/// <summary>
/// Copy another gene to this one.
/// </summary>
/// <param name="gene">The other gene.</param>
public override void Copy(IGene gene)
{
NEATNeuronGene other = (NEATNeuronGene)gene;
activationResponse = other.activationResponse;
Id = other.Id;
neuronType = other.neuronType;
recurrent = other.recurrent;
splitX = other.splitX;
splitY = other.splitY;
}
/// <summary>
/// Get the specified neuron's index.
/// </summary>
/// <param name="neuronID">The neuron id to check for.</param>
/// <returns>The index.</returns>
private int GetElementPos(long neuronID)
{
for (int i = 0; i < Neurons.Genes.Count; i++)
{
NEATNeuronGene neuronGene = (NEATNeuronGene)neuronsChromosome.Genes[i];
if (neuronGene.Id == neuronID)
{
return(i);
}
}
return(-1);
}
/// <summary>
/// Construct an innovation.
/// </summary>
/// <param name="neuronGene">The neuron gene.</param>
/// <param name="innovationID">The innovation id.</param>
/// <param name="neuronID">The neuron id.</param>
public NEATInnovation(NEATNeuronGene neuronGene,
long innovationID, long neuronID)
{
this.neuronID = neuronID;
InnovationID = innovationID;
splitX = neuronGene.SplitX;
splitY = neuronGene.SplitY;
neuronType = neuronGene.NeuronType;
innovationType = NEATInnovationType.NewNeuron;
fromNeuronID = -1;
toNeuronID = -1;
}
/// <summary>
/// Mutate the activation response.
/// </summary>
/// <param name="mutateRate">The mutation rate.</param>
/// <param name="maxPertubation">The maximum to perturb it by.</param>
public void MutateActivationResponse(double mutateRate,
double maxPertubation)
{
foreach (IGene gene in neuronsChromosome.Genes)
{
if (ThreadSafeRandom.NextDouble() < mutateRate)
{
NEATNeuronGene neuronGene = (NEATNeuronGene)gene;
neuronGene.ActivationResponse = neuronGene
.ActivationResponse
+ RangeRandomizer.Randomize(-1, 1) * maxPertubation;
}
}
}
/// <summary>
/// Do we already have this neuron id?
/// </summary>
/// <param name="id">The id to check for.</param>
/// <returns>True if we already have this neuron id.</returns>
public bool AlreadyHaveThisNeuronID(long id)
{
foreach (IGene gene in neuronsChromosome.Genes)
{
NEATNeuronGene neuronGene = (NEATNeuronGene)gene;
if (neuronGene.Id == id)
{
return(true);
}
}
return(false);
}
/// <summary>
/// Convert the genes to an actual network.
/// </summary>
public override void Decode()
{
NEATPattern pattern = new NEATPattern();
IList <NEATNeuron> neurons = pattern.Neurons;
foreach (IGene gene in Neurons.Genes)
{
NEATNeuronGene neuronGene = (NEATNeuronGene)gene;
NEATNeuron neuron = new NEATNeuron(
neuronGene.NeuronType, neuronGene.Id, neuronGene
.SplitY, neuronGene.SplitX, neuronGene
.ActivationResponse);
neurons.Add(neuron);
}
// now to create the links.
foreach (IGene gene in Links.Genes)
{
NEATLinkGene linkGene = (NEATLinkGene)gene;
if (linkGene.Enabled)
{
int element = GetElementPos(linkGene.FromNeuronID);
NEATNeuron fromNeuron = neurons[element];
element = GetElementPos(linkGene.ToNeuronID);
NEATNeuron toNeuron = neurons[element];
NEATLink link = new NEATLink(linkGene.Weight,
fromNeuron, toNeuron, linkGene.IsRecurrent);
fromNeuron.OutputboundLinks.Add(link);
toNeuron.InboundLinks.Add(link);
}
}
pattern.NEATActivation = (((NEATTraining)GA).NeatActivationFunction);
pattern.ActivationFunction = (((NEATTraining)GA).OutputActivationFunction);
pattern.InputNeurons = (inputCount);
pattern.OutputNeurons = (outputCount);
pattern.Snapshot = ((NEATTraining)GA).Snapshot;
Organism = pattern.Generate();
}
/// <summary>
/// Choose a random neuron.
/// </summary>
/// <param name="includeInput">Should the input neurons be included.</param>
/// <returns>The random neuron.</returns>
private NEATNeuronGene ChooseRandomNeuron(bool includeInput)
{
int start;
if (includeInput)
{
start = 0;
}
else
{
start = inputCount + 1;
}
int neuronPos = RangeRandomizer.RandomInt(start, Neurons
.Genes.Count - 1);
NEATNeuronGene neuronGene = (NEATNeuronGene)neuronsChromosome.Genes[neuronPos];
return(neuronGene);
}
/// <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)
{
NEATNeuronGene result = new NEATNeuronGene(NEATNeuronType.Hidden,
0, 0, 0);
foreach (IInnovation i in Innovations)
{
NEATInnovation 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);
}
}
return(result);
}
/// <summary>
/// Construct a genome by copying another.
/// </summary>
/// <param name="other">The other genome.</param>
public NEATGenome(NEATGenome other)
: base(other.GA)
{
neuronsChromosome = new Chromosome();
linksChromosome = new Chromosome();
this.Chromosomes.Add(neuronsChromosome);
this.Chromosomes.Add(linksChromosome);
GenomeID = other.GenomeID;
networkDepth = other.networkDepth;
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)
{
NEATNeuronGene oldGene = (NEATNeuronGene)gene;
NEATNeuronGene newGene = new NEATNeuronGene(oldGene.NeuronType
, oldGene.Id, oldGene.SplitX,
oldGene.SplitY, oldGene.Recurrent, oldGene
.ActivationResponse);
this.neuronsChromosome.Genes.Add(newGene);
}
// copy links
foreach (IGene gene in other.Links.Genes)
{
NEATLinkGene oldGene = (NEATLinkGene)gene;
NEATLinkGene newGene = new NEATLinkGene(oldGene
.FromNeuronID, oldGene.ToNeuronID, oldGene
.Enabled, oldGene.InnovationId, oldGene
.Weight, oldGene.IsRecurrent);
Links.Genes.Add(newGene);
}
}
/// <summary>
/// Construct an innovation list.
/// </summary>
/// <param name="population">The population.</param>
/// <param name="links">The links.</param>
/// <param name="neurons">The neurons.</param>
public NEATInnovationList(IPopulation population, Chromosome links, Chromosome neurons)
{
this.population = population;
foreach (IGene gene in neurons.Genes)
{
NEATNeuronGene neuronGene = (NEATNeuronGene)gene;
NEATInnovation innovation = new NEATInnovation(neuronGene,
population.AssignInnovationID(), AssignNeuronID());
Innovations.Add(innovation);
}
foreach (IGene gene in links.Genes)
{
NEATLinkGene linkGene = (NEATLinkGene)gene;
NEATInnovation innovation = new NEATInnovation(linkGene
.FromNeuronID, linkGene.ToNeuronID,
NEATInnovationType.NewLink, this.population.AssignInnovationID());
Innovations.Add(innovation);
}
}
/// <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>
public void AddNeuron(double mutationRate, int numTrysToFindOldLink)
{
// should we add a neuron?
if (ThreadSafeRandom.NextDouble() > mutationRate)
{
return;
}
// the link to split
NEATLinkGene splitLink = null;
int sizeThreshold = inputCount + outputCount + 10;
// if there are not at least
int upperLimit;
if (linksChromosome.Genes.Count < sizeThreshold)
{
upperLimit = NumGenes - 1 - (int)Math.Sqrt(NumGenes);
}
else
{
upperLimit = NumGenes - 1;
}
while ((numTrysToFindOldLink--) > 0)
{
// choose a link, use the square root to prefer the older links
int i = RangeRandomizer.RandomInt(0, upperLimit);
NEATLinkGene link = (NEATLinkGene)linksChromosome.Genes[i];
// get the from neuron
long fromNeuron = link.FromNeuronID;
if ((link.Enabled)
&& (!link.IsRecurrent)
&& (((NEATNeuronGene)Neurons.Genes[
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;
NEATNeuronGene fromGene = (NEATNeuronGene)Neurons.Genes[
GetElementPos(from)];
NEATNeuronGene toGene = (NEATNeuronGene)Neurons.Genes[
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.Genes.Add(new NEATNeuronGene(NEATNeuronType.Hidden,
newNeuronID, newDepth, newWidth));
// add the first link
long link1ID = ((NEATTraining)GA).Population.AssignInnovationID();
((NEATTraining)GA).Innovations.CreateNewInnovation(from, newNeuronID,
NEATInnovationType.NewLink);
NEATLinkGene link1 = new NEATLinkGene(from, newNeuronID,
true, link1ID, 1.0, false);
linksChromosome.Genes.Add(link1);
// add the second link
long link2ID = ((NEATTraining)GA).Population.AssignInnovationID();
((NEATTraining)GA).Innovations.CreateNewInnovation(newNeuronID, to,
NEATInnovationType.NewLink);
NEATLinkGene link2 = new NEATLinkGene(newNeuronID, to, true,
link2ID, originalWeight, false);
linksChromosome.Genes.Add(link2);
}
else
{
// existing innovation
long newNeuronID = innovation.NeuronID;
NEATInnovation innovationLink1 = ((NEATTraining)GA).Innovations
.CheckInnovation(from, newNeuronID,
NEATInnovationType.NewLink);
NEATInnovation innovationLink2 = ((NEATTraining)GA).Innovations
.CheckInnovation(newNeuronID, to,
NEATInnovationType.NewLink);
if ((innovationLink1 == null) || (innovationLink2 == null))
{
throw new NeuralNetworkError("NEAT Error");
}
NEATLinkGene link1 = new NEATLinkGene(from, newNeuronID,
true, innovationLink1.InnovationID, 1.0, false);
NEATLinkGene link2 = new NEATLinkGene(newNeuronID, to, true,
innovationLink2.InnovationID, originalWeight, false);
linksChromosome.Genes.Add(link1);
linksChromosome.Genes.Add(link2);
NEATNeuronGene newNeuron = new NEATNeuronGene(
NEATNeuronType.Hidden, newNeuronID, newDepth, newWidth);
neuronsChromosome.Genes.Add(newNeuron);
}
return;
}
/// <summary>
/// Construct a genome by copying another.
/// </summary>
/// <param name="other">The other genome.</param>
public NEATGenome(NEATGenome other)
: base(other.GA)
{
neuronsChromosome = new Chromosome();
linksChromosome = new Chromosome();
this.Chromosomes.Add(neuronsChromosome);
this.Chromosomes.Add(linksChromosome);
GenomeID = other.GenomeID;
networkDepth = other.networkDepth;
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)
{
NEATNeuronGene oldGene = (NEATNeuronGene)gene;
NEATNeuronGene newGene = new NEATNeuronGene(oldGene.NeuronType
, oldGene.Id, oldGene.SplitX,
oldGene.SplitY, oldGene.Recurrent, oldGene
.ActivationResponse);
this.neuronsChromosome.Genes.Add(newGene);
}
// copy links
foreach (IGene gene in other.Links.Genes)
{
NEATLinkGene oldGene = (NEATLinkGene)gene;
NEATLinkGene newGene = new NEATLinkGene(oldGene
.FromNeuronID, oldGene.ToNeuronID, oldGene
.Enabled, oldGene.InnovationId, oldGene
.Weight, oldGene.IsRecurrent);
Links.Genes.Add(newGene);
}
}
/// <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>
public void AddNeuron(double mutationRate, int numTrysToFindOldLink)
{
// should we add a neuron?
if (ThreadSafeRandom.NextDouble() > mutationRate)
{
return;
}
// the link to split
NEATLinkGene splitLink = null;
int sizeThreshold = inputCount + outputCount + 10;
// if there are not at least
int upperLimit;
if (linksChromosome.Genes.Count < sizeThreshold)
{
upperLimit = NumGenes - 1 - (int)Math.Sqrt(NumGenes);
}
else
{
upperLimit = NumGenes - 1;
}
while ((numTrysToFindOldLink--) > 0)
{
// choose a link, use the square root to prefer the older links
int i = RangeRandomizer.RandomInt(0, upperLimit);
NEATLinkGene link = (NEATLinkGene)linksChromosome.Genes[i];
// get the from neuron
long fromNeuron = link.FromNeuronID;
if ((link.Enabled) &&
(!link.IsRecurrent) &&
(((NEATNeuronGene)Neurons.Genes[
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;
NEATNeuronGene fromGene = (NEATNeuronGene)Neurons.Genes[
GetElementPos(from)];
NEATNeuronGene toGene = (NEATNeuronGene)Neurons.Genes[
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.Genes.Add(new NEATNeuronGene(NEATNeuronType.Hidden,
newNeuronID, newDepth, newWidth));
// add the first link
long link1ID = ((NEATTraining)GA).Population.AssignInnovationID();
((NEATTraining)GA).Innovations.CreateNewInnovation(from, newNeuronID,
NEATInnovationType.NewLink);
NEATLinkGene link1 = new NEATLinkGene(from, newNeuronID,
true, link1ID, 1.0, false);
linksChromosome.Genes.Add(link1);
// add the second link
long link2ID = ((NEATTraining)GA).Population.AssignInnovationID();
((NEATTraining)GA).Innovations.CreateNewInnovation(newNeuronID, to,
NEATInnovationType.NewLink);
NEATLinkGene link2 = new NEATLinkGene(newNeuronID, to, true,
link2ID, originalWeight, false);
linksChromosome.Genes.Add(link2);
}
else
{
// existing innovation
long newNeuronID = innovation.NeuronID;
NEATInnovation innovationLink1 = ((NEATTraining)GA).Innovations
.CheckInnovation(from, newNeuronID,
NEATInnovationType.NewLink);
NEATInnovation innovationLink2 = ((NEATTraining)GA).Innovations
.CheckInnovation(newNeuronID, to,
NEATInnovationType.NewLink);
if ((innovationLink1 == null) || (innovationLink2 == null))
{
throw new NeuralNetworkError("NEAT Error");
}
NEATLinkGene link1 = new NEATLinkGene(from, newNeuronID,
true, innovationLink1.InnovationID, 1.0, false);
NEATLinkGene link2 = new NEATLinkGene(newNeuronID, to, true,
innovationLink2.InnovationID, originalWeight, false);
linksChromosome.Genes.Add(link1);
linksChromosome.Genes.Add(link2);
NEATNeuronGene newNeuron = new NEATNeuronGene(
NEATNeuronType.Hidden, newNeuronID, newDepth, newWidth);
neuronsChromosome.Genes.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>
public void AddLink(double mutationRate, double chanceOfLooped,
int numTrysToFindLoop, int numTrysToAddLink)
{
// should we even add the link
if (ThreadSafeRandom.NextDouble() > mutationRate)
{
return;
}
// 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 ((numTrysToFindLoop--) > 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 = neuron2ID = neuronGene.Id;
neuronGene.Recurrent = true;
recurrent = true;
numTrysToFindLoop = 0;
}
}
}
else
{
// try to add a regular link
while ((numTrysToAddLink--) > 0)
{
NEATNeuronGene neuron1 = ChooseRandomNeuron(true);
NEATNeuronGene neuron2 = ChooseRandomNeuron(false);
if (!IsDuplicateLink(neuron1ID, neuron2ID) &&
(neuron1.Id != neuron2.Id) &&
(neuron2.NeuronType != NEATNeuronType.Bias))
{
neuron1ID = -1;
neuron2ID = -1;
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
NEATNeuronGene neuronGene2 = (NEATNeuronGene)neuronsChromosome.Genes
[GetElementPos(neuron1ID)];
if (neuronGene2.SplitY > neuronGene2.SplitY)
{
recurrent = true;
}
// is this a new innovation?
if (innovation == null)
{
// new innovation
((NEATTraining)GA).Innovations.CreateNewInnovation(neuron1ID, neuron2ID,
NEATInnovationType.NewLink);
long id2 = ((NEATTraining)GA).Population.AssignInnovationID();
NEATLinkGene linkGene = new NEATLinkGene(neuron1ID,
neuron2ID, true, id2, RangeRandomizer.Randomize(-1, 1),
recurrent);
linksChromosome.Genes.Add(linkGene);
}
else
{
// existing innovation
NEATLinkGene linkGene = new NEATLinkGene(neuron1ID,
neuron2ID, true, innovation.InnovationID,
RangeRandomizer.Randomize(-1, 1), recurrent);
linksChromosome.Genes.Add(linkGene);
}
}
/// <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)
{
NEATNeuronGene result = new NEATNeuronGene(NEATNeuronType.Hidden,
0, 0, 0);
foreach (IInnovation i in Innovations)
{
NEATInnovation 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;
}
}
return result;
}
/// <summary>
/// Construct an innovation.
/// </summary>
/// <param name="neuronGene">The neuron gene.</param>
/// <param name="innovationID">The innovation id.</param>
/// <param name="neuronID">The neuron id.</param>
public NEATInnovation(NEATNeuronGene neuronGene,
long innovationID, long neuronID)
{
this.neuronID = neuronID;
InnovationID = innovationID;
splitX = neuronGene.SplitX;
splitY = neuronGene.SplitY;
neuronType = neuronGene.NeuronType;
innovationType = NEATInnovationType.NewNeuron;
fromNeuronID = -1;
toNeuronID = -1;
}
