class MHL::IntegerVectorGenotypeSpace

This class implements a genotype with integer space representation

Public Class Methods

new(opts, logger) click to toggle source
# 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() click to toggle source
# 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) click to toggle source

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) click to toggle source

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) click to toggle source

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) click to toggle source

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) click to toggle source
# 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