Package adams.opt.genetic

Class AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.opt.genetic.AbstractGeneticAlgorithm

adams.opt.genetic.AbstractClassifierBasedGeneticAlgorithm

adams.opt.genetic.AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation

All Implemented Interfaces:

Destroyable, GlobalInfoSupporter, LoggingLevelHandler, LoggingSupporter, OptionHandler, Pausable, Randomizable, ShallowCopySupporter<AbstractGeneticAlgorithm>, SizeOfHandler, Stoppable, StoppableWithFeedback, ThreadLimiter, GeneticFitnessChangeNotifier, Serializable

Direct Known Subclasses:

DarkLord, Hermione

public abstract class AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation
extends AbstractClassifierBasedGeneticAlgorithm

Ancestor for genetic algorithms that offer a second evaluation using a different seed value. The fitness value of the first evaluation only gets added if it the best one so far and the evaluation with the second seed value also generates the best value so far (using a second set of stored results).

Version:

$Revision$

Author:

FracPete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation.ClassifierBasedGeneticAlgorithmWithSecondEvaluationJob<T extends AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation>	Job class for algorithms with datasets.

Nested classes/interfaces inherited from class adams.opt.genetic.AbstractClassifierBasedGeneticAlgorithm

AbstractClassifierBasedGeneticAlgorithm.ClassifierBasedGeneticAlgorithmJob<T extends AbstractClassifierBasedGeneticAlgorithm>

Nested classes/interfaces inherited from class adams.opt.genetic.AbstractGeneticAlgorithm

AbstractGeneticAlgorithm.FitnessContainer, AbstractGeneticAlgorithm.GeneticAlgorithmJob<T extends AbstractGeneticAlgorithm>

Field Summary

Fields

Modifier and Type	Field	Description
protected double	m_SecondBestFitness	the best fitness so far (second evaluation).
protected Object	m_SecondBestSetup	the best setup so far (second evaluation).
protected int[]	m_SecondBestWeights	the best weights/bits so far (second evaluation).
protected int	m_SecondCrossValidationSeed	the cross-validation seed (second evaluation).
protected int	m_SecondFolds	the number of folds for cross-validation (second evaluation).
Hashtable<String,Double>	m_SecondStoredResults	the cache for results (second evaluation).
protected boolean	m_UseSecondEvaluation	whether to use second evaluation with different seed.

Fields inherited from class adams.opt.genetic.AbstractClassifierBasedGeneticAlgorithm

m_BitsPerGene, m_Classifier, m_ClassIndex, m_ClassLabelIndex, m_CrossValidationSeed, m_EvaluationPostProcessor, m_FlowContext, m_Folds, m_Generator, m_Instances, m_JobRunner, m_JobRunnerSetup, m_Measure, m_OutputDirectory, m_OutputPrefixType, m_OutputType, m_SetupUpload, m_StoredResults, m_SuppliedPrefix, m_TestInstances, PROPS_FILTER, PROPS_MASK, PROPS_RELATION

Fields inherited from class adams.opt.genetic.AbstractGeneticAlgorithm

m_ActualNumChrom, m_BestFitness, m_BestRange, m_BestSetup, m_BestWeights, m_CurrentIteration, m_FavorZeroes, m_Fitness, m_FitnessChangeListeners, m_FitnessHistory, m_Genes, m_InitialSetupsProvider, m_InitialWeights, m_LastNotificationTime, m_MaxFitnessHistorySize, m_NotificationInterval, m_NumChrom, m_NumGenes, m_NumThreads, m_Paused, m_Random, m_Running, m_Seed, m_Stopped, m_StoppingCriterion

Fields inherited from class adams.core.option.AbstractOptionHandler

m_OptionManager

Fields inherited from class adams.core.logging.LoggingObject

m_Logger, m_LoggingIsEnabled, m_LoggingLevel

Constructor Summary

Constructors

Constructor	Description
AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation()

Method Summary

Modifier and Type	Method	Description
protected void	addSecondResult(String key, Double val)	Adds a result to the cache (second evaluation).
protected void	clearResults()	Clears all currently stored results.
void	defineOptions()	Adds options to the internal list of options.
int	getSecondCrossValidationSeed()	Returns the current seed value for cross-validation (second evaluation).
int	getSecondFolds()	Returns the number of folds to use in cross-validation (second evaluation).
protected Double	getSecondResult(String key)	Returns a value from the cache (second evaluation).
boolean	getUseSecondEvaluation()	Returns whether to use the second evaluation.
protected void	initialize()	Initializes the members.
boolean	isSecondBetterFitness(double fitness)	Checks whether the fitness is better (second evaluation).
protected void	preRun()	Further initializations in derived classes.
String	secondCrossValidationSeedTipText()	Returns the tip text for this property.
String	secondFoldsTipText()	Returns the tip text for this property.
void	setSecondCrossValidationSeed(int value)	Sets the seed value to use for cross-validation (second evaluation).
void	setSecondFolds(int value)	Sets the number of folds to use in cross-validation (second evaluation).
boolean	setSecondNewFitness(double fitness, Object setup, int chromosome, int[] weights)	Sets a fitness and keep it if better (second evaluation).
void	setUseSecondEvaluation(boolean value)	Sets whether to use the second evaluation.
String	useSecondEvaluationTipText()	Returns the tip text for this property.

Methods inherited from class adams.opt.genetic.AbstractClassifierBasedGeneticAlgorithm

addResult, bitsPerGeneTipText, calcFitness, classifierTipText, classIndexTipText, classLabelIndexTipText, crossValidationSeedTipText, evaluationPostProcessorTipText, foldsTipText, generatorTipText, getBitsPerGene, getClassifier, getClassIndex, getClassLabelIndex, getCrossValidationSeed, getCurrentFitness, getDefaultClassifier, getDefaultOutputType, getEvaluationPostProcessor, getFlowContext, getFolds, getGenerator, getInstances, getJobRunnerSetup, getMeasure, getOutputDirectory, getOutputPrefixType, getOutputType, getResult, getSetupUpload, getSuppliedPrefix, getTestInstances, measureTipText, newJob, outputDirectoryTipText, outputPrefixTypeTipText, outputTypeTipText, postRun, setBitsPerGene, setClassifier, setClassIndex, setClassLabelIndex, setCrossValidationSeed, setEvaluationPostProcessor, setFlowContext, setFolds, setGenerator, setInstances, setJobRunnerSetup, setMeasure, setOutputDirectory, setOutputPrefixType, setOutputType, setSetupUpload, setSuppliedPrefix, setTestInstances, setupUploadTipText, stopExecution, storeSetup, suppliedPrefixTipText, toString, updateHeader

Methods inherited from class adams.opt.genetic.AbstractGeneticAlgorithm

addFitnessChangeListener, addToFitnessHistory, bestRangeTipText, copyGene, doCrossovers, doMutations, doMutations2, favorZeroesTipText, forCommandLine, forName, getBestRange, getCurrentIteration, getCurrentSetup, getCurrentWeights, getDefaultInitialSetupsProvider, getFavorZeroes, getFitness, getFitnessHistory, getGene, getGeneticAlgorithms, getInitialSetups, getInitialSetupsProvider, getInitialWeights, getMaxFitnessHistorySize, getNotificationInterval, getNumChrom, getNumGenes, getNumThreads, getSeed, getStoppingCriterion, hasMoreZeroes, init, initialSetupsProviderTipText, initialWeightsTipText, isBetterFitness, isPaused, isRunning, isStopped, logChromosomes, maxFitnessHistorySizeTipText, notificationIntervalTipText, notifyFitnessChangeListeners, notifyFitnessChangeListeners, numChromTipText, numThreadsTipText, pauseExecution, removeFitnessChangeListener, reset, resumeExecution, run, runGeneticAlgorithm, seedTipText, setBestRange, setBestRange, setFavorZeroes, setGene, setGene, setInitialSetupsProvider, setInitialWeights, setMaxFitnessHistorySize, setNewFitness, setNotificationInterval, setNumChrom, setNumThreads, setSeed, setStoppingCriterion, shallowCopy, shallowCopy, sort, stoppingCriterionTipText

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, destroy, finishInit, getDefaultLoggingLevel, getOptionManager, globalInfo, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine

Methods inherited from class adams.core.logging.LoggingObject

configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

Methods inherited from class java.lang.Object

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

Methods inherited from interface adams.event.GeneticFitnessChangeNotifier

addFitnessChangeListener, removeFitnessChangeListener

Methods inherited from interface adams.core.logging.LoggingLevelHandler

getLoggingLevel

Field Detail

m_UseSecondEvaluation

protected boolean m_UseSecondEvaluation

whether to use second evaluation with different seed.

m_SecondFolds

protected int m_SecondFolds

the number of folds for cross-validation (second evaluation).

m_SecondCrossValidationSeed

protected int m_SecondCrossValidationSeed

the cross-validation seed (second evaluation).

m_SecondStoredResults

public Hashtable<String,Double> m_SecondStoredResults

the cache for results (second evaluation).

m_SecondBestFitness

protected double m_SecondBestFitness

the best fitness so far (second evaluation).

m_SecondBestSetup

protected Object m_SecondBestSetup

the best setup so far (second evaluation).

m_SecondBestWeights

protected int[] m_SecondBestWeights

the best weights/bits so far (second evaluation).

Constructor Detail

AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation

public AbstractClassifierBasedGeneticAlgorithmWithSecondEvaluation()

Method Detail

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractClassifierBasedGeneticAlgorithm

initialize

protected void initialize()

Initializes the members.

Overrides:

initialize in class AbstractGeneticAlgorithm

setUseSecondEvaluation

public void setUseSecondEvaluation(boolean value)

Sets whether to use the second evaluation.

Parameters:

value - true if to use second evaluation

getUseSecondEvaluation

public boolean getUseSecondEvaluation()

Returns whether to use the second evaluation.

Returns:

true if to use second evaluation

useSecondEvaluationTipText

public String useSecondEvaluationTipText()

Returns the tip text for this property.

Returns:

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

setSecondFolds

public void setSecondFolds(int value)

Sets the number of folds to use in cross-validation (second evaluation).

Parameters:

value - the number of folds

getSecondFolds

public int getSecondFolds()

Returns the number of folds to use in cross-validation (second evaluation).

Returns:

the number of folds

secondFoldsTipText

public String secondFoldsTipText()

Returns the tip text for this property.

Returns:

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

setSecondCrossValidationSeed

public void setSecondCrossValidationSeed(int value)

Sets the seed value to use for cross-validation (second evaluation).

Parameters:

value - the seed to use

getSecondCrossValidationSeed

public int getSecondCrossValidationSeed()

Returns the current seed value for cross-validation (second evaluation).

Returns:

the seed value

secondCrossValidationSeedTipText

public String secondCrossValidationSeedTipText()

Returns the tip text for this property.

Returns:

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

addSecondResult

protected void addSecondResult(String key,
                               Double val)

Adds a result to the cache (second evaluation).

Parameters:

key - the key of the result

val - the value to add

getSecondResult

protected Double getSecondResult(String key)

Returns a value from the cache (second evaluation).

Parameters:

key - the key of the result

Returns:

the result or null if not present

clearResults

protected void clearResults()

Clears all currently stored results.

Overrides:

clearResults in class AbstractClassifierBasedGeneticAlgorithm

isSecondBetterFitness

public boolean isSecondBetterFitness(double fitness)

Checks whether the fitness is better (second evaluation).

Parameters:

fitness - the new fitness

Returns:

true if the new fitness is better

setSecondNewFitness

public boolean setSecondNewFitness(double fitness,
                                   Object setup,
                                   int chromosome,
                                   int[] weights)

Sets a fitness and keep it if better (second evaluation).

Parameters:

fitness - the new fitness

setup - the new setup

chromosome - the chromosome responsible

weights - the new weights

Returns:

true if the new fitness was better

preRun

protected void preRun()

Further initializations in derived classes.

Overrides:

preRun in class AbstractClassifierBasedGeneticAlgorithm