gap
Class GPPopulation

java.lang.Object
  |
  +--gap.GPPopulation

All Implemented Interfaces:

java.io.Serializable

public class GPPopulation

extends java.lang.Object

implements java.io.Serializable

A population of GPPrograms.

Author:

Pietro Berkes, Samuele Pedroni

See Also:

Serialized Form

Field Summary

static int	ADF_EXCL Used in methods with a "mask" argument.
GPProgram	bestOfRun Best individual since the creation of the population.
double	bestOfRunFitness Fitness of the individual since the creation of the population.
static int	EMPTY_MASK Used in methods with a "mask" argument.
double[]	fitness The adjusted fitness for each individual.
Evaluator	judge The fitness evaluator.
LogBook	lb A log book.
boolean	open Flag, true after actions which invalidate the current state of the population.
protected float	overSelBoundary Percent of the population in which to apply over-selection.
protected boolean	overSelection Flag for over-selection.
GPParams	params The parameters shared by all the individuals.
float	pMutation Probability of mutation.
GPProgram[]	pop The population.
float	pXOver Probability of crossover.
static int	REPLACE_BRANCH Replacing method.
static int	REPLACE_PROGRAM Default replacing method.
static int	REPLACE_TREE Replacing method.
int	size Number of individuals.
double	totFitness The sum of all the adjusted fitnesses.

Constructor Summary

	GPPopulation(int size, GPParams params, Evaluator judge) Create a brand new population.
protected	GPPopulation(int size, GPParams params, Evaluator judge, int internal) Create a void population.

Method Summary

int	addADF(int type, int[] ct, java.lang.Class[] fSet, java.lang.Class[] tSet, int[] links) Add an ADF to the function set.
void	addArg(int type) Add an argument.
void	addFunction(java.lang.Class f) Add a function to the function set.
void	addTerminal(java.lang.Class t) Add a terminal to the terminal set.
protected static void	allign(GPFunction f, int[] perm, int[] specPerm) Allign the indices of a subtree.
protected static void	allign(GPProgram ind, int[] perm, int[] specPerm, int[][] adfPerm, int[][] adfSpecPerm) Allign the indices of an individual.
protected void	clearBestOfRun() Clear the BestOfRun data after a change of the parameters.
void	closeLogBook() Stop using a log book.
void	closePopulation() Do what must be done after changes in the parameters and before evaluation.
void	eval() Evaluate the fitness by mean of an Evaluator, transforms the standarized- in the adjusted fitness, sort the individuals and print the results.
protected int	fitnessDependentChoice() Select an individual.
double	getBestFitness() Return the fitness of the best individual.
GPProgram	getBestIndividual() Return the best individual.
protected java.lang.String	getMethodName(int method) Return the name of a replacing method.
boolean	getOverSelection() Return true if the over-selection option is on.
float	getOverSelectionBoundary() Return the over-selected percentual of the population, or -1 if the over-selection option is off.
int	getSize() Return the number of individuals.
static GPPopulation	load(java.io.File f) Load a population.
static GPPopulation	load(java.lang.String filename) Load a population.
static GPPopulation	merge(GPPopulation[] p, GPParams mparams, Evaluator judge, int size, double prc) Merge some populations.
protected static GPProgram	mergeChooseProgram(GPPopulation cp) Choose a program from a population (while merging).
protected GPProgram	modifyProgram(GPProgram progr, int method, java.util.ArrayList refs, java.util.ArrayList adfRefList) Modify an individual.
protected GPProgram	newIndividual() Create a new individual.
void	nextGeneration() Create a new generation.
protected void	quickSortByFitness(int b, int t) Sort the population by fitness, in decreasing order.
void	removeADF(int adfNo, int method) Remove an ADF.
void	removeArg(int argNo, int method) Remove an argument.
void	removeFunction(java.lang.Class func, int method) Remove a function.
void	removeFunction(int funcNo, int method) Remove a function.
void	removeTerminal(java.lang.Class term, int method) Remove a terminal.
void	removeTerminal(int termNo, int method) Remove a terminal.
void	save(java.io.File f) Save the population.
void	save(java.lang.String filename) Save the population.
void	setLogBook(LogBook lb) Set the log book.
void	setOverSelection(float boundary) Set the over-selection option on.
void	stopOverSelection() Set the over-selection option off.
protected static void	verifyParamsComp(GPParams p, GPParams mp, int[] perm, int[] specPerm, int[][] adfPerm, int[][] adfSpecPerm, int mask) Verify that two parameters are equivalent.

Methods inherited from class java.lang.Object

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

Field Detail

pop

public GPProgram[] pop

The population.

params

public GPParams params

The parameters shared by all the individuals.

judge

public Evaluator judge

The fitness evaluator.

lb

public transient LogBook lb

A log book.

open

public boolean open

Flag, true after actions which invalidate the current state of the population.

fitness

public double[] fitness

The adjusted fitness for each individual.

The adjusted fitness is 0.0 for the worst individual, 1.0 for the best. The adjusted fitness is 1.0/(1.0+standarized_fitness).

totFitness

public double totFitness

The sum of all the adjusted fitnesses.

bestOfRun

public GPProgram bestOfRun

Best individual since the creation of the population.

bestOfRunFitness

public double bestOfRunFitness

Fitness of the individual since the creation of the population.

size

public int size

Number of individuals.

pXOver

public float pXOver

Probability of crossover.

pMutation

public float pMutation

Probability of mutation.

overSelection

protected boolean overSelection

Flag for over-selection. Empirical rule: over-select if #individuals >= 1000.

overSelBoundary

protected float overSelBoundary

Percent of the population in which to apply over-selection.

EMPTY_MASK

public static final int EMPTY_MASK

Used in methods with a "mask" argument. No special modifiers.

ADF_EXCL

public static final int ADF_EXCL

Used in methods with a "mask" argument. The ADF are excluded from the computation.

REPLACE_PROGRAM

public static final int REPLACE_PROGRAM

Default replacing method. Replace the program by a new one.

REPLACE_TREE

public static final int REPLACE_TREE

Replacing method. Replace the (main- or ADF-) tree by a new one.

REPLACE_BRANCH

public static final int REPLACE_BRANCH

Replacing method. Replace only the no more valid branches.

Constructor Detail

GPPopulation

public GPPopulation(int size,
                    GPParams params,
                    Evaluator judge)
             throws ParametersNotProperlySetException

Create a brand new population.

Parameters:

size - The number of individuals.

params - The parameters shared by all the individuals.

judge - The fitness evaluator.

GPPopulation

protected GPPopulation(int size,
                       GPParams params,
                       Evaluator judge,
                       int internal)

Create a void population.

Parameters:

size - The number of individuals.

params - The parameters shared by all the individuals.

judge - The fitness evaluator.

Method Detail

setLogBook

public void setLogBook(LogBook lb)

Set the log book.

closeLogBook

public void closeLogBook()

Stop using a log book.

getSize

public int getSize()

Return the number of individuals.

setOverSelection

public void setOverSelection(float boundary)

Set the over-selection option on. The request is refused if #individuals<500.

Parameters:

boundary - The over selection boundary. If <0.0 or >0.5, an automatical choice following the empirical rule 320.0/#individuals will be made.

stopOverSelection

public void stopOverSelection()

Set the over-selection option off.

getOverSelection

public boolean getOverSelection()

Return true if the over-selection option is on.

getOverSelectionBoundary

public float getOverSelectionBoundary()

Return the over-selected percentual of the population, or -1 if the over-selection option is off.

clearBestOfRun

protected void clearBestOfRun()

Clear the BestOfRun data after a change of the parameters. Some classes could be missing...

newIndividual

protected GPProgram newIndividual()
                           throws ParametersNotProperlySetException

Create a new individual.

merge

public static GPPopulation merge(GPPopulation[] p,
                                 GPParams mparams,
                                 Evaluator judge,
                                 int size,
                                 double prc)
                          throws ParametersNotProperlySetException

Merge some populations.

In each population choose 1/(no. populations)*size*prc individuals and put a clone in the new population. The selection is weighted by the fitness, overselection allowed.

Warning: if the fitness of the populations to merge isn't uptodate, the populations are going to be evaluated.

Parameters:

p - The populations to merge.

mparams - The parameters of the new population.

judge - The evaluator of the new population.

size - The size of the new population.

prc - The percent of the population that is not created ex novo (<1.0).

Throws:

ParametersNotProperlySetException - If the parameters of the source populations aren't compatible with those of the new population.

See Also:

overSelection

mergeChooseProgram

protected static GPProgram mergeChooseProgram(GPPopulation cp)

Choose a program from a population (while merging).

verifyParamsComp

protected static void verifyParamsComp(GPParams p,
                                       GPParams mp,
                                       int[] perm,
                                       int[] specPerm,
                                       int[][] adfPerm,
                                       int[][] adfSpecPerm,
                                       int mask)
                                throws ParametersNotProperlySetException

Verify that two parameters are equivalent. If not, throw a detailed exception.

allign

protected static void allign(GPProgram ind,
                             int[] perm,
                             int[] specPerm,
                             int[][] adfPerm,
                             int[][] adfSpecPerm)

Allign the indices of an individual.

allign

protected static void allign(GPFunction f,
                             int[] perm,
                             int[] specPerm)

Allign the indices of a subtree.

eval

public void eval()

Evaluate the fitness by mean of an Evaluator, transforms the standarized- in the adjusted fitness, sort the individuals and print the results.

See Also:

judge

getBestFitness

public double getBestFitness()

Return the fitness of the best individual. If the population is open, close it and eval the individuals.

getBestIndividual

public GPProgram getBestIndividual()

Return the best individual. If the population is open, close it and eval the individuals.

quickSortByFitness

protected void quickSortByFitness(int b,
                                  int t)

Sort the population by fitness, in decreasing order.

closePopulation

public void closePopulation()

Do what must be done after changes in the parameters and before evaluation.

nextGeneration

public void nextGeneration()
                    throws ParametersNotProperlySetException

Create a new generation.

The pXOver per cent of the new population is the result of cross-overs, another pMutation per cent is generated by mutation, and the rest is breeded by simple reproduction. In all the genetic operations the individual are selected in a fitness-dependent way.

If the population is open, it is closed and the individuals are evaluated.

See Also:

pXOver, pMutation, fitnessDependentChoice()

fitnessDependentChoice

protected int fitnessDependentChoice()

Select an individual.

The selection is weighted by the fitness. If the overselection option is set, the 80% of the selected individuals are under the overselection boundary.

See Also:

overSelection

removeADF

public void removeADF(int adfNo,
                      int method)
               throws RemoveFailureException

Remove an ADF.

Parameters:

adfNo - The number of the ADF to be removed.

method - REPLACE_PROGRAM, REPLACE_TREE or REPLACE_BRANCH allowed.

See Also:

REPLACE_PROGRAM, REPLACE_TREE, REPLACE_BRANCH

removeFunction

public void removeFunction(java.lang.Class func,
                           int method)
                    throws RemoveFailureException

Remove a function.

Parameters:

func - Class of the function to remove.

method - REPLACE_PROGRAM, REPLACE_TREE or REPLACE_BRANCH allowed.

See Also:

REPLACE_PROGRAM, REPLACE_TREE, REPLACE_BRANCH

removeFunction

public void removeFunction(int funcNo,
                           int method)
                    throws RemoveFailureException

Remove a function.

Parameters:

method - REPLACE_PROGRAM, REPLACE_TREE or REPLACE_BRANCH allowed.

See Also:

REPLACE_PROGRAM, REPLACE_TREE, REPLACE_BRANCH

removeTerminal

public void removeTerminal(java.lang.Class term,
                           int method)
                    throws RemoveFailureException

Remove a terminal.

Parameters:

term - Class of the terminal to remove.

method - REPLACE_PROGRAM, REPLACE_TREE or REPLACE_BRANCH allowed.

See Also:

REPLACE_PROGRAM, REPLACE_TREE, REPLACE_BRANCH

removeTerminal

public void removeTerminal(int termNo,
                           int method)
                    throws RemoveFailureException

Remove a terminal.

Parameters:

method - REPLACE_PROGRAM, REPLACE_TREE or REPLACE_BRANCH allowed.

See Also:

REPLACE_PROGRAM, REPLACE_TREE, REPLACE_BRANCH

removeArg

public void removeArg(int argNo,
                      int method)
               throws RemoveFailureException

Remove an argument.

Parameters:

method - REPLACE_PROGRAM, REPLACE_TREE or REPLACE_BRANCH allowed.

See Also:

REPLACE_PROGRAM, REPLACE_TREE, REPLACE_BRANCH

modifyProgram

protected GPProgram modifyProgram(GPProgram progr,
                                  int method,
                                  java.util.ArrayList refs,
                                  java.util.ArrayList adfRefList)
                           throws RemoveFailureException

Modify an individual.

Parameters:

progr - The program to modify.

method - REPLACE_PROGRAM, REPLACE_TREE or REPLACE_BRANCH allowed.

refs - A list of Refs to invalid points in the main programs.

adfRefLis - A list of lists (one for each ADF) to invalid points in the ADFs.

See Also:

REPLACE_PROGRAM, REPLACE_TREE, REPLACE_BRANCH

getMethodName

protected java.lang.String getMethodName(int method)

Return the name of a replacing method.

addADF

public int addADF(int type,
                  int[] ct,
                  java.lang.Class[] fSet,
                  java.lang.Class[] tSet,
                  int[] links)
           throws ParametersNotProperlySetException

Add an ADF to the function set.

Parameters:

type - Type of the root of the new ADF.

ct - Type of each argument.

fSet - A function set. If null, use the function set of the main program.

tSet - A terminal set. If null, use the terminal set of the main program.

links - Links to other ADFs. If null, no link will be established.

Returns:

The position to which the ADF is inserted.

addFunction

public void addFunction(java.lang.Class f)
                 throws ParametersNotProperlySetException

Add a function to the function set.

Parameters:

f - A subclass of GPFunction.

addTerminal

public void addTerminal(java.lang.Class t)
                 throws ParametersNotProperlySetException

Add a terminal to the terminal set.

Parameters:

t - A subclass of GPTerminal.

addArg

public void addArg(int type)
            throws ParametersNotProperlySetException

Add an argument.

Parameters:

type - Type of the new agument.

save

public void save(java.lang.String filename)
          throws java.io.IOException

Save the population.

save

public void save(java.io.File f)
          throws java.io.IOException

Save the population.

load

public static GPPopulation load(java.lang.String filename)
                         throws java.io.IOException,
                                java.lang.ClassNotFoundException

Load a population.

load

public static GPPopulation load(java.io.File f)
                         throws java.io.IOException,
                                java.lang.ClassNotFoundException

Load a population.