class MHL::IntegerVectorGenotypeSpace
This class implements a genotype with integer space representation
Public Class Methods
new(opts, logger)
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# File lib/mhl/integer_vector_genotype_space.rb, line 5 def initialize(opts, logger) @random_func = opts[:random_func] @dimensions = opts[:dimensions].to_i unless @dimensions and @dimensions > 0 raise ArgumentError, 'Must have positive integer dimensions' end # TODO: enable to choose which recombination function to use case opts[:recombination_type].to_s when /intermediate/i @recombination_func = :extended_intermediate_recombination_int when /line/i @recombination_func = :extended_line_recombination_int else raise ArgumentError, 'Recombination function must be either line or intermediate!' end @constraints = opts[:constraints] if @constraints and @constraints.size != @dimensions raise ArgumentError, 'Constraints must be provided for every dimension!' end @logger = logger end
Public Instance Methods
get_random()
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# File lib/mhl/integer_vector_genotype_space.rb, line 31 def get_random if @random_func @random_func.call else if @constraints @constraints.map{|x| x[:from] + SecureRandom.random_number(x[:to] - x[:from]) } else raise 'Automated random genotype generation when no constraints are provided is not implemented yet!' end end end
reproduce_from(p1, p2, mutation_rv, recombination_rv)
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reproduction with random geometric mutation and intermediate recombination
# File lib/mhl/integer_vector_genotype_space.rb, line 45 def reproduce_from(p1, p2, mutation_rv, recombination_rv) # make copies of p1 and p2 # (we're only interested in the :genotype key) c1 = { genotype: p1[:genotype].dup } c2 = { genotype: p2[:genotype].dup } # mutation comes first random_delta_mutation(c1[:genotype], mutation_rv) random_delta_mutation(c2[:genotype], mutation_rv) # and then recombination send(@recombination_func, c1[:genotype], c2[:genotype], recombination_rv) if @constraints repair_chromosome(c1[:genotype]) repair_chromosome(c2[:genotype]) end return c1, c2 end
Private Instance Methods
extended_intermediate_recombination_int(g1, g2, recombination_rv)
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integer variant of extended intermediate recombination [MUHLENBEIN93] (see [LUKE15] page 65)
# File lib/mhl/integer_vector_genotype_space.rb, line 87 def extended_intermediate_recombination_int(g1, g2, recombination_rv) # TODO: disable this check in non-debugging mode raise ArgumentError, 'g1 and g2 must have the same dimension' unless g1.size == g2.size # recombination g1.each_index do |i| begin alpha = recombination_rv.next beta = recombination_rv.next t = (alpha * g1[i] + (1.0 - alpha) * g2[i] + 0.5).floor s = ( beta * g2[i] + (1.0 - beta) * g1[i] + 0.5).floor end g1[i] = t g2[i] = s end end
extended_line_recombination_int(g1, g2, recombination_rv)
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integer variant of extended line recombination [MUHLENBEIN93] (see
- LUKE15
-
page 64)
# File lib/mhl/integer_vector_genotype_space.rb, line 106 def extended_line_recombination_int(g1, g2, recombination_rv) # TODO: disable this check in non-debugging mode raise ArgumentError, 'g1 and g2 must have the same dimension' unless g1.size == g2.size alpha = recombination_rv.next beta = recombination_rv.next # recombination g1.each_index do |i| t = (alpha * g1[i] + (1.0 - alpha) * g2[i] + 0.5).floor s = ( beta * g2[i] + (1.0 - beta) * g1[i] + 0.5).floor g1[i] = t g2[i] = s end end
random_delta_mutation(g, mutation_rv)
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mutation based on random perturbations of (all) the individual's chromosomes, according to a geometric distribution [TORTONESI16]
# File lib/mhl/integer_vector_genotype_space.rb, line 71 def random_delta_mutation(g, mutation_rv) g.each_index do |i| delta = mutation_rv.next if rand() >= 0.5 # half of the times the variation will be positive ... g[i] += delta else # ... and half of the times it will be negative g[i] -= delta end end end
repair_chromosome(g)
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# File lib/mhl/integer_vector_genotype_space.rb, line 122 def repair_chromosome(g) g.each_index do |i| if g[i] < @constraints[i][:from] range = "[#{@constraints[i][:from]},#{@constraints[i][:to]}]" @logger.debug "repairing g[#{i}] #{g[i]} to fit within #{range}" if @logger g[i] = @constraints[i][:from] @logger.debug "g[#{i}] repaired as: #{g[i]}" if @logger elsif g[i] > @constraints[i][:to] range = "[#{@constraints[i][:from]},#{@constraints[i][:to]}]" @logger.debug "repairing g[#{i}] #{g[i]} to fit within #{range}" if @logger g[i] = @constraints[i][:to] @logger.debug "g[#{i}] repaired as: #{g[i]}" if @logger end end end