public override double CompatibilityDistance(SpeciatedGenome <CPPNNEATGeneCollection, PType> genome)
{
var differences = new DifferenceAnalysis(this.GeneCollection, genome.GeneCollection);
var totalExcess = differences.FirstCollection.Excess.Count + differences.SecondCollection.Excess.Count;
var totalDisjoint = differences.FirstCollection.Disjoint.Count + differences.SecondCollection.Disjoint.Count;
var averageWeightDifference = differences.Matches
.Select(match =>
(match.FirstCollection.Weight - match.SecondCollection.Weight)
.Magnitude)
.Average();
var n = (double)Math.Max(this.GeneCollection.LinkGenes.Count(),
genome.GeneCollection.LinkGenes.Count());
if (n <= SMALL_GENOME_THRESHOLD)
{
n = 1;
}
var parent = Parent as ICPPNNEATGA;
var averageFunctionDifference = GetAverageFunctionDifference(this, (CPPNNEATGenome <PType>)genome);
return(parent.ExcessGenesWeight * (totalExcess / n) +
parent.DisjointGenesWeight * (totalDisjoint / n) +
parent.MatchingGenesWeight * averageWeightDifference +
parent.FunctionDifferenceWeight * averageFunctionDifference);
}
public CPPNNEATGenome(ICPPNNEATGA parentGA, CPPNNEATGenome <PType> parent, CPPNNEATGenome <PType> partner)
: this(parentGA)
{
var differences = new DifferenceAnalysis(parent.GeneCollection, partner.GeneCollection);
var disjointAndExcessSource = differences.FirstCollection;
if (partner.Score > parent.Score)
{
disjointAndExcessSource = differences.SecondCollection;
}
else if (partner.Score == parent.Score)
{
disjointAndExcessSource = (MathExtensions.RandomNumber() <= 0.5) ? differences.FirstCollection :
differences.SecondCollection;
}
Func <CPPNNEATLinkGene, CPPNNEATLinkGene, Complex> weightSelector = null;
if (MathExtensions.RandomNumber() <= parentGA.MateByAveragingRate)
{
weightSelector = (first, second) => (first.Weight + second.Weight) / 2;
}
else
{
weightSelector = (first, second) => (MathExtensions.RandomNumber() <= 0.5) ? first.Weight : second.Weight;
}
foreach (var match in differences.Matches)
{
var geneToCopy = match.FirstCollection;
var newGene = geneToCopy.Copy();
newGene.Enabled = true;
newGene.Weight = weightSelector(match.FirstCollection, match.SecondCollection);
GeneCollection.TryAddLinkGene(newGene);
if ((!match.FirstCollection.Enabled || !match.SecondCollection.Enabled) &&
MathExtensions.RandomNumber() <= parentGA.DisableGeneRate)
{
GeneCollection.DisableLinkGene(newGene.InnovationNumber);
}
}
foreach (var linkGene in disjointAndExcessSource
.Disjoint.Union(disjointAndExcessSource.Excess))
{
GeneCollection.TryAddLinkGene(linkGene.Copy());
}
}