private static NeatPopulation <double> CreateNeatPopulation(
int count,
double defaultFitness,
IRandomSource rng)
{
MetaNeatGenome <double> metaNeatGenome = new MetaNeatGenome <double>(
inputNodeCount: 3,
outputNodeCount: 2,
isAcyclic: true,
activationFn: new NeuralNets.Double.ActivationFunctions.ReLU());
NeatPopulation <double> neatPop = NeatPopulationFactory <double> .CreatePopulation(metaNeatGenome, 1.0, count, rng);
Assert.Equal(count, neatPop.GenomeList.Count);
Assert.Equal(count, neatPop.GenomeIdSeq.Peek);
// Assign the default fitness to all genomes.
var genomeList = neatPop.GenomeList;
for (int i = 0; i < count; i++)
{
var genome = genomeList[i];
genome.FitnessInfo = new FitnessInfo(defaultFitness);
}
// Init species.
InitialiseSpecies(neatPop);
return(neatPop);
}
/// <summary>
/// Create a new instance of <see cref="NeatEvolutionAlgorithm{T}"/> for the given neat experiment, and neat population.
/// </summary>
/// <param name="neatExperiment">A neat experiment instance; this conveys everything required to create a new evolution algorithm instance that is ready to be run.</param>
/// <param name="neatPop">A pre constructed/loaded neat population; this must be compatible with the provided neat experiment, otherwise an exception will be thrown.</param>
/// <returns>A new instance of <see cref="NeatEvolutionAlgorithm{T}"/>.</returns>
public static NeatEvolutionAlgorithm <double> CreateNeatEvolutionAlgorithm(
INeatExperiment <double> neatExperiment,
NeatPopulation <double> neatPop)
{
// Validate MetaNeatGenome and NeatExperiment are compatible; normally the former should have been created based on the latter, but this is not enforced.
MetaNeatGenome <double> metaNeatGenome = neatPop.MetaNeatGenome;
ValidateCompatible(neatExperiment, metaNeatGenome);
// Create a genomeList evaluator based on the experiment's configuration settings.
var genomeListEvaluator = CreateGenomeListEvaluator(neatExperiment);
// Create a speciation strategy based on the experiment's configuration settings.
var speciationStrategy = CreateSpeciationStrategy(neatExperiment);
// Create an instance of the default connection weight mutation scheme.
var weightMutationScheme = WeightMutationSchemeFactory.CreateDefaultScheme(neatExperiment.ConnectionWeightScale);
// Pull all of the parts together into an evolution algorithm instance.
var ea = new NeatEvolutionAlgorithm <double>(
neatExperiment.NeatEvolutionAlgorithmSettings,
genomeListEvaluator,
speciationStrategy,
neatPop,
neatExperiment.ComplexityRegulationStrategy,
neatExperiment.ReproductionAsexualSettings,
neatExperiment.ReproductionSexualSettings,
weightMutationScheme);
return(ea);
}
public void VerifyPopulationStats()
{
IRandomSource rng = RandomDefaults.CreateRandomSource(0);
// Create a test population.
NeatPopulation <double> pop = CreateNeatPopulation(100, 10.0, rng);
// Modify a few genome fitnesses.
pop.GenomeList[10].FitnessInfo = new FitnessInfo(100.0);
pop.GenomeList[20].FitnessInfo = new FitnessInfo(0.0);
// Initialise the NEAT population species; the wider population stats are dependent on this occurring.
InitialiseSpecies(pop);
// Calc/update stats.
pop.UpdateStats(PrimaryFitnessInfoComparer.Singleton, rng);
// Validate stats.
// Fitness stats.
PopulationStatistics stats = pop.Stats;
Assert.Equal(10, stats.BestGenomeIndex);
Assert.Equal(100.0, stats.BestFitness.PrimaryFitness);
Assert.Equal(10.8, stats.MeanFitness);
Assert.Equal(1, stats.BestFitnessHistory.Length);
Assert.Equal(100.0, stats.BestFitnessHistory.Total);
// Complexity stats.
Assert.Equal(6.0, stats.BestComplexity);
Assert.Equal(6.0, stats.MeanComplexity);
Assert.Equal(1, stats.MeanComplexityHistory.Length);
Assert.Equal(6.0, stats.MeanComplexityHistory.Total);
}
private static int CalcSpeciesTargetSizes(
NeatPopulation <T> pop, double totalMeanFitness, IRandomSource rng)
{
// Handle specific case where all genomes/species have a zero fitness.
// Assign all species an equal targetSize.
if (0.0 == totalMeanFitness)
{
return(CalcSpeciesTargetSizes_ZeroTotalMeanFitness(pop, rng));
}
// Calculate the new target size of each species using fitness sharing.
double popSizeReal = pop.GenomeList.Count;
Species <T>[] speciesArr = pop.SpeciesArray;
int totalTargetSizeInt = 0;
// The size of each specie is based on its fitness relative to the other species.
for (int i = 0; i < speciesArr.Length; i++)
{
SpeciesStats stats = speciesArr[i].Stats;
stats.TargetSizeReal = (stats.MeanFitness / totalMeanFitness) * popSizeReal;
// Discretize targetSize (stochastic rounding).
stats.TargetSizeInt = (int)NumericsUtils.ProbabilisticRound(stats.TargetSizeReal, rng);
// Total up discretized target sizes.
totalTargetSizeInt += stats.TargetSizeInt;
}
return(totalTargetSizeInt);
}
/// <summary>
/// Create a new instance of <see cref="NeatEvolutionAlgorithm{T}"/> for the given neat experiment.
/// </summary>
/// <param name="neatExperiment">A neat experiment instance; this conveys everything required to create a new evolution algorithm instance that is ready to be run.</param>
/// <returns>A new instance of <see cref="NeatEvolutionAlgorithm{T}"/>.</returns>
public static NeatEvolutionAlgorithm <double> CreateNeatEvolutionAlgorithm(
INeatExperiment <double> neatExperiment)
{
// Create a genomeList evaluator based on the experiment's configuration settings.
var genomeListEvaluator = CreateGenomeListEvaluator(neatExperiment);
// Create a MetaNeatGenome.
var metaNeatGenome = CreateMetaNeatGenome(neatExperiment);
// Create an initial population of genomes.
NeatPopulation <double> neatPop = NeatPopulationFactory <double> .CreatePopulation(
metaNeatGenome,
connectionsProportion : neatExperiment.InitialInterconnectionsProportion,
popSize : neatExperiment.PopulationSize);
// Create a speciation strategy based on the experiment's configuration settings.
var speciationStrategy = CreateSpeciationStrategy(neatExperiment);
// Create an instance of the default connection weight mutation scheme.
var weightMutationScheme = WeightMutationSchemeFactory.CreateDefaultScheme(neatExperiment.ConnectionWeightScale);
// Pull all of the parts together into an evolution algorithm instance.
var ea = new NeatEvolutionAlgorithm <double>(
neatExperiment.NeatEvolutionAlgorithmSettings,
genomeListEvaluator,
speciationStrategy,
neatPop,
neatExperiment.ComplexityRegulationStrategy,
neatExperiment.ReproductionAsexualSettings,
neatExperiment.ReproductionSexualSettings,
weightMutationScheme);
return(ea);
}
/// <summary>
/// Handle specific case where all genomes/species have a zero fitness.
/// </summary>
private static int CalcSpeciesTargetSizes_ZeroTotalMeanFitness(NeatPopulation <T> pop, IRandomSource rng)
{
// Assign all species an equal targetSize.
Species <T>[] speciesArr = pop.SpeciesArray;
double popSizeReal = pop.GenomeList.Count;
double targetSizeReal = popSizeReal / speciesArr.Length;
// Keep a total of all allocated target sizes, typically this will vary slightly from the
// required target population size due to rounding of each real valued target size.
int totalTargetSizeInt = 0;
for (int i = 0; i < speciesArr.Length; i++)
{
SpeciesStats stats = speciesArr[i].Stats;
stats.TargetSizeReal = targetSizeReal;
// Stochastic rounding will result in equal allocation if targetSizeReal is a whole
// number, otherwise it will help to distribute allocations fairly.
stats.TargetSizeInt = (int)NumericsUtils.ProbabilisticRound(targetSizeReal, rng);
// Total up discretized target sizes.
totalTargetSizeInt += stats.TargetSizeInt;
}
return(totalTargetSizeInt);
}
public void CreatePopulation()
{
MetaNeatGenome <double> metaNeatGenome = new(
inputNodeCount : 3,
outputNodeCount : 2,
isAcyclic : true,
activationFn : new NeuralNets.Double.ActivationFunctions.ReLU());
int count = 10;
NeatPopulation <double> neatPop = NeatPopulationFactory <double> .CreatePopulation(metaNeatGenome, 1.0, count, RandomDefaults.CreateRandomSource());
Assert.Equal(count, neatPop.GenomeList.Count);
Assert.Equal(count, neatPop.GenomeIdSeq.Peek);
// The population factory assigns the same innovation IDs to matching structures in the genomes it creates.
// In this test there are 5 nodes and 6 connections in each genome, and they are each identifiably
// the same structure in each of the genomes (e.g. input 0 or whatever) and so have the same innovation ID
// across all of the genomes.
// Thus in total although we created N genomes there are only 5 innovation IDs allocated (5 nodes).
Assert.Equal(5, neatPop.InnovationIdSeq.Peek);
// Loop the created genomes.
for (int i = 0; i < count; i++)
{
var genome = neatPop.GenomeList[i];
Assert.Equal(i, genome.Id);
Assert.Equal(0, genome.BirthGeneration);
TestGenome(genome);
}
}
public void SaveAndLoadPopulationToZipArchive()
{
// Create a test population.
NeatPopulation <double> pop = NestGenomeTestUtils.CreateNeatPopulation();
// Build path to test population folder.
string parentPath = Path.Combine(Directory.GetCurrentDirectory(), "test-pops");
// Delete folder if it already exists.
if (Directory.Exists(parentPath))
{
Directory.Delete(parentPath, true);
}
// Create an empty parent folder to save populations into.
Directory.CreateDirectory(parentPath);
// Save the population to the unit test output folder.
NeatPopulationSaver <double> .SaveToZipArchive(pop.GenomeList, parentPath, "pop2", System.IO.Compression.CompressionLevel.Optimal);
// Load the population.
NeatPopulationLoader <double> loader = NeatPopulationLoaderFactory.CreateLoaderDouble(pop.MetaNeatGenome);
string populationZipPath = Path.Combine(parentPath, "pop2.zip");
List <NeatGenome <double> > genomeListLoaded = loader.LoadFromZipArchive(populationZipPath);
// Compare the loaded genomes with the original genome list.
IOTestUtils.CompareGenomeLists(pop.GenomeList, genomeListLoaded);
}
private static void CalcAndStoreSpeciesTargetSizes(
NeatPopulation <T> pop, IRandomSource rng)
{
double totalMeanFitness = pop.TotalSpeciesMeanFitness;
int totalTargetSizeInt = 0;
// Handle specific case where all genomes/species have a zero fitness.
// Assign all species an equal targetSize.
if (0.0 == totalMeanFitness)
{
totalTargetSizeInt = CalcSpeciesTargetSizesInner_ZeroTotalMeanFitness(pop, rng);
}
else
{
// Calculate the new target size of each species using fitness sharing.
double popSizeReal = pop.GenomeList.Count;
Species <T>[] speciesArr = pop.SpeciesArray;
// The size of each specie is based on its fitness relative to the other species.
for (int i = 0; i < speciesArr.Length; i++)
{
SpeciesStats stats = speciesArr[i].Stats;
stats.TargetSizeReal = (stats.MeanFitness / totalMeanFitness) * popSizeReal;
// Discretize targetSize (stochastic rounding).
stats.TargetSizeInt = (int)NumericsUtils.ProbabilisticRound(stats.TargetSizeReal, rng);
// Total up discretized target sizes.
totalTargetSizeInt += stats.TargetSizeInt;
}
}
// Adjust each species' target allocation such that the sum total matches the required population size.
AdjustSpeciesTargetSizes(pop, totalTargetSizeInt, rng);
}
private static void AdjustSpeciesTargetSizes(
NeatPopulation <T> pop,
int totalTargetSizeInt,
IRandomSource rng)
{
// Discretized target sizes may total up to a value that is not equal to the required population size.
// Here we check this and if the total does not match the required population size then we adjust the
// species' targetSizeInt values to compensate for the difference.
int popSize = pop.GenomeList.Count;
int targetSizeDeltaInt = totalTargetSizeInt - popSize;
if (targetSizeDeltaInt < 0)
{
// Target size is too low; adjust up.
AdjustSpeciesTargetSizesUp(pop.SpeciesArray, targetSizeDeltaInt, rng);
}
else if (targetSizeDeltaInt > 0)
{
// Target size is too high; adjust down.
AdjustSpeciesTargetSizesDown(pop.SpeciesArray, targetSizeDeltaInt, rng);
}
// Assert that Sum(TargetSizeInt) == popSize.
Debug.Assert(pop.SpeciesArray.Sum(x => x.Stats.TargetSizeInt) == popSize);
}
private static void AdjustSpeciesTargetSizes_AccommodateBestGenomeSpecies(
NeatPopulation <T> pop, IRandomSource rng)
{
// Test if the best genome is in a species with a zero target size allocation.
int bestGenomeSpeciesIdx = pop.NeatPopulationStats.BestGenomeSpeciesIdx;
Species <T>[] speciesArr = pop.SpeciesArray !;
if (speciesArr[bestGenomeSpeciesIdx].Stats.TargetSizeInt > 0)
{
// Nothing to do. The best genome is in a species with a non-zero allocation.
return;
}
// Set the target size of the best genome species to a allow the best genome to survive to the next generation.
speciesArr[bestGenomeSpeciesIdx].Stats.TargetSizeInt++;
// Adjust down the target size of one of the other species to compensate.
// Pick a species at random (but not the champ species). Note that this may result in a species with a zero
// target size, this is OK at this stage. We handle allocations of zero elsewhere.
// Create an array of shuffled indexes to select from, i.e. all of the species except for the one with the best genome in it.
int speciesCount = speciesArr.Length;
int[] speciesIdxArr = new int[speciesCount - 1];
for (int i = 0; i < bestGenomeSpeciesIdx; i++)
{
speciesIdxArr[i] = i;
}
for (int i = bestGenomeSpeciesIdx + 1; i < speciesCount; i++)
{
speciesIdxArr[i - 1] = i;
}
SpanUtils.Shuffle(speciesIdxArr.AsSpan(), rng);
// Loop the species indexes.
bool success = false;
foreach (int speciesIdx in speciesIdxArr)
{
if (speciesArr[speciesIdx].Stats.TargetSizeInt > 0)
{
speciesArr[speciesIdx].Stats.TargetSizeInt--;
success = true;
break;
}
}
if (!success)
{
throw new Exception("All species have a zero target size.");
}
}
/// <summary>
/// Construct a new instance.
/// </summary>
/// <param name="eaSettings">NEAT evolution algorithm settings.</param>
/// <param name="evaluator">An evaluator of lists of genomes.</param>
/// <param name="speciationStrategy">Speciation strategy.</param>
/// <param name="population">An initial population of genomes.</param>
/// <param name="complexityRegulationStrategy">Complexity regulation strategy.</param>
/// <param name="reproductionAsexualSettings">Asexual reproduction settings.</param>
/// <param name="reproductionSexualSettings">Sexual reproduction settings.</param>
/// <param name="weightMutationScheme">Connection weight mutation scheme.</param>
/// <param name="rng">Random source.</param>
public NeatEvolutionAlgorithm(
NeatEvolutionAlgorithmSettings eaSettings,
IGenomeListEvaluator <NeatGenome <T> > evaluator,
ISpeciationStrategy <NeatGenome <T>, T> speciationStrategy,
NeatPopulation <T> population,
IComplexityRegulationStrategy complexityRegulationStrategy,
NeatReproductionAsexualSettings reproductionAsexualSettings,
NeatReproductionSexualSettings reproductionSexualSettings,
WeightMutationScheme <T> weightMutationScheme,
IRandomSource rng)
{
_eaSettingsCurrent = eaSettings ?? throw new ArgumentNullException(nameof(eaSettings));
_eaSettingsComplexifying = eaSettings;
_eaSettingsSimplifying = eaSettings.CreateSimplifyingSettings();
_evaluator = evaluator ?? throw new ArgumentNullException(nameof(evaluator));
_speciationStrategy = speciationStrategy ?? throw new ArgumentNullException(nameof(speciationStrategy));
_pop = population ?? throw new ArgumentNullException(nameof(population));
_complexityRegulationStrategy = complexityRegulationStrategy ?? throw new ArgumentNullException(nameof(complexityRegulationStrategy));
if (reproductionAsexualSettings == null)
{
throw new ArgumentNullException(nameof(reproductionAsexualSettings));
}
if (reproductionSexualSettings == null)
{
throw new ArgumentNullException(nameof(reproductionSexualSettings));
}
_rng = rng;
_genomeComparerDescending = new GenomeComparerDescending(evaluator.FitnessComparer);
if (eaSettings.SpeciesCount > population.PopulationSize)
{
throw new ArgumentException("Species count is higher then the population size.");
}
_generationSeq = new Int32Sequence();
_reproductionAsexual = new NeatReproductionAsexual <T>(
_pop.MetaNeatGenome, _pop.GenomeBuilder,
_pop.GenomeIdSeq, population.InnovationIdSeq, _generationSeq,
_pop.AddedNodeBuffer, reproductionAsexualSettings, weightMutationScheme);
_reproductionSexual = new NeatReproductionSexual <T>(
_pop.MetaNeatGenome, _pop.GenomeBuilder,
_pop.GenomeIdSeq, _generationSeq,
reproductionSexualSettings);
_offspringBuilder = new OffspringBuilder <T>(
_reproductionAsexual,
_reproductionSexual,
eaSettings.InterspeciesMatingProportion,
evaluator.FitnessComparer);
}
/// <summary>
/// Calc and store species target sizes based on relative mean fitness of each species, i.e. as per NEAT fitness sharing method.
/// Then calc and store the elite, selection and offspring allocations/counts, per species.
/// </summary>
public static void CalcAndStoreSpeciesAllocationSizes(
NeatPopulation <T> pop,
NeatEvolutionAlgorithmSettings eaSettings,
IRandomSource rng)
{
// Calculate the new target size of each species using fitness sharing.
CalcAndStoreSpeciesTargetSizes(pop, rng);
// Calculate elite, selection and offspring counts, per species.
CalculateAndStoreEliteSelectionOffspringCounts(pop, eaSettings, rng);
}
/// <summary>
/// Calculate and update a number of statistical values and target size values on each species in the givben population.
/// </summary>
/// <param name="pop">The population to update species statistics on.</param>
/// <param name="eaSettings">Evolution algorithm settings.</param>
/// <param name="rng">Random source.</param>
public static void CalcAndStoreSpeciesStats(
NeatPopulation <T> pop,
NeatEvolutionAlgorithmSettings eaSettings,
IRandomSource rng)
{
// Calc and store the mean fitness of each species.
CalcAndStoreSpeciesFitnessMeans(pop);
// Calc and store the target size of each species (based on the NEAT fitness sharing method).
SpeciesAllocationCalcs <T> .CalcAndStoreSpeciesAllocationSizes(pop, eaSettings, rng);
}
/// <summary>
/// Calc species target sizes based on relative mean fitness of each species, i.e. as per NEAT fitness sharing method.
/// </summary>
public static void CalcSpeciesTargetSizes(NeatPopulation <T> pop, IRandomSource rng)
{
// Calc mean fitness of all species, and get sum of all species means.
double totalMeanFitness = UpdateSpeciesFitnessMeans(pop.SpeciesArray);
// Calculate the new target size of each species using fitness sharing.
int totalTargetSizeInt = CalcSpeciesTargetSizes(pop, totalMeanFitness, rng);
// Adjust each species' target allocation such that the sum total matches the required population size.
AdjustSpeciesTargetSizes(pop, totalTargetSizeInt, rng);
}
//private IGenomeCollectionEvaluator<NeatGenome<double>> CreateGenomeListEvaluator()
//{
// var genomeDecoder = new NeatGenomeAcyclicDecoder(false);
// var phenomeEvaluator = new BinaryElevenMultiplexerEvaluator();
// var genomeCollectionEvaluator = new SerialGenomeListEvaluator<NeatGenome<double>, IPhenome<double>>(genomeDecoder, phenomeEvaluator);
// return genomeListEvaluator;
//}
private static NeatPopulation <double> CreatePopulation(
MetaNeatGenome <double> metaNeatGenome,
int popSize)
{
NeatPopulation <double> pop = NeatPopulationFactory <double> .CreatePopulation(
metaNeatGenome,
connectionsProportion : 1.0,
popSize : popSize,
rng : RandomDefaults.CreateRandomSource());
return(pop);
}
private static void InitialiseSpecies(NeatPopulation <double> neatPop)
{
// Create a speciation strategy instance.
var distanceMetric = new ManhattanDistanceMetric(1.0, 0.0, 10.0);
var speciationStrategy = new Speciation.GeneticKMeans.Parallelized.GeneticKMeansSpeciationStrategy <double>(distanceMetric, 5, 4);
// Apply the speciation strategy.
var genomeComparerDescending = new GenomeComparerDescending(PrimaryFitnessInfoComparer.Singleton);
IRandomSource rng = RandomDefaults.CreateRandomSource(0);
neatPop.InitialiseSpecies(speciationStrategy, 3, genomeComparerDescending, rng);
}
/// <summary>
/// For each species, allocate the EliteSizeInt, OffspringCount (broken down into OffspringAsexualCount and OffspringSexualCount),
/// and SelectionSizeInt values.
/// </summary>
/// <param name="pop"></param>
/// <param name="eaSettings"></param>
/// <param name="rng"></param>
private static void CalculateAndStoreEliteSelectionOffspringCounts(
NeatPopulation <T> pop,
NeatEvolutionAlgorithmSettings eaSettings,
IRandomSource rng)
{
Species <T>[] speciesArr = pop.SpeciesArray;
// Loop the species, calculating and storing the various size/count properties.
for (int i = 0; i < speciesArr.Length; i++)
{
bool isBestGenomeSpecies = (pop.BestGenomeSpeciesIdx == i);
AllocateEliteSelectionOffspringCounts(speciesArr[i], eaSettings, isBestGenomeSpecies, rng);
}
}
/// <summary>
/// Construct a new instance.
/// </summary>
/// <param name="eaSettings">NEAT evolution algorithm settings.</param>
/// <param name="evaluator">An evaluator of lists of genomes.</param>
/// <param name="speciationStrategy">Speciation strategy.</param>
/// <param name="population">An initial population of genomes.</param>
/// <param name="reproductionAsexualSettings">Asexual reproduction settings.</param>
/// <param name="reproductionSexualSettings">Sexual reproduction settings.</param>
/// <param name="weightMutationScheme">Connection weight mutation scheme.</param>
public NeatEvolutionAlgorithm(
NeatEvolutionAlgorithmSettings eaSettings,
IGenomeListEvaluator <NeatGenome <T> > evaluator,
ISpeciationStrategy <NeatGenome <T>, T> speciationStrategy,
NeatPopulation <T> population,
NeatReproductionAsexualSettings reproductionAsexualSettings,
NeatReproductionSexualSettings reproductionSexualSettings,
WeightMutationScheme <T> weightMutationScheme)
: this(eaSettings, evaluator, speciationStrategy, population,
reproductionAsexualSettings, reproductionSexualSettings,
weightMutationScheme,
RandomDefaults.CreateRandomSource())
{
}
private void btnCreateRandomPop_Click(object sender, EventArgs e)
{
INeatExperiment <double> neatExperiment = GetNeatExperiment();
MetaNeatGenome <double> metaNeatGenome = NeatUtils.CreateMetaNeatGenome(neatExperiment);
// Create an initial population of genomes.
_neatPop = NeatPopulationFactory <double> .CreatePopulation(
metaNeatGenome,
connectionsProportion : neatExperiment.InitialInterconnectionsProportion,
popSize : neatExperiment.PopulationSize);
// Update UI.
UpdateUIState();
}
public void CreateGenome()
{
var metaNeatGenome = new MetaNeatGenome <double>(
inputNodeCount: 10,
outputNodeCount: 20,
isAcyclic: true,
activationFn: new NeuralNets.Double.ActivationFunctions.ReLU());
var genomeBuilder = NeatGenomeBuilderFactory <double> .Create(metaNeatGenome);
int count = 100;
NeatPopulation <double> pop = NeatPopulationFactory <double> .CreatePopulation(metaNeatGenome, 0.1, count, RandomDefaults.CreateRandomSource());
var generationSeq = new Int32Sequence();
var strategy = new UniformCrossoverReproductionStrategy <double>(
pop.MetaNeatGenome.IsAcyclic,
0.02,
genomeBuilder,
pop.GenomeIdSeq, generationSeq);
IRandomSource rng = RandomDefaults.CreateRandomSource(0);
var cyclicGraphCheck = new CyclicGraphCheck();
for (int i = 0; i < 1000; i++)
{
// Randomly select two parents from the population.
var genome1 = pop.GenomeList[rng.Next(count)];
var genome2 = pop.GenomeList[rng.Next(count)];
var childGenome = strategy.CreateGenome(genome1, genome2, rng);
// The connection genes should be sorted.
Assert.True(SortUtils.IsSortedAscending <DirectedConnection>(childGenome.ConnectionGenes._connArr));
// The child genome should describe an acyclic graph, i.e. the new connection should not have
// formed a cycle in the graph.
var digraph = childGenome.DirectedGraph;
Assert.False(cyclicGraphCheck.IsCyclic(digraph));
// The child genome node IDs should be a superset of those from parent1 + parent2.
var childNodeIdSet = GetNodeIdSet(childGenome);
var parentIdSet = GetNodeIdSet(genome1);
parentIdSet.IntersectWith(GetNodeIdSet(genome2));
Assert.True(childNodeIdSet.IsSupersetOf(parentIdSet));
}
}
public void VerifyNeatPopulationStats()
{
IRandomSource rng = RandomDefaults.CreateRandomSource(0);
// Create test population and apply speciation strategy.
NeatPopulation <double> neatPop = CreateNeatPopulation(30, 10.0, rng);
// Loop the species; assign the same fitness to genomes within each species.
for (int i = 0; i < neatPop.SpeciesArray.Length; i++)
{
double fitness = (i + 1) * 10.0;
neatPop.SpeciesArray[i].GenomeList.ForEach(x => x.FitnessInfo = new FitnessInfo(fitness));
}
// Calc NeatPopulation statistics.
neatPop.UpdateStats(PrimaryFitnessInfoComparer.Singleton, rng);
// Validate expected mean fitness for each species.
for (int i = 0; i < neatPop.SpeciesArray.Length; i++)
{
double expectedMeanFitness = (i + 1) * 10.0;
Assert.Equal(expectedMeanFitness, neatPop.SpeciesArray[i].Stats.MeanFitness);
}
// Validate SumSpeciesMeanFitness.
double expectedSumSpeciesMeanFitness = 10.0 + 20.0 + 30.0;
Assert.Equal(expectedSumSpeciesMeanFitness, neatPop.NeatPopulationStats.SumSpeciesMeanFitness);
// Validate BestGenomeSpeciesIdx.
Assert.Equal(2, neatPop.NeatPopulationStats.BestGenomeSpeciesIdx);
// Assign a high fitness to one of the genomes, and check that BestGenomeSpeciesIdx is updated accordingly.
neatPop.SpeciesArray[0].GenomeList[2].FitnessInfo = new FitnessInfo(100.0);
// Note. The species must be re-initialised in order for the fit genome to be sorted correctly within its
// containing species.
InitialiseSpecies(neatPop);
neatPop.UpdateStats(PrimaryFitnessInfoComparer.Singleton, rng);
Assert.Equal(0, neatPop.NeatPopulationStats.BestGenomeSpeciesIdx);
// Perform the same test again with the best genome in the second species.
neatPop.SpeciesArray[1].GenomeList[3].FitnessInfo = new FitnessInfo(200.0);
InitialiseSpecies(neatPop);
neatPop.UpdateStats(PrimaryFitnessInfoComparer.Singleton, rng);
Assert.Equal(1, neatPop.NeatPopulationStats.BestGenomeSpeciesIdx);
}
private static NeatPopulation <double> CreateNeatPopulation(
int count,
int inputNodeCount,
int outputNodeCount,
double connectionsProportion)
{
MetaNeatGenome <double> metaNeatGenome = new MetaNeatGenome <double>(
inputNodeCount: inputNodeCount,
outputNodeCount: outputNodeCount,
isAcyclic: true,
activationFn: new SharpNeat.NeuralNet.Double.ActivationFunctions.ReLU());
NeatPopulation <double> neatPop = NeatPopulationFactory <double> .CreatePopulation(metaNeatGenome, 1.0, count, RandomDefaults.CreateRandomSource());
return(neatPop);
}
public void UpdateSpeciesAllocationSizes()
{
IRandomSource rng = RandomDefaults.CreateRandomSource(0);
NeatEvolutionAlgorithmSettings eaSettings = new()
{
SpeciesCount = 4
};
// Create population.
NeatPopulation <double> neatPop = CreateNeatPopulation(100, eaSettings.SpeciesCount, 2, 2, 1.0);
// Manually set-up some species.
var speciesArr = neatPop.SpeciesArray;
speciesArr[0].GenomeList.AddRange(neatPop.GenomeList.Take(25));
speciesArr[1].GenomeList.AddRange(neatPop.GenomeList.Skip(25).Take(25));
speciesArr[2].GenomeList.AddRange(neatPop.GenomeList.Skip(50).Take(25));
speciesArr[3].GenomeList.AddRange(neatPop.GenomeList.Skip(75).Take(25));
// Manually assign fitness scores to the genomes.
speciesArr[0].GenomeList.ForEach(x => x.FitnessInfo = new FitnessInfo(100.0));
speciesArr[1].GenomeList.ForEach(x => x.FitnessInfo = new FitnessInfo(200.0));
speciesArr[2].GenomeList.ForEach(x => x.FitnessInfo = new FitnessInfo(400.0));
speciesArr[3].GenomeList.ForEach(x => x.FitnessInfo = new FitnessInfo(800.0));
// Invoke species target size calcs.
neatPop.UpdateStats(PrimaryFitnessInfoComparer.Singleton, rng);
SpeciesAllocationCalcs <double> .UpdateSpeciesAllocationSizes(
neatPop, eaSettings, RandomDefaults.CreateRandomSource());
// Species target sizes should be relative to the species mean fitness.
double totalMeanFitness = 1500.0;
double popSize = 100.0;
Assert.Equal((100.0 / totalMeanFitness) * popSize, speciesArr[0].Stats.TargetSizeReal);
Assert.Equal((200.0 / totalMeanFitness) * popSize, speciesArr[1].Stats.TargetSizeReal);
Assert.Equal((400.0 / totalMeanFitness) * popSize, speciesArr[2].Stats.TargetSizeReal);
Assert.Equal((800.0 / totalMeanFitness) * popSize, speciesArr[3].Stats.TargetSizeReal);
// Note. Discretized target sizes will generally be equal to ceil(TargetSizeReal) or floor(TargetSizeReal),
// but may not be due to the target size adjustment logic that is used to ensure that sum(TargetSizeInt) is equal
// to the required population size.
// Check that sum(TargetSizeInt) is equal to the required population size.
Assert.Equal(speciesArr.Sum(x => x.Stats.TargetSizeInt), neatPop.GenomeList.Count);
}
/// <summary>
/// Calc mean fitness of all species, and store the results on each species' stats object.
/// </summary>
/// <param name="pop">The population.</param>
/// <returns>Sum of species mean fitnesses.</returns>
private static void CalcAndStoreSpeciesFitnessMeans(NeatPopulation <T> pop)
{
Species <T>[] speciesArr = pop.SpeciesArray;
// Calc mean fitness of all species, and sum of all species means.
double totalMeanFitness = 0.0;
for (int i = 0; i < speciesArr.Length; i++)
{
var species = speciesArr[i];
double meanFitness = species.GenomeList.Average(x => x.FitnessInfo.PrimaryFitness);
species.Stats.MeanFitness = meanFitness;
totalMeanFitness += meanFitness;
}
pop.TotalSpeciesMeanFitness = totalMeanFitness;
}
public static void TestSpeciateAdd(
int popSize,
int inputNodeCount,
int outputNodeCount,
double connectionsProportion,
IDistanceMetric <double> distanceMetric,
ISpeciationStrategy <NeatGenome <double>, double> speciationStrategy,
IRandomSource rng,
bool validateNearestSpecies = true)
{
// Create population.
NeatPopulation <double> neatPop = CreateNeatPopulation(popSize, inputNodeCount, outputNodeCount, connectionsProportion);
// Split the population into three.
int popSize1 = popSize / 3;
int popSize2 = popSize / 3;
int popSize3 = popSize - (popSize1 + popSize2);
var genomeList1 = neatPop.GenomeList.GetRange(0, popSize1);
var genomeList2 = neatPop.GenomeList.GetRange(popSize1, popSize2);
var genomeList3 = neatPop.GenomeList.GetRange(popSize1 + popSize2, popSize3);
for (int i = 0; i < 6; i++)
{
int speciesCount = rng.Next(1, (neatPop.GenomeList.Count / 4) + 1);
var fullGenomeList = new List <NeatGenome <double> >(genomeList1);
// Invoke speciation strategy, and run tests
var speciesArr = speciationStrategy.SpeciateAll(genomeList1, speciesCount, rng);
ValidationTests(speciesArr, distanceMetric, speciesCount, fullGenomeList, validateNearestSpecies);
// Add second batch of genomes, and re-run tests.
speciationStrategy.SpeciateAdd(genomeList2, speciesArr, rng);
fullGenomeList.AddRange(genomeList2);
ValidationTests(speciesArr, distanceMetric, speciesCount, fullGenomeList, validateNearestSpecies);
// Add third batch of genomes, and re-run tests.
speciationStrategy.SpeciateAdd(genomeList3, speciesArr, rng);
fullGenomeList.AddRange(genomeList3);
ValidationTests(speciesArr, distanceMetric, speciesCount, fullGenomeList, validateNearestSpecies);
}
}
/// <summary>
/// Create a new instance of <see cref="NeatEvolutionAlgorithm{T}"/> for the given neat experiment.
/// </summary>
/// <param name="neatExperiment">A neat experiment; conveys everything required to create a new evolution algorithm instance that is ready to be run.</param>
/// <returns>A new instance of <see cref="NeatEvolutionAlgorithm{T}"/>.</returns>
public static NeatEvolutionAlgorithm <double> CreateNeatEvolutionAlgorithm(
INeatExperiment <double> neatExperiment)
{
// Create a genomeList evaluator based on the experiment's configuration settings.
var genomeListEvaluator = CreateGenomeListEvaluator(neatExperiment);
// Resolve the configured activation function name to an activation function instance.
var actFnFactory = new DefaultActivationFunctionFactory <double>(neatExperiment.EnableHardwareAcceleratedActivationFunctions);
var activationFn = actFnFactory.GetActivationFunction(neatExperiment.ActivationFnName);
// Construct a MetaNeatGenome.
var metaNeatGenome = new MetaNeatGenome <double>(
inputNodeCount: neatExperiment.EvaluationScheme.InputCount,
outputNodeCount: neatExperiment.EvaluationScheme.OutputCount,
isAcyclic: neatExperiment.IsAcyclic,
activationFn: activationFn);
// Create an initial population of genomes.
NeatPopulation <double> neatPop = NeatPopulationFactory <double> .CreatePopulation(
metaNeatGenome,
connectionsProportion : neatExperiment.InitialInterconnectionsProportion,
popSize : neatExperiment.PopulationSize,
rng : RandomDefaults.CreateRandomSource());
// Create a speciation strategy based on the experiment's configuration settings.
var speciationStrategy = CreateSpeciationStrategy(neatExperiment);
// Create an instance of the default connection weight mutation scheme.
var weightMutationScheme = WeightMutationSchemeFactory.CreateDefaultScheme(neatExperiment.ConnectionWeightScale);
// Pull all of the parts together into an evolution algorithm instance.
var ea = new NeatEvolutionAlgorithm <double>(
neatExperiment.NeatEvolutionAlgorithmSettings,
genomeListEvaluator,
speciationStrategy,
neatPop,
neatExperiment.ComplexityRegulationStrategy,
neatExperiment.ReproductionAsexualSettings,
neatExperiment.ReproductionSexualSettings,
weightMutationScheme);
return(ea);
}
private static Species <double> CreateTestSpecies(int genomeCount)
{
// Create the species genomes; we use NeatPopulationFactory for this.
MetaNeatGenome <double> metaNeatGenome = new MetaNeatGenome <double>(
inputNodeCount: 1,
outputNodeCount: 1,
isAcyclic: true,
activationFn: new SharpNeat.NeuralNets.Double.ActivationFunctions.ReLU());
NeatPopulation <double> neatPop = NeatPopulationFactory <double> .CreatePopulation(metaNeatGenome, 1.0, genomeCount, RandomDefaults.CreateRandomSource());
// Create the species object, and assign all of the created genomes to it.
var species = new Species <double>(0, new ConnectionGenes <double>(0));
species.GenomeList.AddRange(neatPop.GenomeList);
// Return the species.
return(species);
}
public void TestInitialConnections()
{
MetaNeatGenome<double> metaNeatGenome = new MetaNeatGenome<double>(
inputNodeCount: 100,
outputNodeCount: 200,
isAcyclic: true,
activationFn: new SharpNeat.NeuralNet.Double.ActivationFunctions.ReLU());
NeatPopulation<double> neatPop = NeatPopulationFactory<double>.CreatePopulation(metaNeatGenome, 0.5, 1, RandomDefaults.CreateRandomSource());
NeatGenome<double> genome = neatPop.GenomeList[0];
Assert.AreEqual(10000, genome.ConnectionGenes.Length);
Assert.IsTrue(SortUtils.IsSortedAscending(genome.ConnectionGenes._connArr));
CalcWeightMinMaxMean(genome.ConnectionGenes._weightArr, out double min, out double max, out double mean);
Assert.IsTrue(min < -genome.MetaNeatGenome.ConnectionWeightRange * 0.98);
Assert.IsTrue(max > genome.MetaNeatGenome.ConnectionWeightRange * 0.98);
Assert.IsTrue(Math.Abs(mean) < 0.1);
}
public void SaveAndLoadPopulationToZipArchive()
{
// Create a test population.
NeatPopulation <double> pop = NestGenomeTestUtils.CreateNeatPopulation();
// Create a parent folder to save populations into.
string parentPath = Path.Combine(TestContext.TestRunDirectory, "test-pops");
Directory.CreateDirectory(parentPath);
// Save the population to the unit test output folder.
NeatPopulationSaver <double> .SaveToZipArchive(pop.GenomeList, parentPath, "pop2", System.IO.Compression.CompressionLevel.Optimal);
// Load the population.
NeatPopulationLoader <double> loader = NeatPopulationLoaderFactory.CreateLoaderDouble(pop.MetaNeatGenome);
string populationZipPath = Path.Combine(parentPath, "pop2.zip");
List <NeatGenome <double> > genomeListLoaded = loader.LoadFromZipArchive(populationZipPath);
// Compare the loaded genomes with the original genome list.
IOTestUtils.CompareGenomeLists(pop.GenomeList, genomeListLoaded);
}
