org.encog.neural.neat.training
Class NEATGenome

java.lang.Object
  org.encog.ml.genetic.genome.BasicGenome
      org.encog.neural.neat.training.NEATGenome

All Implemented Interfaces:

Serializable, Cloneable, Comparable<Genome>, Genome

public class NEATGenome
extends BasicGenome
implements Cloneable, Serializable

Implements a NEAT genome. This is a "blueprint" for creating a neural network. NeuroEvolution of Augmenting Topologies (NEAT) is a genetic algorithm for the generation of evolving artificial neural networks. It was developed by Ken Stanley while at The University of Texas at Austin. http://www.cs.ucf.edu/~kstanley/

See Also:

Serialized Form

Field Summary

static String	PROPERTY_LINKS
static String	PROPERTY_NEURONS
static double	TWEAK_DISJOINT The adjustment factor for disjoint genes.
static double	TWEAK_EXCESS The adjustment factor for excess genes.
static double	TWEAK_MATCHED The adjustment factor for matched genes.

Constructor Summary

NEATGenome()

NEATGenome(long genomeID, Chromosome neurons, Chromosome links, int inputCount, int outputCount)
Create a NEAT gnome.

NEATGenome(long id, int inputCount, int outputCount)
Construct a genome, do not provide links and neurons.

NEATGenome(NEATGenome other)
Construct a genome by copying another.

Method Summary

boolean	alreadyHaveThisNeuronID(long id) Do we already have this neuron id?
void	decode() Convert the genes to an actual network.
void	encode() Convert the network to genes.
double	getCompatibilityScore(NEATGenome genome) Get the compatibility score with another genome.
int	getInputCount()
Chromosome	getLinks()
Chromosome	getLinksChromosome()
int	getNetworkDepth()
Chromosome	getNeurons()
Chromosome	getNeuronsChromosome()
int	getNumGenes()
int	getOutputCount()
long	getSpeciesID()
double	getSplitY(int nd) Get the specified split y.
boolean	isDuplicateLink(long fromNeuronID, long toNeuronID) Determine if this is a duplicate link.
void	mutateActivationResponse(double mutateRate, double maxPertubation) Mutate the activation response.
void	mutateWeights(double mutateRate, double probNewMutate, double maxPertubation) Mutate the weights.
void	setInputCount(int inputCount)
void	setLinksChromosome(Chromosome linksChromosome)
void	setNetworkDepth(int networkDepth)
void	setNeuronsChromosome(Chromosome neuronsChromosome)
void	setOutputCount(int outputCount)
void	setSpeciesID(long species) Set the species id.
void	sortGenes() Sort the genes.

Methods inherited from class org.encog.ml.genetic.genome.BasicGenome

calculateGeneCount, compareTo, equals, getAdjustedScore, getAmountToSpawn, getChromosomes, getGeneticAlgorithm, getGenomeID, getOrganism, getPopulation, getScore, mate, setAdjustedScore, setAmountToSpawn, setGeneticAlgorithm, setGenomeID, setOrganism, setPopulation, setScore, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

PROPERTY_NEURONS

public static final String PROPERTY_NEURONS

See Also:

Constant Field Values

PROPERTY_LINKS

public static final String PROPERTY_LINKS

See Also:

Constant Field Values

TWEAK_DISJOINT

public static final double TWEAK_DISJOINT

The adjustment factor for disjoint genes.

See Also:

Constant Field Values

TWEAK_EXCESS

public static final double TWEAK_EXCESS

The adjustment factor for excess genes.

See Also:

Constant Field Values

TWEAK_MATCHED

public static final double TWEAK_MATCHED

The adjustment factor for matched genes.

See Also:

Constant Field Values

Constructor Detail

NEATGenome

public NEATGenome(NEATGenome other)

Construct a genome by copying another.

Parameters:

other - The other genome.

NEATGenome

public NEATGenome(long genomeID,
                  Chromosome neurons,
                  Chromosome links,
                  int inputCount,
                  int outputCount)

Create a NEAT gnome.

Parameters:

genomeID - The genome id.

neurons - The neurons.

links - The links.

inputCount - The input count.

outputCount - The output count.

NEATGenome

public NEATGenome(long id,
                  int inputCount,
                  int outputCount)

Construct a genome, do not provide links and neurons.

Parameters:

id - The genome id.

inputCount - The input count.

outputCount - The output count.

NEATGenome

public NEATGenome()

Method Detail

alreadyHaveThisNeuronID

public boolean alreadyHaveThisNeuronID(long id)

Do we already have this neuron id?

Parameters:

id - The id to check for.

Returns:

True if we already have this neuron id.

decode

public void decode()

Convert the genes to an actual network.

Specified by:

decode in interface Genome

encode

public void encode()

Convert the network to genes. Not currently supported.

Specified by:

encode in interface Genome

getCompatibilityScore

public double getCompatibilityScore(NEATGenome genome)

Get the compatibility score with another genome. Used to determine species.

Parameters:

genome - The other genome.

Returns:

The score.

getInputCount

public int getInputCount()

Returns:

The number of input neurons.

getLinks

public Chromosome getLinks()

Returns:

THe links chromosome.

getNetworkDepth

public int getNetworkDepth()

Returns:

The network depth.

getNeurons

public Chromosome getNeurons()

Returns:

The neurons chromosome.

getNumGenes

public int getNumGenes()

Returns:

The number of genes in the links chromosome.

getOutputCount

public int getOutputCount()

Returns:

The output count.

getSpeciesID

public long getSpeciesID()

Returns:

The species ID.

getSplitY

public double getSplitY(int nd)

Get the specified split y.

Parameters:

nd - The neuron.

Returns:

The split y.

isDuplicateLink

public boolean isDuplicateLink(long fromNeuronID,
                               long toNeuronID)

Determine if this is a duplicate link.

Parameters:

fromNeuronID - The from neuron id.

toNeuronID - The to neuron id.

Returns:

True if this is a duplicate link.

mutateActivationResponse

public void mutateActivationResponse(double mutateRate,
                                     double maxPertubation)

Mutate the activation response.

Parameters:

mutateRate - The mutation rate.

maxPertubation - The maximum to perturb it by.

mutateWeights

public void mutateWeights(double mutateRate,
                          double probNewMutate,
                          double maxPertubation)

Mutate the weights.

Parameters:

mutateRate - The mutation rate.

probNewMutate - The probability of a whole new weight.

maxPertubation - The max perturbation.

setNetworkDepth

public void setNetworkDepth(int networkDepth)

Parameters:

networkDepth - the networkDepth to set

setSpeciesID

public void setSpeciesID(long species)

Set the species id.

Parameters:

species - The species id.

sortGenes

public void sortGenes()

Sort the genes.

getLinksChromosome

public Chromosome getLinksChromosome()

Returns:

the linksChromosome

setLinksChromosome

public void setLinksChromosome(Chromosome linksChromosome)

Parameters:

linksChromosome - the linksChromosome to set

getNeuronsChromosome

public Chromosome getNeuronsChromosome()

Returns:

the neuronsChromosome

setNeuronsChromosome

public void setNeuronsChromosome(Chromosome neuronsChromosome)

Parameters:

neuronsChromosome - the neuronsChromosome to set

setInputCount

public void setInputCount(int inputCount)

Parameters:

inputCount - the inputCount to set

setOutputCount

public void setOutputCount(int outputCount)

Parameters:

outputCount - the outputCount to set