GeneticSearch (weka-stable 3.6.8 API)

java.lang.Object
- weka.classifiers.bayes.net.search.SearchAlgorithm
- - weka.classifiers.bayes.net.search.local.LocalScoreSearchAlgorithm
  - - weka.classifiers.bayes.net.search.local.GeneticSearch

All Implemented Interfaces:: Serializable, OptionHandler, RevisionHandler

public class GeneticSearch
extends LocalScoreSearchAlgorithm

This Bayes Network learning algorithm uses genetic search for finding a well scoring Bayes network structure. Genetic search works by having a population of Bayes network structures and allow them to mutate and apply cross over to get offspring. The best network structure found during the process is returned.

Valid options are:

 -L <integer>
  Population size

 -A <integer>
  Descendant population size

 -U <integer>
  Number of runs

 -M
  Use mutation.
  (default true)

 -C
  Use cross-over.
  (default true)

 -O
  Use tournament selection (true) or maximum subpopulatin (false).
  (default false)

 -R <seed>
  Random number seed

 -mbc
  Applies a Markov Blanket correction to the network structure, 
  after a network structure is learned. This ensures that all 
  nodes in the network are part of the Markov blanket of the 
  classifier node.

 -S [BAYES|MDL|ENTROPY|AIC|CROSS_CLASSIC|CROSS_BAYES]
  Score type (BAYES, BDeu, MDL, ENTROPY and AIC)

Version:: $Revision: 1.5 $
Author:: Remco Bouckaert (rrb@xm.co.nz)
See Also:: Serialized Form

Field Summary
- Fields inherited from class weka.classifiers.bayes.net.search.local.LocalScoreSearchAlgorithm
  TAGS_SCORE_TYPE
- Fields inherited from class weka.classifiers.bayes.net.search.SearchAlgorithm
  m_bInitAsNaiveBayes, m_bMarkovBlanketClassifier, m_nMaxNrOfParents

Constructor Summary

Constructors
Constructor and Description

GeneticSearch()

Constructors
Constructor and Description
`GeneticSearch()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`descendantPopulationSizeTipText()`
`int`	`getDescendantPopulationSize()`
`String[]`	`getOptions()` Gets the current settings of the search algorithm.
`int`	`getPopulationSize()`
`String`	`getRevision()` Returns the revision string.
`int`	`getRuns()`
`int`	`getSeed()`
`boolean`	`getUseCrossOver()`
`boolean`	`getUseMutation()`
`boolean`	`getUseTournamentSelection()`
`String`	`globalInfo()` This will return a string describing the classifier.
`Enumeration`	`listOptions()` Returns an enumeration describing the available options.
`String`	`populationSizeTipText()`
`String`	`runsTipText()`
`protected void`	`search(BayesNet bayesNet, Instances instances)` search determines the network structure/graph of the network with a genetic search algorithm.
`String`	`seedTipText()`
`void`	`setDescendantPopulationSize(int iDescendantPopulationSize)`
`void`	`setOptions(String[] options)` Parses a given list of options.
`void`	`setPopulationSize(int iPopulationSize)`
`void`	`setRuns(int nRuns)` Sets the number of runs
`void`	`setSeed(int nSeed)` Sets the random number seed
`void`	`setUseCrossOver(boolean bUseCrossOver)`
`void`	`setUseMutation(boolean bUseMutation)`
`void`	`setUseTournamentSelection(boolean bUseTournamentSelection)`
`String`	`useCrossOverTipText()`
`String`	`useMutationTipText()`
`String`	`useTournamentSelectionTipText()`

Methods inherited from class weka.classifiers.bayes.net.search.local.LocalScoreSearchAlgorithm
buildStructure, calcNodeScore, calcScoreOfCounts, calcScoreOfCounts2, calcScoreWithExtraParent, calcScoreWithMissingParent, getMarkovBlanketClassifier, getScoreType, logScore, markovBlanketClassifierTipText, scoreTypeTipText, setMarkovBlanketClassifier, setScoreType

Methods inherited from class weka.classifiers.bayes.net.search.SearchAlgorithm
addArcMakesSense, doMarkovBlanketCorrection, initAsNaiveBayesTipText, isArc, maxNrOfParentsTipText, reverseArcMakesSense, toString

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

- Constructor Detail
  - GeneticSearch
```
public GeneticSearch()
```
- Method Detail
  - search
```
protected void search(BayesNet bayesNet,
                      Instances instances)
               throws Exception
```
    search determines the network structure/graph of the network with a genetic search algorithm.
    
    Overrides:
    
    search in class SearchAlgorithm
    
    Parameters:
    
    bayesNet - the network to use
    
    instances - the data to use
    
    Throws:
    
    Exception - if population size doesn fit or neither cross-over or mutation was chosen
  - getRuns
```
public int getRuns()
```
    Returns:
    
    number of runs
  - setRuns
```
public void setRuns(int nRuns)
```
    Sets the number of runs
    
    Parameters:
    
    nRuns - The number of runs to set
  - listOptions
```
public Enumeration listOptions()
```
    Returns an enumeration describing the available options.
    
    Specified by:
    
    listOptions in interface OptionHandler
    
    Overrides:
    
    listOptions in class LocalScoreSearchAlgorithm
    
    Returns:
    
    an enumeration of all the available options.
  - setOptions
```
public void setOptions(String[] options)
                throws Exception
```
    Parses a given list of options.
    Valid options are:
```
 -L <integer>
  Population size
```
```
 -A <integer>
  Descendant population size
```
```
 -U <integer>
  Number of runs
```
```
 -M
  Use mutation.
  (default true)
```
```
 -C
  Use cross-over.
  (default true)
```
```
 -O
  Use tournament selection (true) or maximum subpopulatin (false).
  (default false)
```
```
 -R <seed>
  Random number seed
```
```
 -mbc
  Applies a Markov Blanket correction to the network structure, 
  after a network structure is learned. This ensures that all 
  nodes in the network are part of the Markov blanket of the 
  classifier node.
```
```
 -S [BAYES|MDL|ENTROPY|AIC|CROSS_CLASSIC|CROSS_BAYES]
  Score type (BAYES, BDeu, MDL, ENTROPY and AIC)
```
    Specified by:
    
    setOptions in interface OptionHandler
    
    Overrides:
    
    setOptions in class LocalScoreSearchAlgorithm
    
    Parameters:
    
    options - the list of options as an array of strings
    
    Throws:
    
    Exception - if an option is not supported
  - getOptions
```
public String[] getOptions()
```
    Gets the current settings of the search algorithm.
    
    Specified by:
    
    getOptions in interface OptionHandler
    
    Overrides:
    
    getOptions in class LocalScoreSearchAlgorithm
    
    Returns:
    
    an array of strings suitable for passing to setOptions
  - getUseCrossOver
```
public boolean getUseCrossOver()
```
    Returns:
    
    whether cross-over is used
  - getUseMutation
```
public boolean getUseMutation()
```
    Returns:
    
    whether mutation is used
  - getDescendantPopulationSize
```
public int getDescendantPopulationSize()
```
    Returns:
    
    descendant population size
  - getPopulationSize
```
public int getPopulationSize()
```
    Returns:
    
    population size
  - setUseCrossOver
```
public void setUseCrossOver(boolean bUseCrossOver)
```
    Parameters:
    
    bUseCrossOver - sets whether cross-over is used
  - setUseMutation
```
public void setUseMutation(boolean bUseMutation)
```
    Parameters:
    
    bUseMutation - sets whether mutation is used
  - getUseTournamentSelection
```
public boolean getUseTournamentSelection()
```
    Returns:
    
    whether Tournament Selection (true) or Maximum Sub-Population (false) should be used
  - setUseTournamentSelection
```
public void setUseTournamentSelection(boolean bUseTournamentSelection)
```
    Parameters:
    
    bUseTournamentSelection - sets whether Tournament Selection or Maximum Sub-Population should be used
  - setDescendantPopulationSize
```
public void setDescendantPopulationSize(int iDescendantPopulationSize)
```
    Parameters:
    
    iDescendantPopulationSize - sets descendant population size
  - setPopulationSize
```
public void setPopulationSize(int iPopulationSize)
```
    Parameters:
    
    iPopulationSize - sets population size
  - getSeed
```
public int getSeed()
```
    Returns:
    
    random number seed
  - setSeed
```
public void setSeed(int nSeed)
```
    Sets the random number seed
    
    Parameters:
    
    nSeed - The number of the seed to set
  - globalInfo
```
public String globalInfo()
```
    This will return a string describing the classifier.
    
    Overrides:
    
    globalInfo in class LocalScoreSearchAlgorithm
    
    Returns:
    
    The string.
  - runsTipText
```
public String runsTipText()
```
    Returns:
    
    a string to describe the Runs option.
  - seedTipText
```
public String seedTipText()
```
    Returns:
    
    a string to describe the Seed option.
  - populationSizeTipText
```
public String populationSizeTipText()
```
    Returns:
    
    a string to describe the Population Size option.
  - descendantPopulationSizeTipText
```
public String descendantPopulationSizeTipText()
```
    Returns:
    
    a string to describe the Descendant Population Size option.
  - useMutationTipText
```
public String useMutationTipText()
```
    Returns:
    
    a string to describe the Use Mutation option.
  - useCrossOverTipText
```
public String useCrossOverTipText()
```
    Returns:
    
    a string to describe the Use Cross-Over option.
  - useTournamentSelectionTipText
```
public String useTournamentSelectionTipText()
```
    Returns:
    
    a string to describe the Use Tournament Selection option.
  - getRevision
```
public String getRevision()
```
    Returns the revision string.
    
    Specified by:
    
    getRevision in interface RevisionHandler
    
    Overrides:
    
    getRevision in class LocalScoreSearchAlgorithm
    
    Returns:
    
    the revision

Class GeneticSearch

Field Summary

Fields inherited from class weka.classifiers.bayes.net.search.local.LocalScoreSearchAlgorithm

Fields inherited from class weka.classifiers.bayes.net.search.SearchAlgorithm

Constructor Summary

Method Summary

Methods inherited from class weka.classifiers.bayes.net.search.local.LocalScoreSearchAlgorithm

Methods inherited from class weka.classifiers.bayes.net.search.SearchAlgorithm

Methods inherited from class java.lang.Object

Constructor Detail

GeneticSearch

Method Detail

search

getRuns

setRuns

listOptions

setOptions

getOptions

getUseCrossOver

getUseMutation

getDescendantPopulationSize

getPopulationSize

setUseCrossOver

setUseMutation

getUseTournamentSelection

setUseTournamentSelection

setDescendantPopulationSize

setPopulationSize

getSeed

setSeed

globalInfo

runsTipText

seedTipText

populationSizeTipText

descendantPopulationSizeTipText

useMutationTipText

useCrossOverTipText

useTournamentSelectionTipText

getRevision