/// <summary>
/// Construct a genome by copying another.
/// </summary>
/// <param name="other">The other genome.</param>
public NEATGenome(NEATGenome other)
{
NetworkDepth = other.NetworkDepth;
Population = other.Population;
Score = other.Score;
AdjustedScore = other.AdjustedScore;
InputCount = other.InputCount;
OutputCount = other.OutputCount;
Species = other.Species;
// copy neurons
foreach (NEATNeuronGene oldGene in other.NeuronsChromosome)
{
var newGene = new NEATNeuronGene(oldGene);
_neuronsList.Add(newGene);
}
// copy links
foreach (var oldGene in other.LinksChromosome)
{
var newGene = new NEATLinkGene(
oldGene.FromNeuronId, oldGene.ToNeuronId,
oldGene.Enabled, oldGene.InnovationId,
oldGene.Weight);
_linksList.Add(newGene);
}
}
/// <summary>
/// Validate the structure of this genome.
/// </summary>
public void Validate()
{
// make sure that the bias neuron is where it should be
NEATNeuronGene g = _neuronsList[0];
if (g.NeuronType != NEATNeuronType.Bias)
{
throw new EncogError("NEAT Neuron Gene 0 should be a bias gene.");
}
// make sure all input neurons are at the beginning
for (int i = 1; i <= InputCount; i++)
{
NEATNeuronGene gene = _neuronsList[i];
if (gene.NeuronType != NEATNeuronType.Input)
{
throw new EncogError("NEAT Neuron Gene " + i
+ " should be an input gene.");
}
}
// make sure that there are no double links
IDictionary <String, NEATLinkGene> map = new Dictionary <String, NEATLinkGene>();
foreach (NEATLinkGene nlg in _linksList)
{
String key = nlg.FromNeuronId + "->" + nlg.ToNeuronId;
if (map.ContainsKey(key))
{
throw new EncogError("Double link found: " + key);
}
map[key] = nlg;
}
}
/// <summary>
/// Copy another gene to this one.
/// </summary>
/// <param name="gene">The other gene.</param>
public void Copy(NEATNeuronGene gene)
{
NEATNeuronGene other = gene;
Id = other.Id;
NeuronType = other.NeuronType;
ActivationFunction = other.ActivationFunction;
InnovationId = other.InnovationId;
}
/// <summary>
/// Create a new genome with the specified connection density. This
/// constructor is typically used to create the initial population.
/// </summary>
/// <param name="rnd">Random number generator.</param>
/// <param name="pop">The population.</param>
/// <param name="inputCount">The input count.</param>
/// <param name="outputCount">The output count.</param>
/// <param name="connectionDensity">The connection density.</param>
public NEATGenome(EncogRandom rnd, NEATPopulation pop,
int inputCount, int outputCount,
double connectionDensity)
{
AdjustedScore = 0;
InputCount = inputCount;
OutputCount = outputCount;
// get the activation function
IActivationFunction af = pop.ActivationFunctions.PickFirst();
// first bias
int innovationId = 0;
var biasGene = new NEATNeuronGene(NEATNeuronType.Bias, af,
inputCount, innovationId++);
_neuronsList.Add(biasGene);
// then inputs
for (var i = 0; i < inputCount; i++)
{
var gene = new NEATNeuronGene(NEATNeuronType.Input, af,
i, innovationId++);
_neuronsList.Add(gene);
}
// then outputs
for (int i = 0; i < outputCount; i++)
{
var gene = new NEATNeuronGene(NEATNeuronType.Output, af,
i + inputCount + 1, innovationId++);
_neuronsList.Add(gene);
}
// and now links
for (var i = 0; i < inputCount + 1; i++)
{
for (var j = 0; j < outputCount; j++)
{
// make sure we have at least one connection
if (_linksList.Count < 1 ||
rnd.NextDouble() < connectionDensity)
{
long fromId = this._neuronsList[i].Id;
long toId = this._neuronsList[inputCount + j + 1].Id;
double w = RangeRandomizer.Randomize(rnd, -pop.WeightRange, pop.WeightRange);
var gene = new NEATLinkGene(fromId, toId, true,
innovationId++, w);
_linksList.Add(gene);
}
}
}
}
/// <summary>
/// Construct an innovation.
/// </summary>
///
/// <param name="neuronGene">The neuron gene.</param>
/// <param name="innovationID">The innovation id.</param>
/// <param name="neuronID_0">The neuron id.</param>
public NEATInnovation(NEATNeuronGene neuronGene,
long innovationID, long neuronID_0)
{
neuronID = neuronID_0;
InnovationID = innovationID;
splitX = neuronGene.SplitX;
splitY = neuronGene.SplitY;
neuronType = neuronGene.NeuronType;
innovationType = NEATInnovationType.NewNeuron;
fromNeuronID = -1;
toNeuronID = -1;
}
/// <summary>
/// Construct a genome by copying another.
/// </summary>
///
/// <param name="other">The other genome.</param>
public NEATGenome(NEATGenome other)
{
neuronsChromosome = new Chromosome();
linksChromosome = new Chromosome();
GA = other.GA;
Chromosomes.Add(neuronsChromosome);
Chromosomes.Add(linksChromosome);
GenomeID = other.GenomeID;
networkDepth = other.networkDepth;
Population = other.Population;
Score = other.Score;
AdjustedScore = other.AdjustedScore;
AmountToSpawn = other.AmountToSpawn;
inputCount = other.inputCount;
outputCount = other.outputCount;
speciesID = other.speciesID;
// copy neurons
foreach (IGene gene in other.Neurons.Genes)
{
var oldGene = (NEATNeuronGene)gene;
var newGene = new NEATNeuronGene(
oldGene.NeuronType, oldGene.Id,
oldGene.SplitY, oldGene.SplitX,
oldGene.Recurrent, oldGene.ActivationResponse);
Neurons.Add(newGene);
}
// copy links
foreach (IGene gene_0 in other.Links.Genes)
{
var oldGene_1 = (NEATLinkGene)gene_0;
var newGene_2 = new NEATLinkGene(
oldGene_1.FromNeuronID, oldGene_1.ToNeuronID,
oldGene_1.Enabled, oldGene_1.InnovationId,
oldGene_1.Weight, oldGene_1.Recurrent);
Links.Add(newGene_2);
}
}
/// <summary>
/// Create a new neuron gene from an id.
/// </summary>
///
/// <param name="neuronID">The neuron id.</param>
/// <returns>The neuron gene.</returns>
public NEATNeuronGene CreateNeuronFromID(long neuronID)
{
var result = new NEATNeuronGene(NEATNeuronType.Hidden,
0, 0, 0);
foreach (IInnovation i in Innovations)
{
var innovation = (NEATInnovation)i;
if (innovation.NeuronID == neuronID)
{
result.NeuronType = innovation.NeuronType;
result.Id = innovation.NeuronID;
result.SplitY = innovation.SplitY;
result.SplitX = innovation.SplitX;
return(result);
}
}
throw new TrainingError("Failed to find innovation for neuron: "
+ neuronID);
}
/// <inheritdoc/>
public Object Read(Stream istream)
{
long nextInnovationId = 0;
long nextGeneId = 0;
var result = new NEATPopulation();
var innovationList = new NEATInnovationList {Population = result};
result.Innovations = innovationList;
var reader = new EncogReadHelper(istream);
EncogFileSection section;
while ((section = reader.ReadNextSection()) != null)
{
if (section.SectionName.Equals("NEAT-POPULATION")
&& section.SubSectionName.Equals("INNOVATIONS"))
{
foreach (String line in section.Lines)
{
IList<String> cols = EncogFileSection
.SplitColumns(line);
var innovation = new NEATInnovation();
var innovationId = int.Parse(cols[1]);
innovation.InnovationId = innovationId;
innovation.NeuronId = int.Parse(cols[2]);
result.Innovations.Innovations[cols[0]] = innovation;
nextInnovationId = Math.Max(nextInnovationId, innovationId + 1);
}
}
else if (section.SectionName.Equals("NEAT-POPULATION")
&& section.SubSectionName.Equals("SPECIES"))
{
NEATGenome lastGenome = null;
BasicSpecies lastSpecies = null;
foreach (String line in section.Lines)
{
IList<String> cols = EncogFileSection.SplitColumns(line);
if (String.Compare(cols[0], "s", StringComparison.OrdinalIgnoreCase) == 0)
{
lastSpecies = new BasicSpecies
{
Population = result,
Age = int.Parse(cols[1]),
BestScore = CSVFormat.EgFormat.Parse(cols[2]),
GensNoImprovement = int.Parse(cols[3])
};
result.Species.Add(lastSpecies);
}
else if (String.Compare(cols[0], "g", StringComparison.OrdinalIgnoreCase) == 0)
{
bool isLeader = lastGenome == null;
lastGenome = new NEATGenome
{
InputCount = result.InputCount,
OutputCount = result.OutputCount,
Species = lastSpecies,
AdjustedScore = CSVFormat.EgFormat.Parse(cols[1]),
Score = CSVFormat.EgFormat.Parse(cols[2]),
BirthGeneration = int.Parse(cols[3])
};
lastSpecies.Add(lastGenome);
if (isLeader)
{
lastSpecies.Leader = lastGenome;
}
}
else if (String.Compare(cols[0], "n", StringComparison.OrdinalIgnoreCase) == 0)
{
var neuronGene = new NEATNeuronGene();
int geneId = int.Parse(cols[1]);
neuronGene.Id = geneId;
IActivationFunction af = EncogFileSection.ParseActivationFunction(cols[2]);
neuronGene.ActivationFunction = af;
neuronGene.NeuronType = PersistNEATPopulation.StringToNeuronType(cols[3]);
neuronGene.InnovationId = int.Parse(cols[4]);
lastGenome.NeuronsChromosome.Add(neuronGene);
nextGeneId = Math.Max(geneId + 1, nextGeneId);
}
else if (String.Compare(cols[0], "l", StringComparison.OrdinalIgnoreCase) == 0)
{
var linkGene = new NEATLinkGene
{
Id = int.Parse(cols[1]),
Enabled = (int.Parse(cols[2]) > 0),
FromNeuronId = int.Parse(cols[3]),
ToNeuronId = int.Parse(cols[4]),
Weight = CSVFormat.EgFormat.Parse(cols[5]),
InnovationId = int.Parse(cols[6])
};
lastGenome.LinksChromosome.Add(linkGene);
}
}
}
else if (section.SectionName.Equals("NEAT-POPULATION")
&& section.SubSectionName.Equals("CONFIG"))
{
IDictionary<string, string> prm = section.ParseParams();
string afStr = prm[NEATPopulation.PropertyNEATActivation];
if (String.Compare(afStr, TypeCppn, StringComparison.OrdinalIgnoreCase) == 0)
{
HyperNEATGenome.BuildCPPNActivationFunctions(result.ActivationFunctions);
}
else
{
result.NEATActivationFunction = EncogFileSection.ParseActivationFunction(prm,
NEATPopulation.PropertyNEATActivation);
}
result.ActivationCycles = EncogFileSection.ParseInt(prm,
PersistConst.ActivationCycles);
result.InputCount = EncogFileSection.ParseInt(prm,
PersistConst.InputCount);
result.OutputCount = EncogFileSection.ParseInt(prm,
PersistConst.OutputCount);
result.PopulationSize = EncogFileSection.ParseInt(prm,
NEATPopulation.PropertyPopulationSize);
result.SurvivalRate = EncogFileSection.ParseDouble(prm,
NEATPopulation.PropertySurvivalRate);
result.ActivationCycles = EncogFileSection.ParseInt(prm,
NEATPopulation.PropertyCycles);
}
}
// set factories
if (result.IsHyperNEAT)
{
result.GenomeFactory = new FactorHyperNEATGenome();
result.CODEC = new HyperNEATCODEC();
}
else
{
result.GenomeFactory = new FactorNEATGenome();
result.CODEC = new NEATCODEC();
}
// set the next ID's
result.InnovationIDGenerate.CurrentID = nextInnovationId;
result.GeneIdGenerate.CurrentID = nextGeneId;
// find first genome, which should be the best genome
if (result.Species.Count > 0)
{
ISpecies species = result.Species[0];
if (species.Members.Count > 0)
{
result.BestGenome = species.Members[0];
}
}
return result;
}
/// <summary>
/// Copy another gene to this one.
/// </summary>
/// <param name="gene">The other gene.</param>
public void Copy(NEATNeuronGene gene)
{
NEATNeuronGene other = gene;
Id = other.Id;
NeuronType = other.NeuronType;
ActivationFunction = other.ActivationFunction;
InnovationId = other.InnovationId;
}
/// <summary>
/// Construct this gene by comping another.
/// </summary>
/// <param name="other">The other gene to copy.</param>
public NEATNeuronGene(NEATNeuronGene other)
{
Copy(other);
}
/// <summary>
/// Mutate the genome by adding a neuron.
/// </summary>
///
/// <param name="mutationRate">The mutation rate.</param>
/// <param name="numTrysToFindOldLink">The number of tries to find a link to split.</param>
internal void AddNeuron(double mutationRate, int numTrysToFindOldLink)
{
// should we add a neuron?
if (ThreadSafeRandom.NextDouble() > mutationRate)
{
return;
}
int countTrysToFindOldLink = numTrysToFindOldLink;
// the link to split
NEATLinkGene splitLink = null;
int sizeBias = inputCount + outputCount + 10;
// if there are not at least
int upperLimit;
if (linksChromosome.Size() < sizeBias)
{
upperLimit = NumGenes - 1 - (int)Math.Sqrt(NumGenes);
}
else
{
upperLimit = NumGenes - 1;
}
while ((countTrysToFindOldLink--) > 0)
{
// choose a link, use the square root to prefer the older links
int i = RangeRandomizer.RandomInt(0, upperLimit);
var link = (NEATLinkGene)linksChromosome
.Get(i);
// get the from neuron
long fromNeuron = link.FromNeuronID;
if ((link.Enabled) &&
(!link.Recurrent) &&
(((NEATNeuronGene)Neurons.Get(
GetElementPos(fromNeuron))).NeuronType != NEATNeuronType.Bias))
{
splitLink = link;
break;
}
}
if (splitLink == null)
{
return;
}
splitLink.Enabled = false;
double originalWeight = splitLink.Weight;
long from = splitLink.FromNeuronID;
long to = splitLink.ToNeuronID;
var fromGene = (NEATNeuronGene)Neurons.Get(
GetElementPos(from));
var toGene = (NEATNeuronGene)Neurons.Get(
GetElementPos(to));
double newDepth = (fromGene.SplitY + toGene.SplitY) / 2;
double newWidth = (fromGene.SplitX + toGene.SplitX) / 2;
// has this innovation already been tried?
NEATInnovation innovation = ((NEATTraining)GA).Innovations.CheckInnovation(from, to,
NEATInnovationType
.NewNeuron);
// prevent chaining
if (innovation != null)
{
long neuronID = innovation.NeuronID;
if (AlreadyHaveThisNeuronID(neuronID))
{
innovation = null;
}
}
if (innovation == null)
{
// this innovation has not been tried, create it
long newNeuronID = ((NEATTraining)GA).Innovations.CreateNewInnovation(from, to,
NEATInnovationType.
NewNeuron,
NEATNeuronType.
Hidden,
newWidth, newDepth);
neuronsChromosome.Add(new NEATNeuronGene(
NEATNeuronType.Hidden, newNeuronID, newDepth, newWidth));
// add the first link
long link1ID = (GA).Population.AssignInnovationID();
((NEATTraining)GA).Innovations
.CreateNewInnovation(from, newNeuronID,
NEATInnovationType.NewLink);
var link1 = new NEATLinkGene(from, newNeuronID,
true, link1ID, 1.0d, false);
linksChromosome.Add(link1);
// add the second link
long link2ID = (GA).Population.AssignInnovationID();
((NEATTraining)GA).Innovations
.CreateNewInnovation(newNeuronID, to,
NEATInnovationType.NewLink);
var link2 = new NEATLinkGene(newNeuronID, to, true,
link2ID, originalWeight, false);
linksChromosome.Add(link2);
}
else
{
// existing innovation
long newNeuronID_0 = innovation.NeuronID;
NEATInnovation innovationLink1 = ((NEATTraining)GA).Innovations.CheckInnovation(from,
newNeuronID_0,
NEATInnovationType
.
NewLink);
NEATInnovation innovationLink2 =
((NEATTraining)GA).Innovations.CheckInnovation(newNeuronID_0, to,
NEATInnovationType.NewLink);
if ((innovationLink1 == null) || (innovationLink2 == null))
{
throw new NeuralNetworkError("NEAT Error");
}
var link1_1 = new NEATLinkGene(from, newNeuronID_0,
true, innovationLink1.InnovationID, 1.0d, false);
var link2_2 = new NEATLinkGene(newNeuronID_0, to, true,
innovationLink2.InnovationID, originalWeight, false);
linksChromosome.Add(link1_1);
linksChromosome.Add(link2_2);
var newNeuron = new NEATNeuronGene(
NEATNeuronType.Hidden, newNeuronID_0, newDepth, newWidth);
neuronsChromosome.Add(newNeuron);
}
return;
}
/// <summary>
/// Mutate the genome by adding a link to this genome.
/// </summary>
///
/// <param name="mutationRate">The mutation rate.</param>
/// <param name="chanceOfLooped">The chance of a self-connected neuron.</param>
/// <param name="numTrysToFindLoop">The number of tries to find a loop.</param>
/// <param name="numTrysToAddLink">The number of tries to add a link.</param>
internal void AddLink(double mutationRate, double chanceOfLooped,
int numTrysToFindLoop, int numTrysToAddLink)
{
// should we even add the link
if (ThreadSafeRandom.NextDouble() > mutationRate)
{
return;
}
int countTrysToFindLoop = numTrysToFindLoop;
int countTrysToAddLink = numTrysToFindLoop;
// the link will be between these two neurons
long neuron1ID = -1;
long neuron2ID = -1;
bool recurrent = false;
// a self-connected loop?
if (ThreadSafeRandom.NextDouble() < chanceOfLooped)
{
// try to find(randomly) a neuron to add a self-connected link to
while ((countTrysToFindLoop--) > 0)
{
NEATNeuronGene neuronGene = ChooseRandomNeuron(false);
// no self-links on input or bias neurons
if (!neuronGene.Recurrent &&
(neuronGene.NeuronType != NEATNeuronType.Bias) &&
(neuronGene.NeuronType != NEATNeuronType.Input))
{
neuron1ID = neuronGene.Id;
neuron2ID = neuronGene.Id;
neuronGene.Recurrent = true;
recurrent = true;
countTrysToFindLoop = 0;
}
}
}
else
{
// try to add a regular link
while ((countTrysToAddLink--) > 0)
{
NEATNeuronGene neuron1 = ChooseRandomNeuron(true);
NEATNeuronGene neuron2 = ChooseRandomNeuron(false);
if (!IsDuplicateLink(neuron1ID, neuron2ID) &&
(neuron1.Id != neuron2.Id) &&
(neuron2.NeuronType != NEATNeuronType.Bias))
{
neuron1ID = neuron1.Id;
neuron2ID = neuron2.Id;
break;
}
}
}
// did we fail to find a link
if ((neuron1ID < 0) || (neuron2ID < 0))
{
return;
}
// check to see if this innovation has already been tried
NEATInnovation innovation = ((NEATTraining)GA).Innovations.CheckInnovation(neuron1ID,
neuron1ID,
NEATInnovationType
.NewLink);
// see if this is a recurrent(backwards) link
var neuronGene_0 = (NEATNeuronGene)neuronsChromosome
.Get(GetElementPos(neuron1ID));
if (neuronGene_0.SplitY > neuronGene_0.SplitY)
{
recurrent = true;
}
// is this a new innovation?
if (innovation == null)
{
// new innovation
((NEATTraining)GA).Innovations
.CreateNewInnovation(neuron1ID, neuron2ID,
NEATInnovationType.NewLink);
long id2 = GA.Population.AssignInnovationID();
var linkGene = new NEATLinkGene(neuron1ID,
neuron2ID, true, id2, RangeRandomizer.Randomize(-1, 1),
recurrent);
linksChromosome.Add(linkGene);
}
else
{
// existing innovation
var linkGene_1 = new NEATLinkGene(neuron1ID,
neuron2ID, true, innovation.InnovationID,
RangeRandomizer.Randomize(-1, 1), recurrent);
linksChromosome.Add(linkGene_1);
}
}
/// <summary>
/// Construct this gene by comping another.
/// </summary>
/// <param name="other">The other gene to copy.</param>
public NEATNeuronGene(NEATNeuronGene other)
{
Copy(other);
}
/// <summary>
/// Construct a genome by copying another.
/// </summary>
/// <param name="other">The other genome.</param>
public NEATGenome(NEATGenome other)
{
NetworkDepth = other.NetworkDepth;
Population = other.Population;
Score = other.Score;
AdjustedScore = other.AdjustedScore;
InputCount = other.InputCount;
OutputCount = other.OutputCount;
Species = other.Species;
// copy neurons
foreach (NEATNeuronGene oldGene in other.NeuronsChromosome)
{
var newGene = new NEATNeuronGene(oldGene);
_neuronsList.Add(newGene);
}
// copy links
foreach (var oldGene in other.LinksChromosome)
{
var newGene = new NEATLinkGene(
oldGene.FromNeuronId, oldGene.ToNeuronId,
oldGene.Enabled, oldGene.InnovationId,
oldGene.Weight);
_linksList.Add(newGene);
}
}
/// <summary>
/// Create a new genome with the specified connection density. This
/// constructor is typically used to create the initial population.
/// </summary>
/// <param name="rnd">Random number generator.</param>
/// <param name="pop">The population.</param>
/// <param name="inputCount">The input count.</param>
/// <param name="outputCount">The output count.</param>
/// <param name="connectionDensity">The connection density.</param>
public NEATGenome(EncogRandom rnd, NEATPopulation pop,
int inputCount, int outputCount,
double connectionDensity)
{
AdjustedScore = 0;
InputCount = inputCount;
OutputCount = outputCount;
// get the activation function
IActivationFunction af = pop.ActivationFunctions.PickFirst();
// first bias
int innovationId = 0;
var biasGene = new NEATNeuronGene(NEATNeuronType.Bias, af,
inputCount, innovationId++);
_neuronsList.Add(biasGene);
// then inputs
for (var i = 0; i < inputCount; i++)
{
var gene = new NEATNeuronGene(NEATNeuronType.Input, af,
i, innovationId++);
_neuronsList.Add(gene);
}
// then outputs
for (int i = 0; i < outputCount; i++)
{
var gene = new NEATNeuronGene(NEATNeuronType.Output, af,
i + inputCount + 1, innovationId++);
_neuronsList.Add(gene);
}
// and now links
for (var i = 0; i < inputCount + 1; i++)
{
for (var j = 0; j < outputCount; j++)
{
// make sure we have at least one connection
if (_linksList.Count < 1
|| rnd.NextDouble() < connectionDensity)
{
long fromId = this._neuronsList[i].Id;
long toId = this._neuronsList[inputCount + j + 1].Id;
double w = RangeRandomizer.Randomize(rnd, -pop.WeightRange, pop.WeightRange);
var gene = new NEATLinkGene(fromId, toId, true,
innovationId++, w);
_linksList.Add(gene);
}
}
}
}