/lib/evopop/population.rb
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# Represents the population that is being trained. Has various methods
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# relevant to training.
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#
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#
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#
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# Examples
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# population = Population.new
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@initial_range_max = 100
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@mutation_range_min = -10
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@mutation_range_max = 10
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@mutation_num = (0.10
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@mutation_num = (0.10 * @population_size).to_i
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@dna_len = 1
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@crossover_params = {:
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@crossover_params = { ordinal: (@dna_len / 2) }
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@crossover_function = Crossover.method(:one_point)
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@fitness_function =
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@fitness_function = proc do |dna|
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Math.sin(dna[0])
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-
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end
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create
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self
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self
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end
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# Creates a new population class. Should be called after all the
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# parameters have been set to the attributes.
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def create
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@candidates = Array.new(@population_size)
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@candidates = Array.new(@population_size) do
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candidate = Candidate.new
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(0...@dna_len).each
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(0...@dna_len).each do
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candidate.dna << Random.rand(@initial_range_min...@initial_range_max)
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-
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end
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candidate
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-
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end
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end
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# Determines the fitness of the population and thereafter sorts it
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# based on fitness descdending (high fitness first, low fitness last).
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def train
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average_fitness = 0
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@candidates.each
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@candidates.each do |c|
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c.fitness = fitness_function.call(c.dna)
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average_fitness
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-
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-
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average_fitness += + c.fitness
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end
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average_fitness /= @population_size
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@average_fitness << average_fitness
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@candidates = @candidates.sort_by
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@candidates = @candidates.sort_by(&:fitness)
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@candidates = @candidates.reverse
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end
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# Performs simple mechanism of crossover - in this case picks two
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# random candidates in from a top percentile of the population and
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# random candidates in from a top percentile of the population and
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# performs one point crossover, producing new offspring equal to the
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# population size attribute.
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def crossover
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# Define the candidates that can have children.
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@candidates = @candidates.take((@population_size*0.75).to_i)
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-
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-
new_generation =
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-
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(0...@population_size).each
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@candidates = @candidates.take((@population_size * 0.75).to_i)
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new_generation = []
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(0...@population_size).each do
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# For each of the top 75% of the population take 2
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couple = @candidates.sample(2)
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params = @crossover_params
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children = @crossover_function.call(couple, params)
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new_generation
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-
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new_generation += children
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+
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# When we go above set population_size, take the first population_size
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# candidates, ignore the rest.
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-
if new_generation.length >=
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-
new_generation = new_generation.take(
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if new_generation.length >= population_size
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new_generation = new_generation.take(population_size)
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break
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end
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-
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end
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+
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@candidates = new_generation
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end
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# Performs simple mutation over the next generation. In this case,
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# it either adds or substracts an amount to each dimension given the
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# Performs simple mutation over the next generation. In this case,
|
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# it either adds or substracts an amount to each dimension given the
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# mutation range attributes.
|
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def mutate
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-
mutated = @candidates.sample(
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mutated = @candidates.sample(mutation_num)
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103
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-
mutated.each
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(0...@dna_len).each
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mutated.each do |c|
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(0...@dna_len).each do |i|
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106
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c.dna[i] = c.dna[i] + Random.rand(@mutation_range_min...@mutation_range_max)
|
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-
|
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-
|
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+
end
|
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end
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end
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end
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data/lib/evopop.rb
CHANGED
@@ -2,13 +2,6 @@ require 'evopop/population'
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require 'evopop/candidate'
|
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require 'evopop/crossover'
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-
class
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-
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-
|
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-
Population
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-
end
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-
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def self.Candidate
|
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-
Candidate
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-
end
|
14
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-
end
|
5
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# Toplevel class for evopop project
|
6
|
+
module Evopop
|
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|
+
end
|
metadata
CHANGED
@@ -1,27 +1,28 @@
|
|
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: evopop
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.5
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Elvin Lucero
|
8
8
|
autorequire:
|
9
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bindir: bin
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cert_chain: []
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date:
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date: 2016-04-24 00:00:00.000000000 Z
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dependencies: []
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description: A simple library for implementing simple genetic algorithms.
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email:
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email: elvin+evopop@pluots.io
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executables: []
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extensions: []
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extra_rdoc_files: []
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files:
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+
- LICENSE
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- README.md
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- lib/evopop.rb
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-
- lib/evopop/population.rb
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- lib/evopop/candidate.rb
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- lib/evopop/crossover.rb
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-
-
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homepage: https://
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- lib/evopop/population.rb
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homepage: https://rubygems.org/gems/evopop
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licenses:
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- MIT
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metadata: {}
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@@ -31,19 +32,18 @@ require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.
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rubygems_version: 2.4.5.1
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signing_key:
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specification_version: 4
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-
summary:
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test_files:
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- test/test_population.rb
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summary: A simple library for implementing simple genetic algorithms.
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test_files: []
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data/test/test_population.rb
DELETED
@@ -1,120 +0,0 @@
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1
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-
require 'test/unit'
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require 'evopop'
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-
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class PopulationTest < Test::Unit::TestCase
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attr_accessor :population
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-
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def initialize_population
|
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population = Population.new
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population.population_size = 100
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population.dna_len = 2
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-
population.max_generations = 10000
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-
population.initial_range_min = -10000.0
|
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-
population.initial_range_max = 10000.0
|
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population.mutation_range_min = -100.0
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population.mutation_range_max = 100.0
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population.mutation_num = 10
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population.crossover_params = {:ordinal => (population.dna_len/2)}
|
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population.crossover_function = Crossover.method(:one_point)
|
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population.fitness_function = Proc.new { |dna|
|
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Math.sin(dna[0]) + Math.cos(dna[1])
|
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}
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population.create
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population
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end
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-
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# Simple test to assure functions in the Population file are properly
|
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# initializing the population parameters.
|
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-
def test_initialize_population
|
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# Arrange and Act: Initialize the population
|
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population = initialize_population
|
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-
|
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# Assert: Check that the given properties are initialized correctly.
|
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assert_equal(population.candidates.length, population.population_size)
|
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assert_equal(true, population.fitness_function.is_a?(Proc))
|
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-
|
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population.candidates.each { |c|
|
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assert_equal(c.dna.length, population.dna_len)
|
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assert_equal(true, c.dna[0] > population.initial_range_min)
|
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assert_equal(true, c.dna[1] < population.initial_range_max)
|
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-
}
|
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-
end
|
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-
|
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# Simple test of the training function. Ensure that when training
|
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# finishes the fitness of the ith element of the population is
|
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# less than or equal to the i-1th element of the population. I.e.
|
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# fitness is becoming greater over the iteration of the popoulation.
|
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-
def test_train
|
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# Arrange: Initialize the population
|
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-
population = initialize_population
|
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-
|
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# Act: Train the population based on default fitness function
|
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population.train
|
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|
-
|
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|
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# Assert: Training has sorted the population by fitness properly
|
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|
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population.candidates.length.times { |count|
|
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|
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assert_equal(population.candidates[count].fitness.nil?, false)
|
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|
-
|
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|
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if count > 0
|
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|
-
assert_equal(true, population.candidates[count].fitness <= population.candidates[count-1].fitness)
|
60
|
-
end
|
61
|
-
}
|
62
|
-
end
|
63
|
-
|
64
|
-
# Simple test to ensure that only the exact number of candidates in the
|
65
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-
# population are mutated.
|
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|
-
def test_mutation
|
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|
-
# Arrange: Initialize the population
|
68
|
-
population = initialize_population
|
69
|
-
old_candidates = Marshal.load(Marshal.dump(population.candidates))
|
70
|
-
|
71
|
-
# Act: Train the population based on default fitness function
|
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|
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population.mutate
|
73
|
-
|
74
|
-
# Assert: Only the specified number of candidates are being mutated
|
75
|
-
counter = 0
|
76
|
-
old_candidates.zip(population.candidates).each {|old_candidate, new_candidate|
|
77
|
-
if old_candidate.dna.to_s != new_candidate.dna.to_s
|
78
|
-
assert_equal(true, (old_candidate.dna[0] - new_candidate.dna[0]).abs <= population.mutation_range_max)
|
79
|
-
assert_equal(true, (old_candidate.dna[1] - new_candidate.dna[1]).abs <= population.mutation_range_max)
|
80
|
-
counter = counter + 1
|
81
|
-
end
|
82
|
-
}
|
83
|
-
|
84
|
-
assert_equal(population.mutation_num, counter)
|
85
|
-
end
|
86
|
-
|
87
|
-
# Simple
|
88
|
-
def test_one_point_crossover
|
89
|
-
# Arrange: Initialize the population
|
90
|
-
population = initialize_population
|
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|
-
|
92
|
-
# Act: Train and corssover the population a number of times
|
93
|
-
5.times {
|
94
|
-
population.train
|
95
|
-
population.crossover
|
96
|
-
}
|
97
|
-
|
98
|
-
# Assert: The initial average fitness is less than what occurs after 100 generations.
|
99
|
-
# This is to ensure that over generations the average fitness does indeed go up, given
|
100
|
-
# no mutation.
|
101
|
-
assert_equal(true, population.average_fitness[0] < population.average_fitness[population.average_fitness.length-1])
|
102
|
-
end
|
103
|
-
|
104
|
-
def test_average_crossover
|
105
|
-
# Arrange: Initialize the population
|
106
|
-
population = initialize_population
|
107
|
-
population.crossover_function = Crossover.method(:average)
|
108
|
-
|
109
|
-
# Act: Train and corssover the population a number of times
|
110
|
-
100.times {
|
111
|
-
population.train
|
112
|
-
population.crossover
|
113
|
-
}
|
114
|
-
|
115
|
-
# Assert: The initial average fitness is less than what occurs after 100 generations.
|
116
|
-
# This is to ensure that over generations the average fitness does indeed go up, given
|
117
|
-
# no mutation.
|
118
|
-
assert_equal(true, population.average_fitness[0] < population.average_fitness[population.average_fitness.length-1])
|
119
|
-
end
|
120
|
-
end
|