adams.optimise
Class GeneticAlgorithm

java.lang.Object
  adams.core.ConsoleObject
      adams.core.option.AbstractOptionHandler
          adams.optimise.AbstractOptimiser
              adams.optimise.genetic.AbstractGeneticAlgorithm
                  adams.optimise.genetic.PackDataGeneticAlgorithm
                      adams.optimise.GeneticAlgorithm

All Implemented Interfaces:

CleanUpHandler, Debuggable, Destroyable, OptionHandler, SizeOfHandler, Serializable, Comparable

public class GeneticAlgorithm
extends PackDataGeneticAlgorithm

Morticia (GEX).

Valid options are:

-D (property: debug)
         If set to true, scheme may output additional info to the console.
 

-num-chrom <int> (property: numChrom)
         The number of chromosomes, ie, the population size.
         default: 50
 

-num-iter <int> (property: numIterations)
         The number of iterations to perform.
         default: 10000000
 

-seed <int> (property: seed)
         The seed value for the random number generator.
         default: 1
 

-favor-zeroes (property: favorZeroes)
         Whether to favor 0s instead of 1s.
 

-best <java.lang.String> (property: bestRange)
         The range of the best attributes.
         default: -none-
 

-max-train <int> (property: maxTrainTime)
         The maximum number of seconds to training time (0 = unlimited time).
         default: 0
 

-notify <int> (property: notificationInterval)
         The time interval in seconds after which notification events about changes
          in the fitness can be sent (-1 = never send notifications; 0 = whenever
          a change occurs).
         default: -1
 

Version:

$Revision: 4584 $

Author:

Dale (dale at cs dot waikato dot ac dot nz), FracPete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Nested Class Summary

static class

GeneticAlgorithm.GAJob Class for multithreading the ga.

Field Summary

protected int	m_bits
protected FitnessFunction	m_fitnessfn
protected Long	m_LastNotificationTime the timestamp the last notification got sent.
protected PackDataDef	m_pdd
Hashtable<String,Double>	m_StoredResults the cache for results.
protected int	m_zerocount

Fields inherited from class adams.optimise.genetic.AbstractGeneticAlgorithm

m_BestRange, m_FavorZeroes, m_Fitness, m_Genes, m_Iterations, m_MaxTrainTime, m_NumChrom, m_NumGenes, m_Random, m_Running, m_Seed, m_TrainStart, PROPS_FILTER, PROPS_MASK, PROPS_RELATION

Fields inherited from class adams.optimise.AbstractOptimiser

m_bestf, m_bestv

Fields inherited from class adams.core.option.AbstractOptionHandler

m_DebugLevel, m_OptionManager

Constructor Summary

GeneticAlgorithm()
The default constructor.

Method Summary

protected void	addResult(String key, Double val) Adds a result to the cache.
String	bitsTipText() Returns the tip text for this property.
void	calcFitness() Calculates the fitness of the population.
double	calcNewFitness(FitnessFunction ff, int[] weights) Calculates the new fitness.
void	checkBest(Double fitness, OptData vars, FitnessFunction ff, int zerocount)
void	cleanUp() Cleans up data structures, frees up memory.
protected void	clearResults() Clears all currently stored results.
void	defineOptions() Adds options to the internal list of options.
int	getBits() Gets the number of bits.
PackDataDef	getDataDef()
Vector<PackData>	getDataSetups()
protected Double	getResult(String key) Returns a value from the cache.
String	globalInfo() Returns a string describing the object.
protected void	initialize() Initializes the members.
static void	main(String[] args)
OptData	optimise(OptData datadef, FitnessFunction fitness)
protected void	preRun() Some more initializations.
void	reset() Resets the genetic algorihtm.
void	setBits(int value) Bits per gene.
String	weightsToString(int[] weights) Turns the weights into a string representation.

Methods inherited from class adams.optimise.genetic.PackDataGeneticAlgorithm

getInitialSetups, init, print, printBits

Methods inherited from class adams.optimise.genetic.AbstractGeneticAlgorithm

bestRangeTipText, copyGene, doCrossovers, doMutations, doMutations2, favorZeroesTipText, forCommandLine, forName, getBestRange, getFavorZeroes, getFitness, getGene, getGeneticAlgorithms, getIterations, getMaxTrainTime, getNumChrom, getNumGenes, getSeed, hasMoreZeroes, init, isRunning, iterationsTipText, maxTrainTimeTipText, numChromTipText, postRun, run, runGeneticAlgorithm, seedTipText, setBestRange, setBestRange, setFavorZeroes, setGene, setGene, setIterations, setMaxTrainTime, setNumChrom, setSeed, sort, stop, storeSetup, updateHeader

Methods inherited from class adams.optimise.AbstractOptimiser

checkBest, compareTo, destroy, equals, getOptimisers, shallowCopy, shallowCopy

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, debug, debug, debugLevelTipText, finishInit, getDebugLevel, getOptionManager, isDebugOn, newOptionManager, setDebugLevel, toCommandLine, toString

Methods inherited from class adams.core.ConsoleObject

getDebugging, getSystemErr, getSystemOut, sizeOf

Methods inherited from class java.lang.Object

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

Field Detail

m_bits

protected int m_bits

m_zerocount

protected int m_zerocount

m_pdd

protected PackDataDef m_pdd

m_fitnessfn

protected FitnessFunction m_fitnessfn

m_LastNotificationTime

protected Long m_LastNotificationTime

the timestamp the last notification got sent.

m_StoredResults

public Hashtable<String,Double> m_StoredResults

the cache for results.

Constructor Detail

GeneticAlgorithm

public GeneticAlgorithm()

The default constructor.

Method Detail

addResult

protected void addResult(String key,
                         Double val)

Adds a result to the cache.

Parameters:

key - the key of the result

val - the value to add

reset

public void reset()

Resets the genetic algorihtm. Derived classes must call this method in set-methods of parameters to assure the invalidation of previously generated data.

Overrides:

reset in class AbstractGeneticAlgorithm

getResult

protected Double getResult(String key)

Returns a value from the cache.

Parameters:

key - the key of the result

Returns:

the result or null if not present

clearResults

protected void clearResults()

Clears all currently stored results.

weightsToString

public String weightsToString(int[] weights)

Turns the weights into a string representation.

Parameters:

weights - the weights to turn into a string

Returns:

the weights as string

calcNewFitness

public double calcNewFitness(FitnessFunction ff,
                             int[] weights)

Calculates the new fitness.

checkBest

public void checkBest(Double fitness,
                      OptData vars,
                      FitnessFunction ff,
                      int zerocount)

globalInfo

public String globalInfo()

Returns a string describing the object.

Specified by:

globalInfo in class AbstractOptionHandler

Returns:

a description suitable for displaying in the gui

initialize

protected void initialize()

Initializes the members.

Overrides:

initialize in class AbstractGeneticAlgorithm

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractGeneticAlgorithm

setBits

public void setBits(int value)

Bits per gene.

Parameters:

value - the number of bits.

getBits

public int getBits()

Gets the number of bits.

Returns:

the number of bits

bitsTipText

public String bitsTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

calcFitness

public void calcFitness()

Calculates the fitness of the population.

Specified by:

calcFitness in class AbstractGeneticAlgorithm

preRun

protected void preRun()

Some more initializations.

Overrides:

preRun in class AbstractGeneticAlgorithm

getDataDef

public PackDataDef getDataDef()

Specified by:

getDataDef in class PackDataGeneticAlgorithm

getDataSetups

public Vector<PackData> getDataSetups()

Specified by:

getDataSetups in class PackDataGeneticAlgorithm

optimise

public OptData optimise(OptData datadef,
                        FitnessFunction fitness)

Specified by:

optimise in class AbstractOptimiser

cleanUp

public void cleanUp()

Cleans up data structures, frees up memory.

Specified by:

cleanUp in interface CleanUpHandler

Overrides:

cleanUp in class AbstractOptimiser

main

public static void main(String[] args)