Source code for species

"""Divides the population into species based on genomic distances."""
from itertools import count

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

[docs]class Species(object): def __init__(self, key, generation): self.key = key self.created = generation self.last_improved = generation self.representative = None self.members = {} self.fitness = None self.adjusted_fitness = None self.fitness_history = []
[docs] def update(self, representative, members): self.representative = representative self.members = members
[docs] def get_fitnesses(self): return [m.fitness for m in itervalues(self.members)]
[docs]class GenomeDistanceCache(object): def __init__(self, config): self.distances = {} self.config = config self.hits = 0 self.misses = 0
[docs] def __call__(self, genome0, genome1): g0 = genome0.key g1 = genome1.key d = self.distances.get((g0, g1)) if d is None: # Distance is not already computed. d = genome0.distance(genome1, self.config) self.distances[g0, g1] = d self.distances[g1, g0] = d self.misses += 1 else: self.hits += 1 return d
[docs]class DefaultSpeciesSet(DefaultClassConfig): """ Encapsulates the default speciation scheme. """ def __init__(self, config, reporters): # pylint: disable=super-init-not-called self.species_set_config = config self.reporters = reporters self.indexer = count(1) self.species = {} self.genome_to_species = {}
[docs] @classmethod def parse_config(cls, param_dict): return DefaultClassConfig(param_dict, [ConfigParameter('compatibility_threshold', float)])
[docs] def speciate(self, config, population, generation): """ Place genomes into species by genetic similarity. Note that this method assumes the current representatives of the species are from the old generation, and that after speciation has been performed, the old representatives should be dropped and replaced with representatives from the new generation. If you violate this assumption, you should make sure other necessary parts of the code are updated to reflect the new behavior. """ assert isinstance(population, dict) compatibility_threshold = self.species_set_config.compatibility_threshold # Find the best representatives for each existing species. unspeciated = set(iterkeys(population)) distances = GenomeDistanceCache(config.genome_config) new_representatives = {} new_members = {} for sid, s in iteritems(self.species): candidates = [] for gid in unspeciated: g = population[gid] d = distances(s.representative, g) candidates.append((d, g)) # The new representative is the genome closest to the current representative. ignored_rdist, new_rep = min(candidates, key=lambda x: x[0]) new_rid = new_rep.key new_representatives[sid] = new_rid new_members[sid] = [new_rid] unspeciated.remove(new_rid) # Partition population into species based on genetic similarity. while unspeciated: gid = unspeciated.pop() g = population[gid] # Find the species with the most similar representative. candidates = [] for sid, rid in iteritems(new_representatives): rep = population[rid] d = distances(rep, g) if d < compatibility_threshold: candidates.append((d, sid)) if candidates: ignored_sdist, sid = min(candidates, key=lambda x: x[0]) new_members[sid].append(gid) else: # No species is similar enough, create a new species, using # this genome as its representative. sid = next(self.indexer) new_representatives[sid] = gid new_members[sid] = [gid] # Update species collection based on new speciation. self.genome_to_species = {} for sid, rid in iteritems(new_representatives): s = self.species.get(sid) if s is None: s = Species(sid, generation) self.species[sid] = s members = new_members[sid] for gid in members: self.genome_to_species[gid] = sid member_dict = dict((gid, population[gid]) for gid in members) s.update(population[rid], member_dict) gdmean = mean(itervalues(distances.distances)) gdstdev = stdev(itervalues(distances.distances)) self.reporters.info( 'Mean genetic distance {0:.3f}, standard deviation {1:.3f}'.format(gdmean, gdstdev))
[docs] def get_species_id(self, individual_id): return self.genome_to_species[individual_id]
[docs] def get_species(self, individual_id): sid = self.genome_to_species[individual_id] return self.species[sid]