FloatVectorSpecies (ECJ 22 API)

java.lang.Object
- ec.Species
- - ec.vector.VectorSpecies
  - - ec.vector.FloatVectorSpecies

All Implemented Interfaces:: Prototype, Setup, Serializable, Cloneable

public class FloatVectorSpecies
extends VectorSpecies

FloatVectorSpecies is a subclass of VectorSpecies with special constraints for floating-point vectors, namely FloatVectorIndividual and DoubleVectorIndividual.

FloatVectorSpecies can specify a number of parameters globally, per-segment, and per-gene. See VectorSpecies for information on how to this works.

FloatVectorSpecies defines a minimum and maximum gene value. These values are used during initialization and, depending on whether mutation-bounded is true, also during various mutation algorithms to guarantee that the gene value will not exceed these minimum and maximum bounds.

FloatVectorSpecies provides support for five ways of mutating a gene.

reset Replacing the gene's value with a value uniformly drawn from the gene's range (the default behavior).
gaussPerturbing the gene's value with gaussian noise; if the gene-by-gene range is used, than the standard deviation is scaled to reflect each gene's range. If the gaussian mutation's standard deviation is too large for the range, than there's a large probability the mutated value will land outside range. We will try again a number of times (100) before giving up and using the previous mutation method.
polynomial Perturbing the gene's value with noise chosen from a polynomial distribution, similar to the gaussian distribution. The polynomial distribution was popularized by Kalyanmoy Deb and is found in many of his publications (see http://www.iitk.ac.in/kangal/deb.shtml). The polynomial distribution has two options. First, there is the index. This variable defines the shape of the distribution and is in some sense the equivalent of the standard deviation in the gaussian distribution. The index is an integer. If it is zero, the polynomial distribution is simply the uniform distribution from [1,-1]. If it is 1, the polynomial distribution is basically a triangular distribution from [1,-1] peaking at 0. If it is 2, the polynomial distribution follows a squared function, again peaking at 0. Larger values result in even more peaking and narrowness. The default values used in nearly all of the NSGA-II and Deb work is 20. Second, there is whether or not the value is intended for bounded genes. The default polynomial distribution is used when we assume the gene can take on literally any value, even beyond the min and max values. For genes which are restricted to be between min and max, there is an alternative version of the polynomial distribution, used by Deb's team but not discussed much in the literature, desiged for that situation. We assume boundedness by default, and have found it to be somewhat better for NSGA-II and SPEA2 problems. For a description of this alternative version, see "A Niched-Penalty Approach for Constraint Handling in Genetic Algorithms" by Kalyanmoy Deb and Samir Agrawal. Deb's default implementation bounds the result to min or max; instead ECJ's implementation of the polynomial distribution retries until it finds a legal value. This will be just fine for ranges like [0,1], but for smaller ranges you may be waiting a long time.
integer-reset Replacing the gene's value with a value uniformly drawn from the gene's range but restricted to only integers.
integer-random-walk Replacing the gene's value by performing a random walk starting at the gene value. The random walk either adds 1 or subtracts 1 (chosen at random), then does a coin-flip to see whether to continue the random walk. When the coin-flip finally comes up false, the gene value is set to the current random walk position.

FloatVectorSpecies provides support for two ways of initializing a gene. The initialization procedure is determined by the choice of mutation procedure as described above. If the mutation is floating-point (reset, gauss, polynomial), then initialization will be done by resetting the gene to uniformly chosen floating-point value between the minimum and maximum legal gene values, inclusive. If the mutation is integer (integer-reset, integer-random-walk), then initialization will be done by performing the same kind of reset, but restricting values to integers only.

Parameters

double (default=0.0)double >= base.min-gene

base.`min-gene` or
base.`segment`.segment-number.`min-gene` or
base.`min-gene`.gene-number 0.0 <= double <= 1.0	(probability that a gene will get mutated over default mutation)
(the minimum gene value)

base.`max-gene` or
base.`segment`.segment-number.`max-gene` or
base.`max-gene`.gene-number 0.0 <= double <= 1.0	(probability that a gene will get mutated over default mutation)
(the maximum gene value)

base.`mutation-type` or
base.`segment`.segment-number.`mutation-type` or
base.`mutation-prob`.gene-number `reset`, `gauss`, `polynomial`, `integer-reset`, or `integer-random-walk` (default=`reset`)	(the mutation type)

base.`mutation-stdev` or
base.`segment`.segment-number.`mutation-stdev` or
base.`mutation-stdev`.gene-number double ≥ 0	(the standard deviation or the gauss perturbation)
base.`distribution-index` or
base.`segment`.segment-number.`distribution-index` or
base.`distribution-index`.gene-number int ≥ 0	(the mutation distribution index for the polynomial mutation distribution)

base.`alternative-polynomial-version` or
base.`segment`.segment-number.`alternative-polynomial-version` or
base.`alternative-polynomial-version`.gene-number boolean (default=true)	(whether to use the "bounded" variation of the polynomial mutation or the standard ("unbounded") version)

base.`random-walk-probability` or
base.`segment`.segment-number.`random-walk-probability` or
base.`random-walk-probability`.gene-number 0.0 <= double <= 1.0	(the probability that a random walk will continue. Random walks go up or down by 1.0 until the coin flip comes up false.)
base.`mutation-bounded` or
base.`segment`.segment-number.`mutation-bounded` or
base.`mutation-bounded`.gene-number boolean (default=true)	(whether mutation is restricted to only being within the min/max gene values. Does not apply to SimulatedBinaryCrossover (which is always bounded))
	base.`out-of-bounds-retries` int ≥ 0 (default=100)	(number of times the gaussian mutation got the gene out of range before we give up and reset the gene's value; 0 means "never give up")

Version:: 2.0
Author:: Sean Luke, Gabriel Balan, Rafal Kicinger
See Also:: Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`C_GAUSS_MUTATION`
`static int`	`C_INTEGER_RANDOM_WALK_MUTATION`
`static int`	`C_INTEGER_RESET_MUTATION`
`static int`	`C_POLYNOMIAL_MUTATION`
`static int`	`C_RESET_MUTATION`
`static int`	`DEFAULT_OUT_OF_BOUNDS_RETRIES`
`protected double[]`	`gaussMutationStdev` Standard deviation for Gaussian Mutation, per gene.
`protected double[]`	`maxGene` Max-gene value, per gene.
`protected double[]`	`minGene` Min-gene value, per gene.
`protected int[]`	`mutationDistributionIndex` The distribution index for Polynomial Mutation, per gene.
`protected boolean[]`	`mutationIsBounded` Whether mutation is bounded to the min- and max-gene values, per gene.
`(package private) boolean`	`mutationIsBoundedDefined` Whether the mutationIsBounded value was defined, per gene.
`protected int[]`	`mutationType` Mutation type, per gene.
`int`	`outOfBoundsRetries` The number of times Polynomial Mutation or Gaussian Mutation retry for valid numbers until they get one.
`static String`	`P_MAXGENE`
`static String`	`P_MINGENE`
`static String`	`P_MUTATION_BOUNDED`
`static String`	`P_MUTATION_DISTRIBUTION_INDEX`
`static String`	`P_MUTATIONTYPE`
`static String`	`P_OUTOFBOUNDS_RETRIES`
`static String`	`P_POLYNOMIAL_ALTERNATIVE`
`static String`	`P_RANDOM_WALK_PROBABILITY`
`static String`	`P_STDEV`
`protected boolean[]`	`polynomialIsAlternative` Whether the Polynomial Mutation method is the "alternative" method, per gene.
`(package private) boolean`	`polynomialIsAlternativeDefined` Whether the polymialIsAlternative value was defined, per gene.
`protected double[]`	`randomWalkProbability` The continuation probability for Integer Random Walk Mutation, per gene.
`(package private) static double`	`SIMULATED_BINARY_CROSSOVER_EPS`
`static String`	`V_GAUSS_MUTATION`
`static String`	`V_INTEGER_RANDOM_WALK_MUTATION`
`static String`	`V_INTEGER_RESET_MUTATION`
`static String`	`V_POLYNOMIAL_MUTATION`
`static String`	`V_RESET_MUTATION`

Fields inherited from class ec.vector.VectorSpecies
C_ANY_POINT, C_GEOMETRIC, C_INTERMED_RECOMB, C_LINE_RECOMB, C_NONE, C_ONE_POINT, C_ONE_POINT_NO_NOP, C_SIMULATED_BINARY, C_TWO_POINT, C_TWO_POINT_NO_NOP, C_UNIFORM, chunksize, crossoverDistributionIndex, crossoverProbability, crossoverType, duplicateRetries, dynamicInitialSize, genomeIncreaseProbability, genomeResizeAlgorithm, genomeSize, lineDistance, maxInitialSize, minInitialSize, mutationProbability, P_CHUNKSIZE, P_CROSSOVER_DISTRIBUTION_INDEX, P_CROSSOVERPROB, P_CROSSOVERTYPE, P_DUPLICATE_RETRIES, P_GENOMESIZE, P_GEOMETRIC_PROBABILITY, P_LINEDISTANCE, P_MUTATIONPROB, P_NUM_SEGMENTS, P_SEGMENT, P_SEGMENT_END, P_SEGMENT_START, P_SEGMENT_TYPE, P_UNIFORM_MAX, P_UNIFORM_MIN, P_VECTORSPECIES, V_ANY_POINT, V_GEOMETRIC, V_INTERMED_RECOMB, V_LINE_RECOMB, V_ONE_POINT, V_ONE_POINT_NO_NOP, V_SIMULATED_BINARY, V_TWO_POINT, V_TWO_POINT_NO_NOP, V_UNIFORM

Fields inherited from class ec.Species
f_prototype, i_prototype, P_FITNESS, P_INDIVIDUAL, P_PIPE, pipe_prototype

Constructor Summary

Constructors
Constructor and Description

FloatVectorSpecies()

Constructors
Constructor and Description
`FloatVectorSpecies()`

Method Summary

Methods
Modifier and Type	Method and Description
`double`	`gaussMutationStdev(int gene)`
`boolean`	`inNumericalTypeRange(double geneVal)`
`protected void`	`loadParametersForGene(EvolutionState state, int index, Parameter base, Parameter def, String postfix)` Called when VectorSpecies is setting up per-gene and per-segment parameters.
`double`	`maxGene(int gene)`
`double`	`minGene(int gene)`
`int`	`mutationDistributionIndex(int gene)`
`boolean`	`mutationIsBounded(int gene)`
`int`	`mutationType(int gene)`
`void`	`outOfRangeRetryLimitReached(EvolutionState state)`
`boolean`	`polynomialIsAlternative(int gene)`
`double`	`randomWalkProbability(int gene)`
`void`	`setup(EvolutionState state, Parameter base)` The default version of setup(...) loads requested pipelines and calls setup(...) on them and normalizes their probabilities.

Methods inherited from class ec.vector.VectorSpecies
contains, contains, contains, contains, defaultBase, duplicateRetries, fill, fill, fill, fill, initializeGenomeSegmentsByEndIndices, initializeGenomeSegmentsByStartIndices, mutationProbability, newIndividual, setupGenome

Methods inherited from class ec.Species
clone, newIndividual, newIndividual

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

- Field Detail
  - P_MINGENE
```
public static final String P_MINGENE
```
    See Also:
    Constant Field Values
  - P_MAXGENE
```
public static final String P_MAXGENE
```
    See Also:
    Constant Field Values
  - P_MUTATIONTYPE
```
public static final String P_MUTATIONTYPE
```
    See Also:
    Constant Field Values
  - P_STDEV
```
public static final String P_STDEV
```
    See Also:
    Constant Field Values
  - P_MUTATION_DISTRIBUTION_INDEX
```
public static final String P_MUTATION_DISTRIBUTION_INDEX
```
    See Also:
    Constant Field Values
  - P_POLYNOMIAL_ALTERNATIVE
```
public static final String P_POLYNOMIAL_ALTERNATIVE
```
    See Also:
    Constant Field Values
  - V_RESET_MUTATION
```
public static final String V_RESET_MUTATION
```
    See Also:
    Constant Field Values
  - V_GAUSS_MUTATION
```
public static final String V_GAUSS_MUTATION
```
    See Also:
    Constant Field Values
  - V_POLYNOMIAL_MUTATION
```
public static final String V_POLYNOMIAL_MUTATION
```
    See Also:
    Constant Field Values
  - V_INTEGER_RANDOM_WALK_MUTATION
```
public static final String V_INTEGER_RANDOM_WALK_MUTATION
```
    See Also:
    Constant Field Values
  - V_INTEGER_RESET_MUTATION
```
public static final String V_INTEGER_RESET_MUTATION
```
    See Also:
    Constant Field Values
  - P_RANDOM_WALK_PROBABILITY
```
public static final String P_RANDOM_WALK_PROBABILITY
```
    See Also:
    Constant Field Values
  - P_OUTOFBOUNDS_RETRIES
```
public static final String P_OUTOFBOUNDS_RETRIES
```
    See Also:
    Constant Field Values
  - P_MUTATION_BOUNDED
```
public static final String P_MUTATION_BOUNDED
```
    See Also:
    Constant Field Values
  - C_RESET_MUTATION
```
public static final int C_RESET_MUTATION
```
    See Also:
    Constant Field Values
  - C_GAUSS_MUTATION
```
public static final int C_GAUSS_MUTATION
```
    See Also:
    Constant Field Values
  - C_POLYNOMIAL_MUTATION
```
public static final int C_POLYNOMIAL_MUTATION
```
    See Also:
    Constant Field Values
  - C_INTEGER_RESET_MUTATION
```
public static final int C_INTEGER_RESET_MUTATION
```
    See Also:
    Constant Field Values
  - C_INTEGER_RANDOM_WALK_MUTATION
```
public static final int C_INTEGER_RANDOM_WALK_MUTATION
```
    See Also:
    Constant Field Values
  - minGene
```
protected double[] minGene
```
    Min-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - maxGene
```
protected double[] maxGene
```
    Max-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - mutationType
```
protected int[] mutationType
```
    Mutation type, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - gaussMutationStdev
```
protected double[] gaussMutationStdev
```
    Standard deviation for Gaussian Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - mutationIsBounded
```
protected boolean[] mutationIsBounded
```
    Whether mutation is bounded to the min- and max-gene values, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - mutationIsBoundedDefined
```
boolean mutationIsBoundedDefined
```
    Whether the mutationIsBounded value was defined, per gene. Used internally only. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - mutationDistributionIndex
```
protected int[] mutationDistributionIndex
```
    The distribution index for Polynomial Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - polynomialIsAlternative
```
protected boolean[] polynomialIsAlternative
```
    Whether the Polynomial Mutation method is the "alternative" method, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - polynomialIsAlternativeDefined
```
boolean polynomialIsAlternativeDefined
```
    Whether the polymialIsAlternative value was defined, per gene. Used internally only. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - randomWalkProbability
```
protected double[] randomWalkProbability
```
    The continuation probability for Integer Random Walk Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.
  - outOfBoundsRetries
```
public int outOfBoundsRetries
```
    The number of times Polynomial Mutation or Gaussian Mutation retry for valid numbers until they get one.
  - DEFAULT_OUT_OF_BOUNDS_RETRIES
```
public static final int DEFAULT_OUT_OF_BOUNDS_RETRIES
```
    See Also:
    Constant Field Values
  - SIMULATED_BINARY_CROSSOVER_EPS
```
static final double SIMULATED_BINARY_CROSSOVER_EPS
```
    See Also:
    Constant Field Values
- Constructor Detail
  - FloatVectorSpecies
```
public FloatVectorSpecies()
```
- Method Detail
  - outOfRangeRetryLimitReached
```
public void outOfRangeRetryLimitReached(EvolutionState state)
```
  - maxGene
```
public double maxGene(int gene)
```
  - minGene
```
public double minGene(int gene)
```
  - mutationType
```
public int mutationType(int gene)
```
  - gaussMutationStdev
```
public double gaussMutationStdev(int gene)
```
  - mutationIsBounded
```
public boolean mutationIsBounded(int gene)
```
  - mutationDistributionIndex
```
public int mutationDistributionIndex(int gene)
```
  - polynomialIsAlternative
```
public boolean polynomialIsAlternative(int gene)
```
  - randomWalkProbability
```
public double randomWalkProbability(int gene)
```
  - inNumericalTypeRange
```
public boolean inNumericalTypeRange(double geneVal)
```
  - setup
```
public void setup(EvolutionState state,
         Parameter base)
```
    Description copied from class: Species
    
    The default version of setup(...) loads requested pipelines and calls setup(...) on them and normalizes their probabilities. If your individual prototype might need to know special things about the species (like parameters stored in it), then when you override this setup method, you'll need to set those parameters BEFORE you call super.setup(...), because the setup(...) code in Species sets up the prototype.
    
    Specified by:
    
    setup in interface Prototype
    
    Specified by:
    
    setup in interface Setup
    
    Overrides:
    
    setup in class VectorSpecies
    
    See Also:
    Prototype.setup(EvolutionState,Parameter)
  - loadParametersForGene
```
protected void loadParametersForGene(EvolutionState state,
                         int index,
                         Parameter base,
                         Parameter def,
                         String postfix)
```
    Description copied from class: VectorSpecies
    
    Called when VectorSpecies is setting up per-gene and per-segment parameters. The index is the current gene whose parameter is getting set up. The Parameters in question are the bases for the gene. The postfix should be appended to the end of any parameter looked up (it often contains a number indicating the gene in question), such as state.parameters.exists(base.push(P_PARAM).push(postfix), def.push(P_PARAM).push(postfix)
    If you override this method, be sure to call super(...) at some point, ideally first.
    
    Overrides:
    
    loadParametersForGene in class VectorSpecies

Class FloatVectorSpecies

Field Summary

Fields inherited from class ec.vector.VectorSpecies

Fields inherited from class ec.Species

Constructor Summary

Method Summary

Methods inherited from class ec.vector.VectorSpecies

Methods inherited from class ec.Species

Methods inherited from class java.lang.Object

Field Detail

P_MINGENE

P_MAXGENE

P_MUTATIONTYPE

P_STDEV

P_MUTATION_DISTRIBUTION_INDEX

P_POLYNOMIAL_ALTERNATIVE

V_RESET_MUTATION

V_GAUSS_MUTATION

V_POLYNOMIAL_MUTATION

V_INTEGER_RANDOM_WALK_MUTATION

V_INTEGER_RESET_MUTATION

P_RANDOM_WALK_PROBABILITY

P_OUTOFBOUNDS_RETRIES

P_MUTATION_BOUNDED

C_RESET_MUTATION

C_GAUSS_MUTATION

C_POLYNOMIAL_MUTATION

C_INTEGER_RESET_MUTATION

C_INTEGER_RANDOM_WALK_MUTATION

minGene

maxGene

mutationType

gaussMutationStdev

mutationIsBounded

mutationIsBoundedDefined

mutationDistributionIndex

polynomialIsAlternative

polynomialIsAlternativeDefined

randomWalkProbability

outOfBoundsRetries

DEFAULT_OUT_OF_BOUNDS_RETRIES

SIMULATED_BINARY_CROSSOVER_EPS

Constructor Detail

FloatVectorSpecies

Method Detail

outOfRangeRetryLimitReached