private void assignNeuronDepth(Gene[] nodeGenes, int depth, Chromosome mutated) {
int i;
NEATNodeGene node;
// ArrayList nodeGenes = this.findOutputNodes(this.candidateNodes(genes));
for (i = 0; i < nodeGenes.length; i++) {
node = (NEATNodeGene) nodeGenes[i];
if (node.getType() == NEATNodeGene.OUTPUT) {
if (depth == 1) {
node.setDepth(depth);
this.assignNeuronDepth(
this.findSourceNodes(node.id(), mutated.genes()), depth + 1, mutated);
}
} else if (node.getType() == NEATNodeGene.HIDDEN) {
if (node.getDepth() == 0) {
// we have an unassigned depth
node.setDepth(depth);
this.assignNeuronDepth(
this.findSourceNodes(node.id(), mutated.genes()), depth + 1, mutated);
}
} else if (node.getType() == NEATNodeGene.INPUT) {
node.setDepth(Integer.MAX_VALUE);
}
}
}
/** Mutates the chromsome based on the set of probabilities. */
public Chromosome mutate(Chromosome mutatee) {
Gene[] genes = mutatee.genes();
int originalSize = genes.length;
NEATChromosome mutated;
int i;
for (i = 0; i < genes.length; i++) {
if (genes[i] instanceof NEATLinkGene) {
genes[i] = this.mutateLink((NEATLinkGene) genes[i]);
} else if (genes[i] instanceof NEATNodeGene) {
genes[i] = this.mutateNode((NEATNodeGene) genes[i]);
} else if (genes[i] instanceof NEATFeatureGene) {
genes[i] = this.mutateFeature((NEATFeatureGene) genes[i]);
}
}
mutated = new NEATChromosome(genes);
mutated.setSpecieId(((NEATChromosome) mutatee).getSpecieId());
this.mutateAddLink(mutated);
this.mutateAddNode(mutated);
// now update chrome for depth and recurrency legality
this.updateDepthInfo(mutated);
mutated.updateChromosome(this.ensureLegalLinks(mutated.genes()));
if (mutated.genes().length < originalSize) {
System.out.println(
"Mutation -- Original: " + originalSize + " new: " + mutated.genes().length);
}
return (mutated);
}
private void mutateAddNode(Chromosome mutatee) {
double nodeRandVal = nodeRand.nextDouble();
ArrayList nodeLinks;
// ArrayList nodes;
NEATLinkGene chosen;
NEATNodeGene newNode;
NEATLinkGene newLower;
NEATLinkGene newUpper;
int newChromoIdx = mutatee.genes().length;
// Gene[] newChromo = new Gene[newChromoIdx + 3];
Gene[] newChromo = new Gene[newChromoIdx + 2];
System.arraycopy(mutatee.genes(), 0, newChromo, 0, newChromoIdx);
int linkIdx;
if (nodeRandVal < this.pAddNode) {
// add a node on an existing enabled connection
// find an existing connection to intercept
nodeLinks = this.candidateLinks(mutatee.genes(), true);
if (nodeLinks.size() > 0) {
// ensure there is a link to split
linkIdx = nodeRand.nextInt(nodeLinks.size());
chosen = (NEATLinkGene) nodeLinks.get(linkIdx);
// disable old link
chosen.setEnabled(false);
newNode = InnovationDatabase.database().submitNodeInnovation(chosen);
// newNode.setBias(MathUtils.nextPlusMinusOne());
newLower =
InnovationDatabase.database().submitLinkInnovation(chosen.getFromId(), newNode.id());
newUpper =
InnovationDatabase.database().submitLinkInnovation(newNode.id(), chosen.getToId());
// set weights according to Stanley et al's NEAT document
newLower.setWeight(1);
newUpper.setWeight(chosen.getWeight());
// now update the chromosome with new node and 2 new links
newChromo[this.findChosenIndex(chosen, mutatee)] = newNode;
// newChromo[newChromoIdx++] = newNode;
newChromo[newChromoIdx++] = newLower;
newChromo[newChromoIdx] = newUpper;
mutatee.updateChromosome(newChromo);
}
}
}
private void mutateAddLink(Chromosome mutatee) {
double linkRandVal = linkRand.nextDouble();
NEATNodeGene from;
NEATNodeGene to;
int rIdx;
int i = 0;
ArrayList links;
ArrayList nodes;
Gene[] genes = new Gene[mutatee.size() + 1];
System.arraycopy(mutatee.genes(), 0, genes, 0, mutatee.genes().length);
Gene newLink = null;
if (linkRandVal < this.pAddLink) {
nodes = this.candidateNodes(mutatee.genes());
links = this.candidateLinks(mutatee.genes(), false);
// find a new available link
while (newLink == null && i < MAX_LINK_ATTEMPTS) {
rIdx = linkRand.nextInt(nodes.size());
from = ((NEATNodeGene) nodes.get(rIdx));
rIdx = linkRand.nextInt(nodes.size());
to = ((NEATNodeGene) nodes.get(rIdx));
// TODO Remove
if (from.getInnovationNumber() == 2 && to.getInnovationNumber() == 5) {
System.out.println("a");
}
if (!this.linkIllegal(from, to, links)) {
// set it to a random value
newLink = InnovationDatabase.database().submitLinkInnovation(from.id(), to.id());
((NEATLinkGene) newLink).setWeight(MathUtils.nextPlusMinusOne());
// add link between 2 unconnected nodes
genes[genes.length - 1] = newLink;
mutatee.updateChromosome(genes);
}
i++;
}
}
}
private int findChosenIndex(NEATLinkGene chosen, Chromosome mutatee) {
int idx = -1;
int i = 0;
Gene[] genes = mutatee.genes();
int mutateeSize = genes.length;
while (i < mutateeSize && idx == -1) {
if (genes[i] instanceof NEATLinkGene
&& ((NEATLinkGene) genes[i]).getFromId() == chosen.getFromId()
&& ((NEATLinkGene) genes[i]).getToId() == chosen.getToId()) {
idx = i;
} else {
i++;
}
}
return (idx);
}
private void updateDepthInfo(Chromosome mutated) {
// use descriptor's chromo to create net
ArrayList nodes = new ArrayList();
ArrayList links = new ArrayList();
int i;
Gene[] genes = mutated.genes();
for (i = 0; i < genes.length; i++) {
if (genes[i] instanceof NEATNodeGene) {
nodes.add(genes[i]);
} else if (genes[i] instanceof NEATLinkGene) {
if (((NEATLinkGene) genes[i]).isEnabled()) {
// only add enabled links to the net structure
links.add(genes[i]);
}
}
}
this.assignNeuronDepth(this.findOutputNodes(this.candidateNodes(genes)), 1, mutated);
}