Source code for reproduction

Handles creation of genomes, either from scratch or by sexual or
asexual reproduction from parents.
from __future__ import division

import math
import random
from itertools import count

from neat.config import ConfigParameter, DefaultClassConfig
from neat.math_util import mean
from neat.six_util import iteritems, itervalues

# TODO: Provide some sort of optional cross-species performance criteria, which
# are then used to control stagnation and possibly the mutation rate
# configuration. This scheme should be adaptive so that species do not evolve
# to become "cautious" and only make very slow progress.

[docs]class DefaultReproduction(DefaultClassConfig): """ Implements the default NEAT-python reproduction scheme: explicit fitness sharing with fixed-time species stagnation. """
[docs] @classmethod def parse_config(cls, param_dict): return DefaultClassConfig(param_dict, [ConfigParameter('elitism', int, 0), ConfigParameter('survival_threshold', float, 0.2), ConfigParameter('min_species_size', int, 2)])
def __init__(self, config, reporters, stagnation): # pylint: disable=super-init-not-called self.reproduction_config = config self.reporters = reporters self.genome_indexer = count(1) self.stagnation = stagnation self.ancestors = {}
[docs] def create_new(self, genome_type, genome_config, num_genomes): new_genomes = {} for i in range(num_genomes): key = next(self.genome_indexer) g = genome_type(key) g.configure_new(genome_config) new_genomes[key] = g self.ancestors[key] = tuple() return new_genomes
[docs] @staticmethod def compute_spawn(adjusted_fitness, previous_sizes, pop_size, min_species_size): """Compute the proper number of offspring per species (proportional to fitness).""" af_sum = sum(adjusted_fitness) spawn_amounts = [] for af, ps in zip(adjusted_fitness, previous_sizes): if af_sum > 0: s = max(min_species_size, af / af_sum * pop_size) else: s = min_species_size d = (s - ps) * 0.5 c = int(round(d)) spawn = ps if abs(c) > 0: spawn += c elif d > 0: spawn += 1 elif d < 0: spawn -= 1 spawn_amounts.append(spawn) # Normalize the spawn amounts so that the next generation is roughly # the population size requested by the user. total_spawn = sum(spawn_amounts) norm = pop_size / total_spawn spawn_amounts = [max(min_species_size, int(round(n * norm))) for n in spawn_amounts] return spawn_amounts
[docs] def reproduce(self, config, species, pop_size, generation): """ Handles creation of genomes, either from scratch or by sexual or asexual reproduction from parents. """ # TODO: I don't like this modification of the species and stagnation objects, # because it requires internal knowledge of the objects. # Filter out stagnated species, collect the set of non-stagnated # species members, and compute their average adjusted fitness. # The average adjusted fitness scheme (normalized to the interval # [0, 1]) allows the use of negative fitness values without # interfering with the shared fitness scheme. all_fitnesses = [] remaining_species = [] for stag_sid, stag_s, stagnant in self.stagnation.update(species, generation): if stagnant: self.reporters.species_stagnant(stag_sid, stag_s) else: all_fitnesses.extend( for m in itervalues(stag_s.members)) remaining_species.append(stag_s) # The above comment was not quite what was happening - now getting fitnesses # only from members of non-stagnated species. # No species left. if not remaining_species: species.species = {} return {} # was [] # Find minimum/maximum fitness across the entire population, for use in # species adjusted fitness computation. min_fitness = min(all_fitnesses) max_fitness = max(all_fitnesses) # Do not allow the fitness range to be zero, as we divide by it below. # TODO: The ``1.0`` below is rather arbitrary, and should be configurable. fitness_range = max(1.0, max_fitness - min_fitness) for afs in remaining_species: # Compute adjusted fitness. msf = mean([ for m in itervalues(afs.members)]) af = (msf - min_fitness) / fitness_range afs.adjusted_fitness = af adjusted_fitnesses = [s.adjusted_fitness for s in remaining_species] avg_adjusted_fitness = mean(adjusted_fitnesses) # type: float"Average adjusted fitness: {:.3f}".format(avg_adjusted_fitness)) # Compute the number of new members for each species in the new generation. previous_sizes = [len(s.members) for s in remaining_species] min_species_size = self.reproduction_config.min_species_size # Isn't the effective min_species_size going to be max(min_species_size, # self.reproduction_config.elitism)? That would probably produce more accurate tracking # of population sizes and relative fitnesses... doing. TODO: document. min_species_size = max(min_species_size,self.reproduction_config.elitism) spawn_amounts = self.compute_spawn(adjusted_fitnesses, previous_sizes, pop_size, min_species_size) new_population = {} species.species = {} for spawn, s in zip(spawn_amounts, remaining_species): # If elitism is enabled, each species always at least gets to retain its elites. spawn = max(spawn, self.reproduction_config.elitism) assert spawn > 0 # The species has at least one member for the next generation, so retain it. old_members = list(iteritems(s.members)) s.members = {} species.species[s.key] = s # Sort members in order of descending fitness. old_members.sort(reverse=True, key=lambda x: x[1].fitness) # Transfer elites to new generation. if self.reproduction_config.elitism > 0: for i, m in old_members[:self.reproduction_config.elitism]: new_population[i] = m spawn -= 1 if spawn <= 0: continue # Only use the survival threshold fraction to use as parents for the next generation. repro_cutoff = int(math.ceil(self.reproduction_config.survival_threshold * len(old_members))) # Use at least two parents no matter what the threshold fraction result is. repro_cutoff = max(repro_cutoff, 2) old_members = old_members[:repro_cutoff] # Randomly choose parents and produce the number of offspring allotted to the species. while spawn > 0: spawn -= 1 parent1_id, parent1 = random.choice(old_members) parent2_id, parent2 = random.choice(old_members) # Note that if the parents are not distinct, crossover will produce a # genetically identical clone of the parent (but with a different ID). gid = next(self.genome_indexer) child = config.genome_type(gid) child.configure_crossover(parent1, parent2, config.genome_config) child.mutate(config.genome_config) new_population[gid] = child self.ancestors[gid] = (parent1_id, parent2_id) return new_population