/// <summary>
/// Speciates the genomes in genomeList into the provided species. It is assumed that
/// the genomeList represents all of the required genomes and that the species are currently empty.
///
/// This method can be used for initialization or completely respeciating an existing genome population.
/// </summary>
public void SpeciateGenomes(IList <TGenome> genomeList, IList <Specie <TGenome> > specieList)
{
Debug.Assert(SpeciationUtils.TestEmptySpecies(specieList), "SpeciateGenomes(IList<TGenome>,IList<Species<TGenome>>) called with non-empty species");
Debug.Assert(genomeList.Count >= specieList.Count, string.Format("SpeciateGenomes(IList<TGenome>,IList<Species<TGenome>>). Specie count [{0}] is greater than genome count [{1}].", specieList.Count, genomeList.Count));
// Make a copy of genomeList and shuffle the items.
List <TGenome> gList = new List <TGenome>(genomeList);
Utilities.Shuffle(gList, _rng);
// We evenly distribute genomes between species.
// Calc how many genomes per specie. Baseline number given by integer division rounding down (by truncating fractional part).
// This is guaranteed to be at least 1 because genomeCount >= specieCount.
int genomeCount = genomeList.Count;
int specieCount = specieList.Count;
int genomesPerSpecie = genomeCount / specieCount;
// Allocate genomes to species.
int genomeIdx = 0;
for (int i = 0; i < specieCount; i++)
{
Specie <TGenome> specie = specieList[i];
for (int j = 0; j < genomesPerSpecie; j++, genomeIdx++)
{
specie.GenomeList.Add(gList[genomeIdx]);
}
}
// Evenly allocate any remaining genomes.
for (int i = 0; i < specieCount && genomeIdx < genomeCount; i++, genomeIdx++)
{
specieList[i].GenomeList.Add(gList[genomeIdx]);
}
}
/// <summary>
/// Speciates the offspring genomes in offspringList into the provided
/// specieList. In contrast to SpeciateGenomes() offspringList is taken
/// to be a list of new genomes (offspring) that should be added to
/// existing species. That is, the species contain genomes that are not
/// in offspringList that we wish to keep; typically these would be elite
/// genomes that are the parents of the offspring.
/// </summary>
public void SpeciateOffspring(IList <TGenome> offspringList,
IList <Specie <TGenome> > specieList)
{
// Each specie should contain at least one genome. We need at least
// one existing genome per specie to act as a specie centroid in order
// to define where the specie is within the encoding space.
Debug.Assert(SpeciationUtils.TestPopulatedSpecies(specieList),
"SpeciateOffspring(IList<TGenome>,IList<Species<TGenome>>) called with an empty specie.");
// Update the centroid of each specie. If we're adding offspring this
// means that old genomes have been removed from the population and
// therefore the centroids are out-of-date.
foreach (Specie <TGenome> specie in specieList)
{
specie.Centroid = CalculateSpecieCentroid(specie);
}
// Allocate each offspring genome to the specie it is closest to.
foreach (TGenome genome in offspringList)
{
Specie <TGenome> closestSpecie = FindClosestSpecie(genome, specieList);
closestSpecie.GenomeList.Add(genome);
genome.SpecieIdx = closestSpecie.Idx;
}
// Recalculate each specie's centroid now that we have additional
// genomes in the specieList.
foreach (Specie <TGenome> specie in specieList)
{
specie.Centroid = CalculateSpecieCentroid(specie);
}
// Accumulate *all* genomes into a flat genome list.
int genomeCount = 0;
foreach (Specie <TGenome> specie in specieList)
{
genomeCount += specie.GenomeList.Count;
}
List <TGenome> genomeList = new List <TGenome>(genomeCount);
foreach (Specie <TGenome> specie in specieList)
{
genomeList.AddRange(specie.GenomeList);
}
// Perform the main k-means loop until convergence.
SpeciateUntilConvergence(genomeList, specieList);
Debug.Assert(SpeciationUtils.PerformIntegrityCheck(specieList));
}
/// <summary>
/// Speciates the genomes in genomeList into the provided specieList.
/// It is assumed that the genomeList represents all of the required
/// genomes and that the species are currently empty.
///
/// This method can be used for initialization or completely respeciating
/// an existing genome population.
/// </summary>
public void SpeciateGenomes(IList <TGenome> genomeList,
IList <Specie <TGenome> > specieList)
{
Debug.Assert(SpeciationUtils.TestEmptySpecies(specieList),
"SpeciateGenomes(IList<TGenome>,IList<Species<TGenome>>) called with non-empty species");
Debug.Assert(genomeList.Count >= specieList.Count,
string.Format("SpeciateGenomes(IList<TGenome>,IList<Species<TGenome>>). Species count [{0}] is greater than genome count [{1}].",
specieList.Count, genomeList.Count));
// Randomly allocate the first k genomes to their own specie.
// Because there is only one genome in these species each genome
// effectively represents a specie centroid. This is necessary to
// ensure we get k specieList. If we randomly assign all genomes to
// species from the outset and then calculate centroids then
// typically some of the species become empty. This approach ensures
// that each species will have at least one genome - because that
// genome is the specie centroid and therefore has distance of zero
// from the centroid (itself).
int specieCount = specieList.Count;
for (int i = 0; i < specieCount; i++)
{
Specie <TGenome> specie = specieList[i];
genomeList[i].SpecieIdx = specie.Idx;
specie.GenomeList.Add(genomeList[i]);
// Just set the specie centroid directly.
specie.Centroid = genomeList[i].Position;
}
// Now allocate the remaining genomes based on their distance from the centroids.
int genomeCount = genomeList.Count;
for (int i = specieCount; i < genomeCount; i++)
{
TGenome genome = genomeList[i];
Specie <TGenome> closestSpecie = FindClosestSpecie(genome, specieList);
genome.SpecieIdx = closestSpecie.Idx;
closestSpecie.GenomeList.Add(genome);
}
// Recalculate each specie's centroid.
foreach (Specie <TGenome> specie in specieList)
{
specie.Centroid = CalculateSpecieCentroid(specie);
}
// Perform the main k-means loop until convergence.
SpeciateUntilConvergence(genomeList, specieList);
Debug.Assert(SpeciationUtils.PerformIntegrityCheck(specieList));
}
/// <summary>
/// Speciates the offspring genomes in offspringList into the provided specieList. In contrast to
/// SpeciateGenomes() offspringList is taken to be a list of new genomes (offspring) that should be
/// added to existing species. That is, the species contain genomes that are not in offspringList
/// that we wish to keep; typically these would be elite genomes that are the parents of the
/// offspring.
/// </summary>
public void SpeciateOffspring(IList <TGenome> offspringList, IList <Specie <TGenome> > specieList)
{
// Each specie should contain at least one genome. We need at least one existing genome per specie to act
// as a specie centroid in order to define where the specie is within the encoding space.
Debug.Assert(SpeciationUtils.TestPopulatedSpecies(specieList), "SpeciateOffspring(IList<TGenome>,IList<Species<TGenome>>) called with an empty specie.");
// Update the centroid of each specie. If we're adding offspring this means that old genomes
// have been removed from the population and therefore the centroids are out-of-date.
Parallel.ForEach(specieList, _parallelOptions, delegate(Specie <TGenome> specie) {
specie.Centroid = CalculateSpecieCentroid(specie);
});
// Allocate each offspring genome to the specie it is closest to.
Parallel.ForEach(offspringList, _parallelOptions, delegate(TGenome genome)
{
Specie <TGenome> closestSpecie = FindClosestSpecie(genome, specieList);
lock (closestSpecie.GenomeList) {
// TODO: Consider using ConcurrentQueue here (and elsewhere in this class).
closestSpecie.GenomeList.Add(genome);
}
genome.SpecieIdx = closestSpecie.Idx;
});
// Recalculate each specie's centroid now that we have additional genomes in the specieList.
Parallel.ForEach(specieList, _parallelOptions, delegate(Specie <TGenome> specie) {
specie.Centroid = CalculateSpecieCentroid(specie);
});
// Accumulate *all* genomes into a flat genome list.
int genomeCount = 0;
foreach (Specie <TGenome> specie in specieList)
{
genomeCount += specie.GenomeList.Count;
}
List <TGenome> genomeList = new List <TGenome>(genomeCount);
foreach (Specie <TGenome> specie in specieList)
{
genomeList.AddRange(specie.GenomeList);
}
// Perform the main k-means loop until convergence.
SpeciateUntilConvergence(genomeList, specieList);
Debug.Assert(SpeciationUtils.TestPopulatedSpecies(specieList), "Speciation must allocate at least one genome to each species.");
}
/// <summary>
/// Speciates the offspring genomes in genomeList into the provided species. In contrast to
/// SpeciateGenomes() genomeList is taken to be a list of new genomes (e.g. offspring) that should be
/// added to existing species. That is, the species contain genomes that are not in genomeList
/// that we wish to keep; typically these would be elite genomes that are the parents of the
/// offspring.
/// </summary>
public void SpeciateOffspring(IList <TGenome> genomeList, IList <Specie <TGenome> > specieList)
{
// Each specie should contain at least one genome. We need at least one existing genome per specie to act
// as a specie centroid in order to define where the specie is within the encoding space.
Debug.Assert(SpeciationUtils.TestPopulatedSpecies(specieList), "SpeciateOffspring(IList<TGenome>,IList<Species<TGenome>>) called with an empty specie.");
// Make a copy of genomeList and shuffle the items.
List <TGenome> gList = new List <TGenome>(genomeList);
SharpNeat.Utility.Utilities.Shuffle(gList, _rng);
// Count how many genomes we have in total.
int genomeCount = gList.Count;
int totalGenomeCount = genomeCount;
foreach (Specie <TGenome> specie in specieList)
{
totalGenomeCount += specie.GenomeList.Count;
}
// We attempt to evenly distribute genomes between species.
// Calc how many genomes per specie. Baseline number given by integer division rounding down (by truncating fractional part).
// This is guaranteed to be at least 1 because genomeCount >= specieCount.
int specieCount = specieList.Count;
int genomesPerSpecie = totalGenomeCount / specieCount;
// Sort species, smallest first. We must make a copy of specieList to do this; Species must remain at
// the correct index in the main specieList. The principle here is that we wish to ensure that genomes are
// allocated to smaller species in preference to larger species, this is motivated by the desire to create
// evenly sized species.
List <Specie <TGenome> > sList = new List <Specie <TGenome> >(specieList);
sList.Sort(delegate(Specie <TGenome> x, Specie <TGenome> y)
{ // We use the difference in size where we aren't expecting that diff value to overflow the range of an int.
return(x.GenomeList.Count - y.GenomeList.Count);
});
// Add genomes into each specie in turn until they each reach genomesPerSpecie in size.
int genomeIdx = 0;
for (int i = 0; i < specieCount && genomeIdx < genomeCount; i++)
{
Specie <TGenome> specie = sList[i];
int fillcount = genomesPerSpecie - specie.GenomeList.Count;
if (fillcount <= 0)
{ // We may encounter species with more than genomesPerSpecie genomes. Since we have
// ordered the species by size we break out of this loop and allocate the remaining
// genomes randomly.
break;
}
// Don't allocate more genomes than there are remaining in genomeList.
fillcount = Math.Min(fillcount, genomeCount - genomeIdx);
// Allocate memory for the genomes we are about to allocate;
// This eliminates potentially having to dynamically resize the list one or more times.
if (specie.GenomeList.Capacity < specie.GenomeList.Count + fillcount)
{
specie.GenomeList.Capacity = specie.GenomeList.Count + fillcount;
}
// genomeIdx test not required. Already taken into account by fillCount.
for (int j = 0; j < fillcount; j++)
{
gList[genomeIdx].SpecieIdx = specie.Idx;
specie.GenomeList.Add(gList[genomeIdx++]);
}
}
// Evenly allocate any remaining genomes.
int[] specieIdxArr = new int[specieCount];
for (int i = 0; i < specieCount; i++)
{
specieIdxArr[i] = i;
}
SharpNeat.Utility.Utilities.Shuffle(specieIdxArr, _rng);
for (int i = 0; i < specieCount && genomeIdx < genomeCount; i++, genomeIdx++)
{
int specieIdx = specieIdxArr[i];
gList[genomeIdx].SpecieIdx = specieIdx;
specieList[specieIdx].GenomeList.Add(gList[genomeIdx]);
}
Debug.Assert(SpeciationUtils.PerformIntegrityCheck(specieList));
}