NEATPopulation

Documentation of 'org.encog.neural.neat.NEATPopulation' Java class NEATPopulation

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Summary:
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Constr |
Method

Detail:
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Method

java.lang.Object
- org.encog.ml.BasicML
- - org.encog.ml.ea.population.BasicPopulation
  - - org.encog.neural.neat.NEATPopulation

All Implemented Interfaces:

java.io.Serializable, Population, MLError, MLInput, MLInputOutput, MLMethod, MLOutput, MLProperties, MLRegression
```
public class NEATPopulation
extends BasicPopulation
implements java.io.Serializable, MLError, MLRegression
```
A population for a NEAT or HyperNEAT system. This population holds the genomes, substrate and other values for a NEAT or HyperNEAT network. ----------------------------------------------------------------------------- http://www.cs.ucf.edu/~kstanley/ Encog's NEAT implementation was drawn from the following three Journal Articles. For more complete BibTeX sources, see NEATNetwork.java. Evolving Neural Networks Through Augmenting Topologies Generating Large-Scale Neural Networks Through Discovering Geometric Regularities Automatic feature selection in neuroevolution

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`DEFAULT_CYCLES` Default number of activation cycles.
`static double`	`DEFAULT_HYPERNEAT_WEIGHT_RANGE` Default link weight range for HyperNEAT networks.
`static double`	`DEFAULT_NEAT_WEIGHT_RANGE` Default link weight range for NEAT networks.
`static double`	`DEFAULT_SURVIVAL_RATE` The default survival rate.
`static java.lang.String`	`PROPERTY_CYCLES` Property to hold the number of cycles.
`static java.lang.String`	`PROPERTY_NEAT_ACTIVATION` The activation function to use.
`static java.lang.String`	`PROPERTY_POPULATION_SIZE` Property tag for the population size.
`static java.lang.String`	`PROPERTY_SURVIVAL_RATE` Property tag for the survival rate.

Constructor Summary

Constructors
Constructor and Description
`NEATPopulation()` An empty constructor for serialization.
`NEATPopulation(int inputCount, int outputCount, int populationSize)` Construct a starting NEAT population.
`NEATPopulation(Substrate theSubstrate, int populationSize)` Construct a starting HyperNEAT population.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`long`	`assignGeneID()`
`long`	`assignInnovationID()`
`double`	`calculateError(MLDataSet data)` Calculate the error of the ML method, given a dataset.
`static double`	`clampWeight(double w, double weightRange)` Change the weight, do not allow the weight to go out of the weight range.
`MLData`	`compute(MLData input)` Compute regression.
`int`	`getActivationCycles()`
`ChooseObject<ActivationFunction>`	`getActivationFunctions()`
`GeneticCODEC`	`getCODEC()`
`GenerateID`	`getGeneIDGenerate()`
`NEATGenomeFactory`	`getGenomeFactory()`
`double`	`getInitialConnectionDensity()`
`GenerateID`	`getInnovationIDGenerate()`
`NEATInnovationList`	`getInnovations()`
`int`	`getInputCount()`
`int`	`getOutputCount()`
`RandomFactory`	`getRandomNumberFactory()`
`Substrate`	`getSubstrate()`
`double`	`getSurvivalRate()`
`double`	`getWeightRange()`
`boolean`	`isHyperNEAT()`
`void`	`reset()` Create an initial random population.
`void`	`setActivationCycles(int activationCycles)` Set the number of activation cycles to use.
`void`	`setCODEC(GeneticCODEC codec)`
`void`	`setInitialConnectionDensity(double initialConnectionDensity)`
`void`	`setInnovations(NEATInnovationList theInnovations)` Set the innovation list to use.
`void`	`setInputCount(int inputCount)`
`void`	`setNEATActivationFunction(ActivationFunction af)` Specify to use a single activation function.
`void`	`setOutputCount(int outputCount)`
`void`	`setRandomNumberFactory(RandomFactory randomNumberFactory)`
`void`	`setSubstrate(Substrate substrate)`
`void`	`setSurvivalRate(double theSurvivalRate)` Set the survival rate, this is the percent of the population allowed to mate.
`void`	`setWeightRange(double weightRange)` Sets the weight range for links in genomes in this population.

Methods inherited from class org.encog.ml.ea.population.BasicPopulation
clear, createSpecies, determineBestSpecies, flatten, getBestGenome, getMaxIndividualSize, getName, getPopulationSize, getRules, getSpecies, purgeInvalidGenomes, setBestGenome, setGenomeFactory, setName, setPopulationSize, setRules, size, updateProperties

Methods inherited from class org.encog.ml.BasicML
getProperties, getPropertyDouble, getPropertyLong, getPropertyString, setProperty, setProperty, setProperty

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - DEFAULT_SURVIVAL_RATE
```
public static final double DEFAULT_SURVIVAL_RATE
```
    The default survival rate.
    
    See Also:
    
    Constant Field Values
  - PROPERTY_NEAT_ACTIVATION
```
public static final java.lang.String PROPERTY_NEAT_ACTIVATION
```
    The activation function to use.
    
    See Also:
    
    Constant Field Values
  - PROPERTY_POPULATION_SIZE
```
public static final java.lang.String PROPERTY_POPULATION_SIZE
```
    Property tag for the population size.
    
    See Also:
    
    Constant Field Values
  - PROPERTY_SURVIVAL_RATE
```
public static final java.lang.String PROPERTY_SURVIVAL_RATE
```
    Property tag for the survival rate.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_CYCLES
```
public static final int DEFAULT_CYCLES
```
    Default number of activation cycles.
    
    See Also:
    
    Constant Field Values
  - PROPERTY_CYCLES
```
public static final java.lang.String PROPERTY_CYCLES
```
    Property to hold the number of cycles.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_NEAT_WEIGHT_RANGE
```
public static final double DEFAULT_NEAT_WEIGHT_RANGE
```
    Default link weight range for NEAT networks.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_HYPERNEAT_WEIGHT_RANGE
```
public static final double DEFAULT_HYPERNEAT_WEIGHT_RANGE
```
    Default link weight range for HyperNEAT networks.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - NEATPopulation
```
public NEATPopulation()
```
    An empty constructor for serialization.
  - NEATPopulation
```
public NEATPopulation(int inputCount,
                      int outputCount,
                      int populationSize)
```
    Construct a starting NEAT population. This does not generate the initial random population of genomes.
    
    Parameters:
    
    inputCount - The input neuron count.
    
    outputCount - The output neuron count.
    
    populationSize - The population size.
  - NEATPopulation
```
public NEATPopulation(Substrate theSubstrate,
                      int populationSize)
```
    Construct a starting HyperNEAT population. This does not generate the initial random population of genomes.
    
    Parameters:
    
    theSubstrate - The substrate ID.
    
    populationSize - The population size.
- Method Detail
  - clampWeight
```
public static double clampWeight(double w,
                                 double weightRange)
```
    Change the weight, do not allow the weight to go out of the weight range.
    
    Parameters:
    
    w - The amount to change the weight by.
    
    weightRange - Specify the weight range. The range is from -weightRange to +weightRange.
    
    Returns:
    
    The new weight value.
  - assignGeneID
```
public long assignGeneID()
```
    Returns:
    
    A newly generated gene id.
  - assignInnovationID
```
public long assignInnovationID()
```
    Returns:
    
    A newly generated innovation id.
  - calculateError
```
public double calculateError(MLDataSet data)
```
    Calculate the error of the ML method, given a dataset.
    
    Specified by:
    
    calculateError in interface MLError
    
    Parameters:
    
    data - The dataset.
    
    Returns:
    
    The error.
  - compute
```
public MLData compute(MLData input)
```
    Compute regression.
    
    Specified by:
    
    compute in interface MLRegression
    
    Parameters:
    
    input - The input data.
    
    Returns:
    
    The output data.
  - getActivationCycles
```
public int getActivationCycles()
```
    Returns:
    
    Get the activation cycles.
  - getActivationFunctions
```
public ChooseObject<ActivationFunction> getActivationFunctions()
```
    Returns:
    
    the activationFunctions
  - getCODEC
```
public GeneticCODEC getCODEC()
```
    Returns:
    
    the codec
  - getGeneIDGenerate
```
public GenerateID getGeneIDGenerate()
```
    Returns:
    
    the geneIDGenerate
  - getGenomeFactory
```
public NEATGenomeFactory getGenomeFactory()
```
    Specified by:
    
    getGenomeFactory in interface Population
    
    Overrides:
    
    getGenomeFactory in class BasicPopulation
    
    Returns:
    
    A factory used to create genomes.
  - getInitialConnectionDensity
```
public double getInitialConnectionDensity()
```
    Returns:
    
    the initialConnectionDensity
  - getInnovationIDGenerate
```
public GenerateID getInnovationIDGenerate()
```
    Returns:
    
    the innovationIDGenerate
  - getInnovations
```
public NEATInnovationList getInnovations()
```
    Returns:
    
    Get the innovations.
  - getInputCount
```
public int getInputCount()
```
    Specified by:
    
    getInputCount in interface MLInput
    
    Returns:
    
    The input.
  - getOutputCount
```
public int getOutputCount()
```
    Specified by:
    
    getOutputCount in interface MLOutput
    
    Returns:
    
    The output count.
  - getRandomNumberFactory
```
public RandomFactory getRandomNumberFactory()
```
    Returns:
    
    the randomNumberFactory
  - getSubstrate
```
public Substrate getSubstrate()
```
    Returns:
    
    Returns the hyper-neat substrate.
  - getSurvivalRate
```
public double getSurvivalRate()
```
    Returns:
    
    The survival rate, this is the number of genomes used to mate.
  - getWeightRange
```
public double getWeightRange()
```
    Returns:
    
    the weightRange
  - isHyperNEAT
```
public boolean isHyperNEAT()
```
    Returns:
    
    Returns true if this is a hyperneat population.
  - reset
```
public void reset()
```
    Create an initial random population.
  - setActivationCycles
```
public void setActivationCycles(int activationCycles)
```
    Set the number of activation cycles to use.
    
    Parameters:
    
    activationCycles - The number of activatino cycles to use.
  - setCODEC
```
public void setCODEC(GeneticCODEC codec)
```
    Parameters:
    
    codec - the codec to set
  - setInitialConnectionDensity
```
public void setInitialConnectionDensity(double initialConnectionDensity)
```
    Parameters:
    
    initialConnectionDensity - the initialConnectionDensity to set
  - setInnovations
```
public void setInnovations(NEATInnovationList theInnovations)
```
    Set the innovation list to use.
    
    Parameters:
    
    theInnovations - The innovation list to use.
  - setInputCount
```
public void setInputCount(int inputCount)
```
    Parameters:
    
    inputCount - the inputCount to set
  - setNEATActivationFunction
```
public void setNEATActivationFunction(ActivationFunction af)
```
    Specify to use a single activation function. This is typically the case for NEAT, but not for HyperNEAT.
    
    Parameters:
    
    af - The activation function to use.
  - setOutputCount
```
public void setOutputCount(int outputCount)
```
    Parameters:
    
    outputCount - the outputCount to set
  - setRandomNumberFactory
```
public void setRandomNumberFactory(RandomFactory randomNumberFactory)
```
    Parameters:
    
    randomNumberFactory - the randomNumberFactory to set
  - setSubstrate
```
public void setSubstrate(Substrate substrate)
```
    Parameters:
    
    substrate - the substrate to set
  - setSurvivalRate
```
public void setSurvivalRate(double theSurvivalRate)
```
    Set the survival rate, this is the percent of the population allowed to mate.
    
    Parameters:
    
    theSurvivalRate - The survival rate.
  - setWeightRange
```
public void setWeightRange(double weightRange)
```
    Sets the weight range for links in genomes in this population.
    
    Parameters:
    
    weightRange - The link weight range.

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All Classes

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

Class NEATPopulation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.encog.ml.ea.population.BasicPopulation

Methods inherited from class org.encog.ml.BasicML

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_SURVIVAL_RATE

PROPERTY_NEAT_ACTIVATION

PROPERTY_POPULATION_SIZE

PROPERTY_SURVIVAL_RATE

DEFAULT_CYCLES

PROPERTY_CYCLES

DEFAULT_NEAT_WEIGHT_RANGE

DEFAULT_HYPERNEAT_WEIGHT_RANGE

Constructor Detail

NEATPopulation

NEATPopulation

NEATPopulation

Method Detail

clampWeight

assignGeneID

assignInnovationID

calculateError

compute

getActivationCycles

getActivationFunctions

getCODEC

getGeneIDGenerate

getGenomeFactory

getInitialConnectionDensity

getInnovationIDGenerate

getInnovations

getInputCount

getOutputCount

getRandomNumberFactory

getSubstrate

getSurvivalRate

getWeightRange

isHyperNEAT

reset

setActivationCycles

setCODEC

setInitialConnectionDensity

setInnovations

setInputCount

setNEATActivationFunction

setOutputCount

setRandomNumberFactory

setSubstrate

setSurvivalRate

setWeightRange