// Assigns the genomes to a species. Returns new collection of species.
//
// Throughout evolution, NEAT maintains a list of species numbered in the order they ap- peared. In
// the first generation, since there are no preexisting species, NEAT begins by creating species 1
// and placing the first genome into that species. All other genomes are placed into species as
// follows: A random member of each existing species is chosen as its permanent representative.
// Genomes are tested one at a time; if a genome’s distance to the representative of any existing
// species is less than δt, a compatibility threshold, it is placed into this species. Otherwise,
// if it is not compatible with any existing species, a new species is created and given a new
// number. After the first generation, genomes are first compared with species from the previous
// generation so that the same species numbers can be used to identify species throughout the run.
// (Stanley, 39)
//
// TODO: Pick a random reprentative each time instead of permanently recording it with the species
// record
func (s Classic) Speciate(curr []neat.Species, genomes []neat.Genome) (next []neat.Species, err error) {
// Copy the species to the new set
next = make([]neat.Species, len(curr))
for i, s := range curr {
next[i] = s
next[i].Age = s.Age + 1
}
// Iterate the genomes, looking for target species
// TODO: This could be made concurrent if it is slow
var δ float64
cnts := make([]int, len(curr))
for i, genome := range genomes {
found := false
for j, species := range next {
δ, err = s.ctx.Comparer().Compare(genome, species.Example)
if err != nil {
return
}
if δ < s.CompatibilityThreshold() {
genomes[i].SpeciesIdx = j
cnts[j] += 1
found = true
break
}
}
if !found {
genomes[i].SpeciesIdx = len(next)
cnts = append(cnts, 1)
species := neat.Species{
Example: neat.CopyGenome(genomes[i]),
}
next = append(next, species)
}
}
// Purge unused species
i := 0
for i < len(next) {
if cnts[i] == 0 {
next = append(next[:i], next[i+1:]...)
cnts = append(cnts[:i], cnts[i+1:]...)
for j := 0; j < len(genomes); j++ {
if genomes[j].SpeciesIdx > i {
genomes[j].SpeciesIdx -= 1
}
}
} else {
i += 1
}
}
return
}
// Creates the pool of potential parents, grouped by species' index. The list of genomes is also
// sorted by fitness in decending order for future operations
func createPool(curr neat.Population) (pool map[int]Improvements) {
pool = make(map[int]Improvements, len(curr.Species))
for _, genome := range curr.Genomes {
pool[genome.SpeciesIdx] = append(pool[genome.SpeciesIdx], neat.CopyGenome(genome))
}
for idx, list := range pool {
sort.Sort(sort.Reverse(list))
pool[idx] = list
}
return
}
func createOffspring(ctx neat.Context, cfg ClassicSettings, cross bool, rng *rand.Rand, pool map[int]Improvements, cnts map[int]int, next *neat.Population) (err error) {
var child neat.Genome
for idx, cnt := range cnts {
l := pool[idx]
for i := 0; i < cnt; i++ {
p1, p2 := pickParents(cfg, cross, rng, l, pool)
if p1.ID == p2.ID {
child = neat.CopyGenome(p1)
} else {
child, err = ctx.Crosser().Cross(p1, p2)
if err != nil {
return
}
}
child.ID = ctx.NextID()
child.Birth = next.Generation
err = ctx.Mutator().Mutate(&child)
next.Genomes = append(next.Genomes, child)
}
}
return
}