internal void CalculatePopulation()
{
// traženje najboljih hromosoma
fitnessMax = 0;
fitnessSum = 0;
if (bestChromosome == null)
{
bestChromosome = chromosomes[0];
}
for (int i = 0; i < gpParameters.popSize; i++)
{
float fitness = (chromosomes[i]).fitness;
// sum calc
fitnessSum += fitness;
// cal the best chromosome
if (fitness > fitnessMax)
{
fitnessMax = fitness;
bestChromosome = chromosomes[i];
}
}
fitnessAvg = fitnessSum / gpParameters.popSize;
}
private void FUSSSelection(int size)
{
// new chromosomes, initially empty
List <GPChromosome> newPopulation = new List <GPChromosome>();
//Maximum fitness
double fitnessMax = chromosomes.Max(x => x.fitness);
double rnd;
double dif;
int selIndex = 0;
for (int j = 0; j < size; j++)
{
rnd = Globals.radn.NextDouble(0, fitnessMax);
dif = Math.Abs(chromosomes[0].fitness - rnd);
selIndex = 0;
for (int i = 1; i < chromosomes.Count; i++)
{
double curDif = Math.Abs(chromosomes[i].fitness - rnd);
if (dif > curDif)
{
dif = curDif;
selIndex = i;
}
}
newPopulation.Add(chromosomes[selIndex].Clone());
}
// survived chromosomes
chromosomes.AddRange(newPopulation);
// old population is goint to die
GPChromosome.DestroyChromosomes(ref chromosomes);
}
private void TournamentSelection(int size)
{
// velicinaPopulacije of current chromosomes
int currentSize = chromosomes.Count;
List <GPChromosome> tourn = new List <GPChromosome>((int)gpParameters.SelParam1);
// new chromosomes, initially empty
List <GPChromosome> newPopulation = new List <GPChromosome>();
for (int j = 0; j < size; j++)
{
currentSize = chromosomes.Count;
for (int i = 0; i < gpParameters.SelParam1 && i < currentSize; i++)
{
int ind = Globals.radn.Next(currentSize);
tourn.Add(chromosomes[ind]);
}
tourn.Sort();
newPopulation.Add(tourn[0].Clone());
chromosomes.Remove(tourn[0]);
tourn.Clear();
}
// survived chromosomes
chromosomes.AddRange(newPopulation);
// old population is goint to die
GPChromosome.DestroyChromosomes(ref chromosomes);
}
/// <summary>
/// HalfAndHalf method of initialization,all chromosomes is grouped in equal number of chromosome
/// and generates with the same levels.
/// </summary>
/// <param name="size"></param>
private void HalfHalfInitialization(int size)
{
//The max init depth of tree
int n = GetMaxInitializeLevel();
//Make equal group for each level
int br = (size / n);
//Create equal number of choromosomes for each level
for (int i = 2; i <= n; i++)
{
if (i == n)//at the end take the rest
{
br = (size - ((i - 2) * br));
}
//Chromosome generation with exact level
for (int j = 0; j < br; j++)
{
// create new chromosome
GPChromosome c = GenerateChromosome(i);
// add to chromosomes
chromosomes.Add(c);
}
}
}
/// <summary>
/// Randomly generate chromosome with exact number of levels
/// </summary>
/// <param name="levels">Tree leveles</param>
/// <returns></returns>
public GPChromosome GenerateChromosome(int levels)
{
GPChromosome ch = GPChromosome.NewChromosome();
ch.expressionTree = GenerateTreeStructure(levels);
return(ch);
}
public static HashSet <IGPChromosome> GenerateAllCombinations(SocialGPChromosome socialChromosome)
{
var allSubCombinations = new GPChromosome[socialChromosome.NumAgents][];
for (var i = 0; i < socialChromosome.NumAgents; i++)
{
//adds sub-element and all its combinations to list
var gpChromosome = (GPChromosome)socialChromosome[i];
var allChromCombs = Learning.IMRL.EC.Util.GenerateAllCombinations(gpChromosome).ToList();
allChromCombs.Add(gpChromosome);
var allChromCombsArray = new GPChromosome[allChromCombs.Count];
for (var j = 0; j < allChromCombs.Count; j++)
{
allChromCombsArray[j] = (GPChromosome)allChromCombs[j];
}
allSubCombinations[i] = allChromCombsArray;
}
//makes combinations with all chromosomes
var chromCombs = allSubCombinations.AllCombinations();
var allCombinations = new HashSet <IGPChromosome>();
foreach (var chromComb in chromCombs)
{
allCombinations.Add(new SocialGPChromosome(chromComb));
}
return(allCombinations);
}
private void SkrgicSelection(int size)
{
// new chromosomes, initially empty
List <GPChromosome> newPopulation = new List <GPChromosome>();
// double k = 0.2; //additionalParameter;
double fitnessMax = chromosomes.Max(x => x.fitness) * (1.0 + gpParameters.SelParam1);
for (int i = 0; i < size; i++)
{
//Slucajni index iz populacije
int randomIndex = Globals.radn.Next(0, chromosomes.Count);
//Slucajni broj izmedju 0-maxFitnes ukljucujuci i maxFitness koje je prethodno vec izracunat kod evaluacije hromosoma
double randomFitness = Globals.radn.NextDouble(0, fitnessMax /*, true include MaxValue*/);
while (true)
{
//Akoje slucajno generirani broj manji ili jednak fitnesu slucajnog hromosoma selektuj hromosom
if (randomFitness <= chromosomes[randomIndex].fitness * (1.0 + gpParameters.SelParam1 / fitnessMax))
{
newPopulation.Add(chromosomes[randomIndex].Clone());
break;
}
randomIndex = Globals.radn.Next(0, chromosomes.Count);
randomFitness = Globals.radn.NextDouble(0, fitnessMax /*, true include MaxValue*/);
}
}
// survived chromosomes
chromosomes.AddRange(newPopulation);
// old population is goint to die
GPChromosome.DestroyChromosomes(ref chromosomes);
}
/// <summary>
/// Randomly generate chromosome with exact number of levels
/// </summary>
/// <param name="levels">Tree leveles</param>
/// <returns></returns>
public GPChromosome GenerateGPChromosome(int levels)
{
GPChromosome ch = GPChromosome.NewChromosome();
ch.Generate(levels);
return(ch);
}
/// <summary>
/// Calculates model/prediction using best chromosome. Also it denormalized valuse if they were normalized
/// </summary>
/// <param name="ch"> bestchromosomes</param>
/// <param name="testData"></param>
/// <returns></returns>
protected virtual double[][] CalculateModel(GPChromosome ch, bool btrainingData = true)
{
if (ch != null)
{
var pts = GPdotNET.Core.Globals.CalculateGPModel(ch.expressionTree, btrainingData);
if (pts == null)
{
return(null);
}
//calculate output
var model = new double[1][];
var outv = new double[1][];
if (m_Experiment != null)
{
outv[0] = new double[1];
model[0] = new double[pts.Length];
for (int i = 0; i < pts.Length; i++)
{
outv[0][0] = pts[i];
var outv1 = m_Experiment.GetDenormalizedOutputRow(outv[0]);
model[0][i] = outv1[0];
}
}
else
{
model[0] = pts;//old version
}
return(model);
}
else
{
return(null);
}
}
/// <summary>
/// Before we start GP prepare all neccessery information
/// </summary>
/// <param name="termSet"></param>
/// <param name="funSet"></param>
/// <param name="gpParams"></param>
public void PrepareAlgorithm(GPTerminalSet termSet, GPFunctionSet funSet, GPParameters gpParams = null)
{
m_IterationCounter = 0;
if (Population == null)
{
Population = new CHPopulation();
}
Population.InitPopulation(termSet, funSet, gpParams);
Population.CalculatePopulation();
IsAlgorthmPrepared = true;
StopIteration = false;
//calculate model and prediction
GPChromosome ch = Population.bestChromosome as GPChromosome;
double[][] model = CalculateModel(ch);
double[][] prediction = CalculateModel(ch, false);
//Report the evolution has been started
if (ReportEvolution != null)
{
ReportEvolution(this,
new ProgressIndicatorEventArgs()
{
ReportType = ProgramState.Started,
AverageFitness = Population.fitnessAvg,
BestChromosome = Population.bestChromosome,
CurrentIteration = 0, LearnOutput = model, PredicOutput = prediction
});
}
}
private void UniversalStohasticSelection(int size)
{
// new chromosomes, initially empty
List <GPChromosome> newPopulation = new List <GPChromosome>();
//chromosomes.Sort();
int currentSize = chromosomes.Count();
float fitnessSum = chromosomes.Sum(c => c.fitness);
// get random distance value
float randDist = (float)Globals.radn.NextDouble(0, 1.0 / (double)size);
float partFitnes = 0;
for (int j = 0; j < size; j++)
{
partFitnes = 0;
for (int i = 0; i < chromosomes.Count; i++)
{
partFitnes += chromosomes[i].fitness / fitnessSum;
if (randDist <= partFitnes)
{
newPopulation.Add(chromosomes[i].Clone());
break;
}
}
randDist += 1.0F / (float)size;
}
// survived chromosomes
chromosomes.AddRange(newPopulation);
// old population is goint to die
GPChromosome.DestroyChromosomes(ref chromosomes);
}
/// <summary>
/// Fitness šproportionate selection.
/// </summary>
/// <param name="size"></param>
private void FitnessProportionateSelection(int size)
{
// new chromosomes, initially empty
List <GPChromosome> newPopulation = new List <GPChromosome>();
int currentSize = chromosomes.Count;
double sumOfFitness = 0;
//calculate sum of fitness
for (int i = 0; i < currentSize; i++)
{
sumOfFitness += chromosomes[i].fitness;
}
// create wheel ranges
double[] rangeMax = new double[currentSize];
double s = 0;
for (int i = 0; i < currentSize; i++)
{
// cumulative normalized fitness
s += (chromosomes[i].fitness / sumOfFitness);
rangeMax[i] = s;
}
// select chromosomes from old chromosomes to the new chromosomes
for (int j = 0; j < size; j++)
{
// get wheel value
double wheelValue = Globals.radn.NextDouble();
// find the chromosome for the wheel value
for (int i = 0; i < currentSize; i++)
{
//double wheelValue = rand.NextDouble();
if (wheelValue <= rangeMax[i] && chromosomes[i].fitness != -1)
{
// add the chromosome to the new population
var ch = chromosomes[i].Clone();
newPopulation.Add(ch);
chromosomes[i].fitness = -1;
break;
}
}
}
// survived chromosomes
chromosomes.AddRange(newPopulation);
// old population is goint to die
GPChromosome.DestroyChromosomes(ref chromosomes);
}
public override void Train(IForecastingDataSets datasets)
{
OnStartRunning(new ComponentRunEventArgs(datasets));
NumberOfVariables = datasets.InputVectorLength;
NumberOfSamples = datasets.Length;
EnvolutionStep = 0;
if (functionSet == null)
{
functionSet = new GPFunctionSet();
}
Initialize();
GenerateFunction();
double [] gpConstraints = GenerateConstants(mGPModelParameter.ConstantsIntervalFrom, mGPModelParameter.ConstantsIntervalTo, mGPModelParameter.ConstantsNumber);
GenerateTerminals(datasets, gpConstraints);
if (population == null)
{
EnvolutionStep = 1;
population = new GPPopulation(mGPModelParameter.PopulationSize, terminalSet, functionSet, parameters, mGPModelParameter.MultipleCore);
}
GPBestHromosome = population.bestChromosome;
while (ProveEnvolution(EnvolutionStep, mGPModelParameter.EnvolveConditionValue, mGPModelParameter.EnvolveIndicator))
{
population.StartEvolution();
OnRunningEpoch(new ComponentRunEpochEventArgs(EnvolutionStep));
EnvolutionStep++;
}
int indexOutput = terminalSet.NumConstants + terminalSet.NumVariables - 1;
List <int> lst = new List <int>();
FunctionTree.ToListExpression(lst, GPBestHromosome.Root);
double y = 0;
datasets.ForecastedData = new double[datasets.Length][];
for (int i = 0; i < terminalSet.RowCount; i++)
{
// evalue the function
y = functionSet.Evaluate(lst, terminalSet, i);
// check for correct numeric value
if (double.IsNaN(y) || double.IsInfinity(y))
{
y = 0;
}
datasets.ForecastedData[i] = new double[1];
datasets.ForecastedData[i][0] = y;
}
OnFinishRunning(new ComponentRunEventArgs(datasets)
{
State = functionSet.DecodeExpression(lst, terminalSet)
});
}
public SocialGPChromosome(uint numAgents, GPChromosome baseChromosome)
{
this.NumAgents = numAgents;
this._chromosomes = new GPChromosome[numAgents];
for (var i = 0; i < numAgents; i++)
{
this._chromosomes[i] = (GPChromosome)baseChromosome.Clone();
}
this.Population = baseChromosome.Population;
this.Init();
}
public override IECChromosome CreateBaseChromosome()
{
var gpChromosome = new GPChromosome(
new FlexibleGPGene(this.AllowedFunctions.ToList(), (int)(this.Constants.Length + this.NumBaseVariables)));
return(this.SameAgentParameters
? (IECChromosome) new SocialCommonGPChromosome(this.NumAgents, gpChromosome)
: new SocialGPChromosome(this.NumAgents, gpChromosome)
{
SymmetryFactor = this.SymmetryFactor
});
}
/// <summary>
/// Full initialization method, all choromosomes have the same level.
/// </summary>
/// <param name="size"></param>
private void FullInitialization(int size)
{
//Chromosome generation with exact level
for (int i = 0; i < size; i++)
{
// generate new chromosome
GPChromosome c = GenerateChromosome(GetMaxInitializeLevel());
//add to poppulation
chromosomes.Add(c);
}
}
/// <summary>
/// Main function for running GP
/// </summary>
/// <param name="terValue">termination value</param>
/// <param name="termType">type of termination</param>
public void StartEvolution(float terValue, int termType)
{
if (!IsAlgorthmPrepared)
{
throw new Exception("Algorithm is not prepared!");
}
if (Population == null)
{
throw new Exception("Population is null!");
}
//before we start set variable to initial value
StopIteration = false;
while (CanContinue(terValue, termType))
{
//increase evolution
m_IterationCounter++;
Population.Crossover();
Population.Mutate();
Population.EvaluatePopulation();
Population.Selection();
Population.CalculatePopulation();
//calculate model and prediction
GPChromosome ch = Population.bestChromosome as GPChromosome;
double[][] model = CalculateModel(ch);
double[][] prediction = CalculateModel(ch, false);
if (ReportEvolution != null)
{
ReportEvolution(this,
new ProgressIndicatorEventArgs()
{
ReportType = CanContinue(terValue, termType) ? ProgramState.Running : ProgramState.Finished,
AverageFitness = Population.fitnessAvg,
BestChromosome = Population.bestChromosome,
CurrentIteration = m_IterationCounter,
LearnOutput = model,
PredicOutput = prediction
});
}
}
}
public static uint GetDepth(GPChromosome chromosome)
{
var nodeStack = GetNodeStack(chromosome.ToString());
if ((nodeStack == null) || (nodeStack.Count == 0))
{
return(0);
}
var rootNode = nodeStack.Pop();
GenerateNodeStructure(rootNode, nodeStack);
return(GetDepth(rootNode, 0));
}
private void ApplyCrossover(GPChromosome ch1, GPChromosome ch2)
{
//Get random numbers between 0 and maximum index
int index1 = GetRandomNode(ch1.expressionTree.NodeCount());
int index2 = GetRandomNode(ch2.expressionTree.NodeCount());
//Exchange the geene material
Crossover(ch1.expressionTree, ch2.expressionTree, index1, index2);
//if some tree exceed the levels trim it
ch1.Trim(GetMaxOperationLevel());
ch2.Trim(GetMaxOperationLevel());
}
public static HashSet <IGPChromosome> GenerateAllCombinations(GPChromosome chromosome)
{
var nodeStack = GetNodeStack(chromosome.ToString());
if ((nodeStack == null) || (nodeStack.Count == 0))
{
return(new HashSet <IGPChromosome>());
}
var rootNode = nodeStack.Pop();
GenerateNodeStructure(rootNode, nodeStack);
return(GenerateAllCombinations(rootNode));
}
private void RankSelection(int size)
{
// new chromosomes, initially empty
List <GPChromosome> newPopulation = new List <GPChromosome>();
// velicinaPopulacije of current chromosomes
int currentSize = chromosomes.Count;
// sort current chromosomes
//chromosomes.Sort();
// calculate amount of ranges in the wheel
double ranges = currentSize * (currentSize + 1) / 2;
// create wheel ranges
double[] rangeMax = new double[currentSize];
double s = 0;
for (int i = 0, n = currentSize; i < currentSize; i++, n--)
{
s += ((double)n / ranges);
rangeMax[i] = s;
}
// select chromosomes from old chromosomes to the new chromosomes
for (int j = 0; j < size; j++)
{
// get wheel value
double wheelValue = Globals.radn.NextDouble();
// find the chromosome for the wheel value
for (int i = 0; i < currentSize; i++)
{
// get wheel value
if (wheelValue <= rangeMax[i])
{
// add the chromosome to the new chromosomes
newPopulation.Add(chromosomes[i].Clone());
break;
}
//Debug.Assert(false);
}
}
// survived chromosomes
chromosomes.AddRange(newPopulation);
// old population is goint to die
GPChromosome.DestroyChromosomes(ref chromosomes);
}
/// <summary>
/// Every chromosome have randomly generated levels between 2 and maximumValue.
/// </summary>
/// <param name="size"></param>
private void GrowInitialization(int size)
{
int levels = 2;
//Chromosome generation with exact level
for (int i = 0; i < size; i++)
{
//Randomly choose which level chromose will have
levels = Globals.radn.Next(2, GetMaxInitializeLevel() + 1);
// generate new chromosome
GPChromosome c = GenerateChromosome(levels);
// pridruzivanje populaciji
chromosomes.Add(c);
}
}
/// <summary>
/// Reports about current evolution. See other reposrt methods
/// </summary>
/// <param name="currentEvolution"></param>
/// <param name="averageFitness"></param>
/// <param name="ch"></param>
/// <param name="repType"></param>
public void ReportProgress(int currentEvolution, float averageFitness, IChromosome ch, int repType)
{
if (ch == null)
{
return;
}
if (prevFitness < ch.Fitness)
{
prevFitness = ch.Fitness;
if (ch is GPChromosome)
{
_gpModel = (GPdotNET.Engine.GPChromosome)ch;
if (Globals.functions != null)
{
enooptMatematickiModel.Text = Globals.functions.DecodeExpression(_gpModel.expressionTree);
}
treeCtrlDrawer1.DrawTreeExpression(_gpModel.expressionTree, Globals.GetGPNodeStringRep);
}
}
}
public IChromosome CreateNew()
{
var newChromosomes = new GPChromosome[this.NumAgents];
//gets symmetry prob
var symmetricProb = Rand.NextDouble();
//creates first (base) individual chromosome
newChromosomes[0] = (GPChromosome)this._chromosomes[0].CreateNew();
//creates new chromosomes or copies base one based on symmetry prob.
for (var i = 1; i < this.NumAgents; i++)
{
newChromosomes[i] = (GPChromosome)(symmetricProb <= this.SymmetryFactor
? newChromosomes[0].Clone()
: this._chromosomes[i].CreateNew());
}
return(new SocialGPChromosome(newChromosomes)
{
Population = this.Population,
SymmetryFactor = this.SymmetryFactor
});
}
public double[][] CalculateTestModel(GPChromosome ch)
{
return(CalculateModel(ch, false));
}
public double[][] CalculateTrainModel(GPChromosome ch)
{
return(CalculateModel(ch, true));
}
public SocialCommonGPChromosome(uint numAgents, GPChromosome commomTestParameters)
: base(commomTestParameters.BaseChromosome ?? commomTestParameters, commomTestParameters.Population)
{
this.NumAgents = numAgents;
}
/// <summary>
/// Resets previous solution
/// </summary>
public void ResetSolution()
{
prevFitness = -1;
_gpModel = null;
}
public void EvaluateChromosome(GPChromosome c)
{
c.fitness = fitnessFunction.Evaluate(c.expressionTree, functionSet);
}
/// <summary>
///
/// </summary>
/// <param name="lines"></param>
/// <param name="factory"></param>
/// <param name="curLine"></param>
/// <param name="typeChromosome"></param>
/// <returns></returns>
private int MainPopulationFromString(string[] lines, GPFactory factory, int curLine)
{
curLine++;
//Line 8: populationSize; maxFitness; BestChromosome
if (lines.Length <= curLine)
{
//MessageBox.Show("Fie is corrupt!");
return(-1);
}
var str = lines[curLine].Split(';');
if (lines[curLine] == "-" || lines[curLine] == "-\r")
{
return(curLine += 2);
}
if (_GPModel == GPModelType.TSP)
{
PrepareTSP(false);
}
else if (_GPModel == GPModelType.AP)
{
PrepareALOC(false);
}
else if (_GPModel == GPModelType.TP)
{
PrepareTrans(false);
}
else
{
PrepareGP(false);
}
int popSize = 0;
if (!int.TryParse(str[0], out popSize))
{
popSize = 0;
}
List <IChromosome> chromosomes = new List <IChromosome>();
for (int i = 0; i < popSize; i++)
{
IChromosome ch = null;
if (_GPModel == GPModelType.TSP || _GPModel == GPModelType.AP)
{
ch = GAVChromosome.CreateFromString(lines[i + curLine + 1]);
}
else if (_GPModel == GPModelType.TP)
{
ch = GAMChromosome.CreateFromString(lines[i + curLine + 1]);
}
else
{
ch = GPChromosome.CreateFromString(lines[i + curLine + 1]);
}
chromosomes.Add(ch);
}
factory.SetChromosomes(chromosomes);
factory.CalculatePopulation();
return(popSize + 7);
}
