// 새로운 노드를 추가함.
// 기존의 연결 중 무작위로 선택해서 기존의 연결은 비활성화시키고,
// 그 사이에 새로운 노드를 추가함.
// in ==(w₁)==> out 이었다면
// in =(w₂)=> new =(w₃)=> out과 같이 변이가 일어남. (w₁w₂w₃는 연결의 가중치)
// 이때 구조적 혁신이 기존 성능에 주는 영향을 최소화하기 위해서 w₂= w₁, w₃= 1로 설정함.
public void MutateNode(Random r)
{
if (Genes.Count == 0)
{
return;
}
Gene gene = RandomGenes(r);
if (gene == null || !gene.Enable)
{
return;
}
gene.Enable = false;
Gene gene1 = gene.Clone();
gene1.Out = NodeIndex;
gene1.Weight = 1.0;
gene1.Innovation = Pool.NewInnovation();
gene1.Enable = true;
Genes.Add(gene1);
Gene gene2 = gene.Clone();
gene2.In = NodeIndex;
gene2.Innovation = Pool.NewInnovation();
gene2.Enable = true;
Genes.Add(gene2);
++NodeIndex;
}
public void Initialize()
{
Genes.Clear();
Fitness = 0;
int genes = _settings.GenomeLength;
// create a random bit string (random genes)
for (int i = 0; i < genes; ++i)
{
var gene = new Gene <TCombinationModel>(_settings);
int initPasses = 0;
// Make sure all genes are unique
do
{
gene.Initialize();
initPasses++;
} while (Genes.Any(g => g.GetActivePartsString().Equals(gene.GetActivePartsString())));
Genes.Add(gene);
Debug.WriteLineIf(initPasses > 1, $"# Re-initialized because of duplicate gene ({initPasses})");
}
RebuildModelFollowingGenes();
UpdateFitnessScore();
}
//Give birth to two children
public Genome(Genome Father, Genome Mother, bool XY, Int64 id)
{
ID = id;
this.Genes = new List <String>();
//Get half the length
int HalfLength = (int)Math.Round((Father.Genes.Count / 2D), 0);
//If XY is true then spawn first three of father and last three of mother otherwise do the opposite
if (XY)
{
//Father
for (int i = 0; i < HalfLength; i++)
{
Genes.Add(Father.Genes[i]);
}
//Mother
for (int i = HalfLength; i < Mother.Genes.Count; i++)
{
Genes.Add(Mother.Genes[i]);
}
}
else
{
//Mother
for (int i = 0; i < HalfLength; i++)
{
Genes.Add(Mother.Genes[i]);
}
//Father
for (int i = HalfLength; i < Father.Genes.Count; i++)
{
Genes.Add(Father.Genes[i]);
}
}
}
/// <summary>
/// Adds gene between two nodes.
/// There cannot be two genes between same nodes.
/// </summary>
private void AddGene(Random rnd, ref int innovation, List <Gene> allGenes)
{
int latter;
int first;
do
{
first = rnd.Next(0, Nodes.Count);
}while(Nodes[first].Type == NodeType.Output);
Node input = Nodes[first];
Node output;
int j = 0;
do
{
latter = rnd.Next(0, Nodes.Count);
output = Nodes[latter];
++j;
if (j > 10 && input.Layer >= output.Layer)
{
for (int i = 0; i < Nodes.Count; i++)
{
if (input.Layer < Nodes[i].Layer)
{
output = Nodes[i];
}
}
}
} // SHOULD NOT PICK THE SAME LAYER
while (input.Layer >= output.Layer);
Gene gene = null;
foreach (var item in allGenes)
{
if (item.In.Number == input.Number && item.Out.Number == output.Number)
{
gene = item.ShallowCopy();
gene.In = input;
gene.Type = GeneType.Enabled;
gene.Out = output;
break;
}
}
if (gene == null)
{
gene = new Gene(input, output, 0f, GeneType.Enabled, ++innovation);
var g = gene.ShallowCopy();
g.Type = GeneType.AddGene;
allGenes.Add(g);
}
if (Genes.ContainsValue(gene))
{
return;
}
gene.Weight = gene.AssignRandomWeight(rnd);
gene.In.OutgoingConnections.Add(gene);
Genes.Add(gene.Innovation, gene);
}
public Chromosome(List <Gene> genes) //Caprazlama yapildiginda yeni kromozom olusturmak icin sadece bu metot taraginda kullanilabilir
{
foreach (var gene in genes)
{
Genes.Add(new Gene(gene.Value));
}
CalculateFittnesFuntion();
}
private void InitGenes()
{
Genes.Add(GeneHelper.CreateCooperationGene(RandomHelper.StandardGeneratorInstance.Next(1, 2)));
Genes.Add(GeneHelper.CreateLibidoGene());
Genes.Add(GeneHelper.CreateEconomyGeneVariations());
Genes.Add(GeneHelper.CreateMilitaryGeneVariations());
}
public Chromosome() //Kromozom ilk olustugunda populasyonda belirtildigi kadar genlere sahip bir sekilde olusturuluyor.
{
for (int i = 0; i < Population.GenesCount; i++)
{
Genes.Add(new Gene());
}
CalculateFittnesFuntion();
}
public void Add(Gene gene)
{
if (!Exists)
{
Genes = new List <Gene>();
}
Genes.Add(gene);
}
public IGene MutateAddGene(IEnumerable <IGene> genePool)
{
// Select two nodes at random to connect
List <INode> nodeOutCandidates = Nodes.ToList();
if (!GenomeParameters.AllowOutputOutGenes)
{
nodeOutCandidates = nodeOutCandidates.Where(n => n.Type != NodeType.Output).ToList();
}
INode nodeOut = nodeOutCandidates[new Random().Next(nodeOutCandidates.Count)];
// Get existing connections for this node
List <IGene> existingConnectionsIn = Genes.Where(cg => cg.NodeIn == nodeOut).ToList();
List <IGene> existingConnectionsOut = Genes.Where(cg => cg.NodeOut == nodeOut).ToList();
// Discover nodes where no connection currently exists
List <INode> nodeInCandidates = Nodes
.Except(existingConnectionsIn.Select(g => g.NodeOut))
.Except(existingConnectionsOut.Select(g => g.NodeIn)).ToList();
// Don't allow input to input or output to output connections
if (nodeOut.Type == NodeType.Input || nodeOut.Type == NodeType.Output)
{
nodeInCandidates = nodeInCandidates.Where(n => n.Type != nodeOut.Type).ToList();
}
if (nodeOut.Type == NodeType.Hidden || nodeOut.Type == NodeType.Output)
{
nodeInCandidates = nodeInCandidates.Where(n => n.Type != NodeType.Input).ToList();
}
if (nodeInCandidates.Count > 0)
{
INode selectedNodeIn = nodeInCandidates[new Random().Next(nodeInCandidates.Count)];
IGene existingGene = genePool.FirstOrDefault(gp => gp.NodeIn.Id == selectedNodeIn.Id &&
gp.NodeOut.Id == nodeOut.Id);
// Create the connection
IGene gene = new Gene(
nodeOut,
selectedNodeIn,
existingGene != null ? existingGene.Innovation : GetNextInnovation()
);
Genes.Add(gene);
return(gene);
}
return(null);
}
public Genome(int inputs, int outputs, double weight = 0) : this()
{
List <INode> inputNodes = Enumerable.Range(0, inputs).Select <int, INode>(i => new Node(NodeType.Input, i)).ToList();
List <INode> outputNodes = Enumerable.Range(0, outputs).Select <int, INode>(i => new Node(NodeType.Output, i)).ToList();
Nodes = inputNodes.Concat(outputNodes).ToList();
inputNodes.ForEach(inputNode => {
outputNodes.ForEach(outputNode =>
Genes.Add(new Gene(inputNode, outputNode, GetNextInnovation(), weight)));
});
}
public void Crossover(ref TestCitizen mate, int slicePosA = -1, int slicePosB = -1)
{
Random rng = new Random();
slicePosA = (slicePosA < 0) ? rng.Next(Genes.Count - 1) : slicePosA;
slicePosB = (slicePosB < 0) ? rng.Next(mate.Genes.Count - 1) : slicePosB;
// Determines if the input parameters are valid
if (slicePosB >= mate.Genes.Count || slicePosA >= Genes.Count)
{
throw new InvalidOperationException("slice position is greater than the maximum index of either the mate, or the subject!");
}
// Initializes each cut List
List <bool> cutA = new List <bool>(Genes.Count - (slicePosA + 1));
List <bool> cutB = new List <bool>(mate.Genes.Count - (slicePosB + 1));
// Removes the data from each subject at the splice Pos
for (int i = 0; i < Genes.Count - (slicePosA + 1); i++)
{
cutA.Add(Genes[Genes.Count - 1]);
Genes.RemoveAt(Genes.Count - 1);
}
cutA.Reverse();
for (int i = 0; i < mate.Genes.Count - (slicePosB + 1); i++)
{
cutB.Add(mate.Genes[mate.Genes.Count - 1]);
mate.Genes.RemoveAt(mate.Genes.Count - 1);
}
cutB.Reverse();
// Adds the cut material back into the opposite subject
foreach (bool b in cutA)
{
mate.Genes.Add(b);
}
foreach (bool b in cutB)
{
Genes.Add(b);
}
}
public TestCitizen(List <bool> genes = null, int geneCount = -1) : base()
{
geneCount = (geneCount > 0) ? GeneCount : geneCount;
// Initializes the genes list with default value
Genes = genes ?? new List <bool>(geneCount);
if (genes == null)
{
for (int i = 0; i < geneCount; i++)
{
Genes.Add(false);
}
}
}
public void MutateLink(bool forceBias)
{
Neuron n1 = forceBias ? this[-66] : RandomNeuron(true);
Neuron n2 = RandomNeuron(false);
foreach (Gene gene in Genes)
{
if (gene.from == n1.Index && gene.axon.destination == n2.Index)
{
return;
}
}
Genes.Add(new Gene(n1.Index, n2.Index, R.NextDouble() * 4 - 2, true, innovation++));
}
private void CopyFrom(Neat parent)
{
lock (ThinkLock) {
for (int i = 0; i < parent.Neurons.Count; i++)
{
Neurons.Add(parent.Neurons[i].Clone(this));
}
}
for (int i = 0; i < parent.Genes.Count; i++)
{
Gene gene = parent.Genes[i];
Genes.Add(new Gene(gene.from, gene.axon.destination, gene.axon.weight, gene.enabled, gene.innovation));
}
innovation = parent.innovation;
}
public void FromParents(Neat parent, Neat other)
{
lock (ThinkLock) {
OnRemove?.Invoke();
Neurons.Clear();
Genes.Clear();
}
if (other == null || R.NextDouble() > mutate_crossover)
{
CopyFrom(parent);
VaryColor(parent, null);
}
else
{
Dictionary <int, Gene> genes = new Dictionary <int, Gene>();
foreach (Gene gene in parent.Genes.Concat(other.Genes))
{
if (!genes.ContainsKey(gene.innovation))
{
Gene mutate = gene;
if (!mutate.enabled && R.NextDouble() < mutate_enable)
{
mutate.enabled = true;
}
genes[gene.innovation] = mutate;
}
}
int max = 0;
foreach (Gene gene in genes.Values)
{
max = Max(max, Max(gene.from, gene.axon.destination));
Genes.Add(gene);
}
addNeurons(max);
innovation = Max(parent.innovation, other.innovation);
VaryColor(parent, other);
}
MutateEnable();
Mutate();
}
public void AddGene(GeneType Gene)
{
#region Validations
if (Genes == null)
{
Genes = new List <GeneType>();
}
if (Genes.Count > NumberOfGene)
{
throw new Exception("Violation of Maximum Number of Genes");
}
if (Gene == null)
{
throw new NullReferenceException();
}
#endregion Validations
Genes.Add(Gene);
}
protected void AddRegion(string id, string typename, int start, int end, Sense sense)
{
try{
if (typename.Equals("gene"))
{
Gene g = new Gene(id, typename, start, end, sense);
Genes.Add(id, g);
}
else
{
Region r = new Region(id, typename, start, end, sense);
Regions.Add(id, r);
}
}
catch (Exception e) {
MainData.ShowMessageWindow("Your Gff3 IDs are not consistent!\n " +
"Change Gff3 loader options to fix them!\n Error: " + e.Message + "\n Offending id:" + id, true);
}
}
// 새로운 연결을 추가하는 변이
// 두 개의 노드를 무작위로 선택해 (단, out에 해당하는 node는 입력 노드가 아님)
// 두 노드 사이를 잇는 연결이 없다면 새로운 연결을 추가함
public void MutateConnection(Random random)
{
int n1 = RandomNode(false, random);
int n2 = RandomNode(true, random);
if (n2 < Pool.Inputs)
{
if (n1 < Pool.Inputs)
{
return;
}
int _tmp = n1;
n1 = n2;
n2 = _tmp;
}
if (n1 == n2)
{
return;
}
if (n1 > n2)
{
int _tmp = n1;
n1 = n2;
n2 = _tmp;
}
if (ContainsLink(n1, n2))
{
return;
}
Gene gene = new Gene(n1, n2)
{
Weight = random.NextDouble() * 4 - 2,
Enable = true,
Innovation = Pool.NewInnovation()
};
Genes.Add(gene);
}
public Genome(int genomeSize, int geneSize, GenomeFunctions <T> functions, GenomeSettings settings = null)
{
if (settings == null)
{
this.settings = new GenomeSettings(genomeSize);
}
else
{
this.settings = settings;
}
this.Generation = 1;
this.Genes = new List <Gene <T> >(genomeSize);
this.geneSize = geneSize;
this.functions = functions;
for (int i = 0; i < Genes.Capacity; i++)
{
Genes.Add(new Gene <T>(geneSize, functions, settings));
}
}
public INode MutateAddNode()
{
int innovation = (int)RandomHelpers.GetRandomBiasingLow(
Genes.Min(g => g.Innovation), Genes.Max(g => g.Innovation)
);
IGene oldGene = Genes.FirstOrDefault(g => g.Innovation <= innovation);
if (oldGene == null)
{
oldGene = Genes[new Random().Next(Genes.Count)];
}
INode newNode = new Node(NodeType.Hidden);
// Disable the old connection
oldGene.IsExpressed = false;
// Add new connections
IGene newGeneIn = new Gene(
oldGene.NodeOut,
newNode,
GetNextInnovation(),
1
);
IGene newGeneOut = new Gene(
newNode,
oldGene.NodeIn,
GetNextInnovation(),
oldGene.Weight
);
Nodes.Add(newNode);
Genes.Add(newGeneIn);
Genes.Add(newGeneOut);
return(newNode);
}
public void MutateNode()
{
if (Genes.Count == 0)
{
return;
}
Gene gene = Genes[R.Next(0, Genes.Count)];
if (!gene.enabled)
{
return;
}
gene.enabled = false;
StdNeuron neuron = new StdNeuron(this, Neurons.Count + 1);
Neurons.Add(neuron);
Genes.Add(new Gene(gene.from, neuron.Index, gene.axon.weight, true, innovation++));
Genes.Add(new Gene(neuron.Index, gene.axon.destination, 1, true, innovation++));
}
/// <summary>
/// Add nodes to random connection gene in genome
/// </summary>
private void AddNode(Random rnd, ref int innovation, ref int number, List <Gene> allGenes)
{
int index = rnd.Next(0, Genes.Count);
var pair = Genes.ElementAt(index);
Gene gene = pair.Value;
gene.Type = GeneType.Disabled;
Node node = null;
Gene firstGene = null;
Gene latterGene = null;
bool exists = FindExistingNode(gene, ref node, ref firstGene, ref latterGene, allGenes, ref innovation, ref number);
if (!exists)
{
node = new Node(NodeType.Hidden, gene.In.Layer + 1, ++number);
firstGene = new Gene(gene.In, node, 1f, GeneType.Enabled, ++innovation);
latterGene = new Gene(node, gene.Out, gene.Weight, GeneType.Enabled, ++innovation);
}
// Check if the latter gene connection cannot be from the same layer to the same layer
if (gene.Out.Layer == node.Layer)
{
IncrementLayer(node);
}
if (!Genes.ContainsKey(firstGene.Innovation)) // should always go to if branch
{
Genes.Add(firstGene.Innovation, firstGene);
firstGene.In.OutgoingConnections.Add(firstGene);
if (!exists)
{
var g = firstGene.ShallowCopy();
g.Type = GeneType.AddNode;
allGenes.Add(g); // still points to nodes in this genome
}
}
else
{
;
}
if (!Genes.ContainsKey(latterGene.Innovation)) // should always go to if branch
{
Genes.Add(latterGene.Innovation, latterGene);
latterGene.In.OutgoingConnections.Add(latterGene);
if (!exists)
{
var g = latterGene.ShallowCopy();
g.Type = GeneType.AddNode;
allGenes.Add(g); // still points to nodes in this genome
}
}
else
{
;
}
if (!Nodes.Contains(node)) // should always go to if branch
{
Nodes.Add(node);
}
else
{
for (int i = 0; i < Nodes.Count; i++)
{
if (node.Number == Nodes[i].Number)
{
if (ReferenceEquals(node, Nodes[i]))
{
;
}
else
{
;
}
}
}
}
}
/// <summary>
/// Processes a feature from a GTF gene model file.
/// </summary>
/// <param name="feature"></param>
/// <param name="oneBasedStart"></param>
/// <param name="oneBasedEnd"></param>
/// <param name="chrom"></param>
/// <param name="attributes"></param>
public void ProcessGtfFeature(MetadataListItem <List <string> > feature, long oneBasedStart, long oneBasedEnd, Chromosome chrom, Dictionary <string, string> attributes)
{
bool hasGeneId = attributes.TryGetValue("gene_id", out string geneId);
bool hasTranscriptId = attributes.TryGetValue("transcript_id", out string transcriptId);
bool hasProteinId = attributes.TryGetValue("protein_id", out string proteinId);
bool hasExonId = attributes.TryGetValue("exon_id", out string exonId);
bool hasSource = feature.SubItems.TryGetValue("source", out List <string> sourceish);
bool hasStrand = feature.SubItems.TryGetValue("strand", out List <string> strandish);
bool hasFrame = feature.SubItems.TryGetValue("frame", out List <string> framey);
string source = hasSource ? sourceish[0] : "";
if (!hasStrand)
{
return;
} // strand is a required to do anything in this program
string strand = strandish[0];
int frame = 0;
if (hasFrame)
{
int.TryParse(framey[0], out frame);
}
// Trim prefixes from the IDs
string genePrefix = "gene:";
string transcriptPrefix = "transcript:";
if (hasGeneId && geneId.StartsWith(genePrefix))
{
string newGeneId = geneId.Substring(genePrefix.Length);
feature.FreeText.Replace(geneId, newGeneId);
geneId = newGeneId;
}
if (hasTranscriptId && transcriptId.StartsWith(transcriptPrefix))
{
string newTranscriptId = transcriptId.Substring(transcriptPrefix.Length);
feature.FreeText.Replace(transcriptId, newTranscriptId);
transcriptId = newTranscriptId;
}
if (hasProteinId && proteinId.StartsWith(transcriptPrefix))
{
proteinId = proteinId.Substring(transcriptPrefix.Length); // transcript id is used for protein id sometimes
}
// Catch the transcript features before they go by if available, i.e. if the file doesn't just have exons
if (feature.Key == "transcript" && (currentTranscript == null || hasTranscriptId && transcriptId != currentTranscript.ID))
{
if (currentGene == null || hasGeneId && geneId != currentGene.ID)
{
currentGene = new Gene(geneId, chrom, source, strand, oneBasedStart, oneBasedEnd, feature);
Genes.Add(currentGene);
GenomeForest.Add(currentGene);
}
currentTranscript = new Transcript(transcriptId, currentGene, source, strand, oneBasedStart, oneBasedEnd, null, null, feature);
currentGene.Transcripts.Add(currentTranscript);
GenomeForest.Add(currentTranscript);
}
if (feature.Key == "exon" || feature.Key == "CDS")
{
if (currentGene == null || hasGeneId && geneId != currentGene.ID)
{
currentGene = new Gene(geneId, chrom, source, strand, oneBasedStart, oneBasedEnd, feature);
Genes.Add(currentGene);
GenomeForest.Add(currentGene);
}
if (currentTranscript == null || hasTranscriptId && transcriptId != currentTranscript.ID)
{
if (currentTranscript != null)
{
Transcript.SetRegions(currentTranscript);
currentTranscript.FrameCorrection();
}
currentTranscript = new Transcript(transcriptId, currentGene, source, strand, oneBasedStart, oneBasedEnd, null, null, feature);
currentGene.Transcripts.Add(currentTranscript);
GenomeForest.Add(currentTranscript);
}
if (feature.Key == "exon")
{
ISequence exon_dna = chrom.Sequence.GetSubSequence(oneBasedStart - 1, oneBasedEnd - oneBasedStart + 1);
Exon exon = new Exon(currentTranscript, currentTranscript.IsStrandPlus() ? exon_dna : exon_dna.GetReverseComplementedSequence(),
source, oneBasedStart, oneBasedEnd, chrom.Sequence.ID, strand, null, feature);
if (exon.Length() > 0)
{
currentTranscript.Exons.Add(exon);
}
}
else if (feature.Key == "CDS")
{
CDS cds = new CDS(currentTranscript, chrom.Sequence.ID, source, strand, oneBasedStart, oneBasedEnd, null, frame);
if (hasProteinId)
{
currentTranscript.ProteinID = proteinId;
}
if (cds.Length() > 0)
{
currentTranscript.CodingDomainSequences.Add(cds);
}
}
else
{ // nothing to do
}
}
}
/// <summary>
/// Processes a feature from a GFF3 gene model file.
/// </summary>
/// <param name="feature"></param>
/// <param name="oneBasedStart"></param>
/// <param name="oneBasedEnd"></param>
/// <param name="chrom"></param>
/// <param name="attributes"></param>
public void ProcessGff3Feature(MetadataListItem <List <string> > feature, long oneBasedStart, long oneBasedEnd, Chromosome chrom, Dictionary <string, string> attributes)
{
bool hasGeneId = attributes.TryGetValue("gene_id", out string geneId);
bool hasTranscriptId = attributes.TryGetValue("transcript_id", out string transcriptId);
bool hasExonId = attributes.TryGetValue("exon_id", out string exonId);
bool hasProteinId = attributes.TryGetValue("protein_id", out string proteinId);
bool hasSource = feature.SubItems.TryGetValue("source", out List <string> sourceish); // false if empty ("." in GFF format)
bool hasStrand = feature.SubItems.TryGetValue("strand", out List <string> strandish); // false if empty ("." in GFF format)
bool hasFrame = feature.SubItems.TryGetValue("frame", out List <string> framey); // false if empty ("." in GFF format)
string source = hasSource ? sourceish[0] : "";
if (!hasStrand)
{
return;
} // strand is a required to do anything in this program
string strand = strandish[0];
int frame = 0;
if (hasFrame)
{
int.TryParse(framey[0], out frame);
}
if (hasGeneId && (currentGene == null || hasGeneId && geneId != currentGene.ID))
{
currentGene = new Gene(geneId, chrom, source, strand, oneBasedStart, oneBasedEnd, feature);
Genes.Add(currentGene);
GenomeForest.Add(currentGene);
}
if (hasTranscriptId && (currentTranscript == null || hasTranscriptId && transcriptId != currentTranscript.ID))
{
if (currentTranscript != null)
{
Transcript.SetRegions(currentTranscript);
currentTranscript.FrameCorrection();
}
currentTranscript = new Transcript(transcriptId, currentGene, source, strand, oneBasedStart, oneBasedEnd, null, null, feature);
currentGene.Transcripts.Add(currentTranscript);
GenomeForest.Add(currentTranscript);
}
if (hasExonId)
{
ISequence exon_dna = chrom.Sequence.GetSubSequence(oneBasedStart - 1, oneBasedEnd - oneBasedStart + 1);
Exon exon = new Exon(currentTranscript, currentTranscript.IsStrandPlus() ? exon_dna : exon_dna.GetReverseComplementedSequence(),
source, oneBasedStart, oneBasedEnd, chrom == null ? "" : chrom.ChromosomeID, strand, null, feature);
if (exon.Length() > 0)
{
currentTranscript.Exons.Add(exon);
}
}
else if (hasProteinId)
{
CDS cds = new CDS(currentTranscript, chrom.Sequence.ID, source, strand, oneBasedStart, oneBasedEnd, null, frame);
if (cds.Length() > 0)
{
currentTranscript.CodingDomainSequences.Add(cds);
currentTranscript.ProteinID = proteinId;
}
}
else // nothing to do
{
}
}
/// <summary>
/// Add a new Gene
/// </summary>
public void addGene()
{
Genes.Add(new Gene());
}