/// <summary>
/// Constructs a chromosome from metadata.
/// </summary>
/// <remarks>This constructor is for neural chromosomes only.</remarks>
/// <param name="chromosomeType">The chromosome type.</param>
/// <param name="nodeGenes">The node genes.</param>
/// <param name="edgeGenes">The edge genes.</param>
/// <returns></returns>
public static IChromosome ConstructChromosome(ChromosomeType chromosomeType,
IList <NeuralChromosome.NodeGene> nodeGenes, IList <NeuralChromosome.EdgeGene> edgeGenes)
{
switch (chromosomeType)
{
case ChromosomeType.Neural:
return(new NeuralChromosome(nodeGenes, edgeGenes, "UT", 1, 1, 1, ActivationFunction.Sigmoid));
default:
throw new ArgumentException($"Error! Invalid chromosome type.");
}
}
/// <summary>Initializes a new instance of the CombinatorialChromosome class.</summary>
/// <param name="numberOfElements">Number of unique genes in the chromosome.</param>
public CombinatorialChromosome(int numberOfElements) : base(numberOfElements)
{
NumberOfElements = numberOfElements;
ChromosomeType = ChromosomeType.CombinatorialChromosome;
var elements = RandomizationProvider.Current.GetUniqueInts(numberOfElements, 0, numberOfElements);
for (int i = 0; i < numberOfElements; i++)
{
ReplaceGene(i, new Gene(elements[i]));
}
}
/// <summary>
/// Constructs a chromosome from metadata.
/// </summary>
/// <remarks>This constructor is for neural chromosomes only.</remarks>
/// <param name="chromosomeType">The chromosome type.</param>
/// <param name="inputSize">The input size.</param>
/// <param name="outputSize">The output size.</param>
/// <param name="innovationTrackerName">The innovation tracker name.</param>
/// <returns></returns>
public static IChromosome ConstructChromosome(ChromosomeType chromosomeType,
uint inputSize, uint outputSize, string innovationTrackerName)
{
switch (chromosomeType)
{
case ChromosomeType.Neural:
return(new NeuralChromosome(inputSize, outputSize, innovationTrackerName));
default:
throw new ArgumentException($"Error! Invalid chromosome type.");
}
}
/// <summary>
/// Constructs a chromosome from metadata.
/// </summary>
/// <typeparam name="T">The array data type.</typeparam>
/// <param name="chromosomeType">The chromosome type.</param>
/// <param name="genes">The chromosome genes genes.</param>
/// <returns>The chromosome.</returns>
public static IChromosome ConstructChromosome <T>(ChromosomeType chromosomeType, T[] genes)
{
switch (chromosomeType)
{
case ChromosomeType.Binary:
return(new BinaryChromosome(genes as bool[]));
case ChromosomeType.Permutation:
return(new PermutationChromosome(genes as uint[]));
default:
throw new ArgumentException($"Error! Invalid chromosome type.");
}
}
/// <summary>Initializes a new instance of the DoubleChromosome class.</summary>
/// <param name="minValues">Minimum values.</param>
/// <param name="maxValues">Maximum values.</param>
public DoubleChromosome(double[] minValues, double[] maxValues)
{
MinValues = minValues;
MaxValues = maxValues;
ChromosomeType = ChromosomeType.DoubleChromosome;
ChromosomeLength = minValues.Count();
Genes = new Gene[ChromosomeLength];
var rnd = RandomizationProvider.Current;
for (int i = 0; i < ChromosomeLength; i++)
{
ReplaceGene(i, new Gene(rnd.GetDouble(minValues[i], maxValues[i])));
}
}
/// <summary>Initializes a new instance of the BinaryChromosome class.</summary>
/// <param name="minValues">Minimum values.</param>
/// <param name="maxValues">Maximum values.</param>
/// <param name="totalBits">Total bits.</param>
/// <param name="fractionDigits">Decimals.</param>
/// <param name="genes">Genes.</param>
public BinaryChromosome(double[] minValues, double[] maxValues, int[] totalBits, int[] fractionDigits, double[] genes) : base(totalBits.Sum())
{
MinValues = minValues;
MaxValues = maxValues;
TotalBits = totalBits;
FractionDigits = fractionDigits;
ChromosomeType = ChromosomeType.BinaryChromosome;
// If values are not supplied, create random values
if (genes == null)
{
genes = new double[minValues.Length];
var rnd = RandomizationProvider.Current;
for (int i = 0; i < genes.Length; i++)
{
genes[i] = rnd.GetDouble(minValues[i], maxValues[i]);
}
}
OriginalValueStringRepresentation = string.Join("", BinaryStringRepresentation.ToRepresentation(genes, totalBits, fractionDigits));
CreateGenes();
}
public static DynamoGeneticAlgorithm CreateGeneticAlgorithm(Population population,
[DefaultArgument("Evo.DynamoGeneticAlgorithm.Default()")] object selection,
[DefaultArgument("Evo.DynamoGeneticAlgorithm.Default()")] object crossover,
[DefaultArgument("Evo.DynamoGeneticAlgorithm.Default()")] object mutation,
[DefaultArgument("Evo.DynamoGeneticAlgorithm.Default()")] object termination,
[DefaultArgument("Evo.DynamoGeneticAlgorithm.Default()")] int?selectionSize,
double crossoverProbability = DynamoGeneticAlgorithm.DefaultCrossoverProbability,
double mutationProbability = DynamoGeneticAlgorithm.DefaultMutationProbability)
{
IChromosome exemplaryChromome = population.CurrentGeneration.Chromosomes[0];
ChromosomeType chromosomeType = 0;
if (exemplaryChromome is BinaryChromosome)
{
chromosomeType = ((BinaryChromosome)exemplaryChromome).ChromosomeType;
}
else if (exemplaryChromome is CombinatorialChromosome)
{
chromosomeType = ((CombinatorialChromosome)exemplaryChromome).ChromosomeType;
}
else if (exemplaryChromome is DoubleChromosome)
{
chromosomeType = ((DoubleChromosome)exemplaryChromome).ChromosomeType;
}
ISelection selectionMethod = null;
if (selection == null)
{
selectionMethod = new EliteSelection();
}
else
{
if (selection is EliteSelection)
{
selectionMethod = selection as EliteSelection;
}
else if (selection is RouletteWheelSelection)
{
selectionMethod = selection as RouletteWheelSelection;
}
else if (selection is StochasticUniversalSamplingSelection)
{
selectionMethod = selection as StochasticUniversalSamplingSelection;
}
else if (selection is TournamentSelection)
{
selectionMethod = selection as TournamentSelection;
}
else
{
throw new CrossoverException("Invalid selection input. A valid object returned by a node of the Selections category should be used.");
}
}
ICrossover crossoverMethod = null;
if (crossover == null)
{
crossoverMethod = new UniformCrossover(0.5f);
}
else
{
if (crossover is AlternatingPositionCrossover)
{
if (chromosomeType != ChromosomeType.CombinatorialChromosome)
{
throw new CrossoverException("The Alternating-position Crossover (AP) can be only used with combinatorial chromosomes. The specified individuals are not combinatorial chromosomes.");
}
crossoverMethod = crossover as AlternatingPositionCrossover;
}
else if (crossover is CutAndSpliceCrossover)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Cut and Splice Crossover (AP) can be only used with binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
crossoverMethod = crossover as CutAndSpliceCrossover;
}
else if (crossover is CycleCrossover)
{
if (chromosomeType != ChromosomeType.CombinatorialChromosome)
{
throw new CrossoverException("The Cycle Crossover (CX) can be only used with combinatorial chromosomes. The specified individuals are not combinatorial chromosomes.");
}
crossoverMethod = crossover as CycleCrossover;
}
else if (crossover is OnePointCrossover)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The One-point Crossover can be only used with binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
crossoverMethod = crossover as OnePointCrossover;
}
else if (crossover is OrderBasedCrossover)
{
if (chromosomeType != ChromosomeType.CombinatorialChromosome)
{
throw new CrossoverException("The Order Based Crossover (OX2) can be only used with combinatorial chromosomes. The specified individuals are not combinatorial chromosomes.");
}
crossoverMethod = crossover as OrderBasedCrossover;
}
else if (crossover is OrderedCrossover)
{
if (chromosomeType != ChromosomeType.CombinatorialChromosome)
{
throw new CrossoverException("The Ordered Crossover (OX1) can be only used with combinatorial chromosomes. The specified individuals are not combinatorial chromosomes.");
}
crossoverMethod = crossover as OrderedCrossover;
}
else if (crossover is PartiallyMappedCrossover)
{
if (chromosomeType != ChromosomeType.CombinatorialChromosome)
{
throw new CrossoverException("The Partially-mapped Crossover (PMX) can be only used with combinatorial chromosomes. The specified individuals are not combinatorial chromosomes.");
}
crossoverMethod = crossover as PartiallyMappedCrossover;
}
else if (crossover is PositionBasedCrossover)
{
if (chromosomeType != ChromosomeType.CombinatorialChromosome)
{
throw new CrossoverException("The Position Based Crossover (POS) can be only used with combinatorial chromosomes. The specified individuals are not combinatorial chromosomes.");
}
crossoverMethod = crossover as PositionBasedCrossover;
}
else if (crossover is SimulatedBinaryCrossover)
{
if (chromosomeType != ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Simulated Binary Crossover (SBX) can be only used with double chromosomes. The specified individuals are not double chromosomes.");
}
crossoverMethod = crossover as SimulatedBinaryCrossover;
}
else if (crossover is ThreeParentCrossover)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Three-parent Crossover can be only used with binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
crossoverMethod = crossover as ThreeParentCrossover;
}
else if (crossover is TwoPointCrossover)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Two-point Crossover can be only used with binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
crossoverMethod = crossover as TwoPointCrossover;
}
else if (crossover is UniformCrossover)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Uniform Crossover can be only used with binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
crossoverMethod = crossover as UniformCrossover;
}
else if (crossover is VotingRecombinationCrossover)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Voting Recombination Crossover (VR) can be only used with binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
crossoverMethod = crossover as VotingRecombinationCrossover;
}
else
{
throw new CrossoverException("Invalid crossover input. A valid object returned by a node of the Crossovers category should be used.");
}
}
IMutation mutationMethod = null;
if (mutation == null)
{
mutationMethod = new FlipBitMutation();
}
else
{
if (mutation is DisplacementMutation)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Displacement Mutation can be only used on binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
mutationMethod = mutation as DisplacementMutation;
}
else if (mutation is FlipBitMutation)
{
if (chromosomeType != ChromosomeType.BinaryChromosome)
{
throw new CrossoverException("The Flip Bit Mutation can be only used on binary chromosomes. The specified individuals are not binary chromosomes.");
}
mutationMethod = mutation as FlipBitMutation;
}
else if (mutation is GaussianMutation)
{
if (chromosomeType != ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Gaussian Mutation can be only used on double chromosomes. The specified individuals are not double chromosomes.");
}
mutationMethod = mutation as GaussianMutation;
}
else if (mutation is InsertionMutation)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Displacement Mutation can be only used on binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
mutationMethod = mutation as InsertionMutation;
}
else if (mutation is PartialShuffleMutation)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Displacement Mutation (PSM) can be only used on binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
mutationMethod = mutation as PartialShuffleMutation;
}
else if (mutation is PolynomialMutation)
{
if (chromosomeType != ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Polynomial Mutation can be only used on double chromosomes. The specified individuals are not double chromosomes.");
}
mutationMethod = mutation as PolynomialMutation;
}
else if (mutation is ReverseSequenceMutation)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Displacement Mutation (RSM) can be only used on binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
mutationMethod = mutation as ReverseSequenceMutation;
}
else if (mutation is TworsMutation)
{
if (chromosomeType == ChromosomeType.DoubleChromosome)
{
throw new CrossoverException("The Displacement Mutation can be only used on binary and combinatorial chromosomes. The specified individuals are double chromosomes.");
}
mutationMethod = mutation as TworsMutation;
}
else if (mutation is UniformMutation)
{
if (chromosomeType != ChromosomeType.BinaryChromosome)
{
throw new CrossoverException("The Uniform Mutation can be only used on binary chromosomes. The specified individuals are not binary chromosomes.");
}
mutationMethod = mutation as UniformMutation;
}
else
{
throw new CrossoverException("Invalid mutation input. A valid object returned by a node of Mutations category should be used.");
}
}
ElitistReinsertion reinsertionMethod = new ElitistReinsertion();
ITermination terminationMethod = null;
if (termination == null)
{
terminationMethod = new FitnessStagnationTermination(100);
}
else
{
if (termination is FitnessStagnationTermination)
{
terminationMethod = termination as FitnessStagnationTermination;
}
else if (termination is FitnessThresholdTermination)
{
terminationMethod = termination as FitnessThresholdTermination;
}
else if (termination is GenerationNumberTermination)
{
terminationMethod = termination as GenerationNumberTermination;
}
else if (termination is TimeEvolvingTermination)
{
terminationMethod = termination as TimeEvolvingTermination;
}
else if (termination is AndTermination)
{
terminationMethod = termination as AndTermination;
}
else if (termination is OrTermination)
{
terminationMethod = termination as OrTermination;
}
else
{
throw new CrossoverException("Invalid termination input. An object returned by nodes of Terminations library should be used.");
}
}
if (selectionSize == null)
{
selectionSize = (int)Math.Round(0.5 * population.MaxSize);
}
else if (!(selectionSize is int))
{
throw new CrossoverException("Defined selection size is not an integer.");
}
else if (selectionSize > population.MaxSize)
{
throw new CrossoverException("Selection size cannot be greater than population size.");
}
var algorithm = new DynamoGeneticAlgorithm(population, selectionMethod, crossoverMethod, mutationMethod, reinsertionMethod, terminationMethod)
{
SelectionSize = (int)selectionSize,
CrossoverProbability = (float)crossoverProbability,
MutationProbability = (float)mutationProbability,
Timer = Stopwatch.StartNew()
};
algorithm.Timer.Start();
return(algorithm);
}
public Chromosome(ChromosomeType type, bool value)
{
this.type = type;
this.increase = value;
}
/// <summary>
/// A mutation will change the type of a chromosome
/// </summary>
public void Mutate()
{
Type = Type == ChromosomeType.OProducer ? ChromosomeType.Oc2Producer : ChromosomeType.OProducer;
}
public MyChromosome(ChromosomeType type)
{
Type = type;
}
