weka.attributeSelection
Class PrincipalComponents

java.lang.Object
  weka.attributeSelection.ASEvaluation
      weka.attributeSelection.UnsupervisedAttributeEvaluator
          weka.attributeSelection.PrincipalComponents

All Implemented Interfaces:

Serializable, AttributeEvaluator, AttributeTransformer, CapabilitiesHandler, OptionHandler, RevisionHandler

public class PrincipalComponents
extends UnsupervisedAttributeEvaluator
implements AttributeTransformer, OptionHandler

Performs a principal components analysis and transformation of the data. Use in conjunction with a Ranker search. Dimensionality reduction is accomplished by choosing enough eigenvectors to account for some percentage of the variance in the original data---default 0.95 (95%). Attribute noise can be filtered by transforming to the PC space, eliminating some of the worst eigenvectors, and then transforming back to the original space.

Valid options are:

 -C
  Center (rather than standardize) the
  data and compute PCA using the covariance (rather
   than the correlation) matrix.

 -R
  Retain enough PC attributes to account 
  for this proportion of variance in the original data.
  (default = 0.95)

 -O
  Transform through the PC space and 
  back to the original space.

 -A
  Maximum number of attributes to include in 
  transformed attribute names. (-1 = include all)

Version:

$Revision: 8034 $

Author:

Mark Hall (mhall@cs.waikato.ac.nz), Gabi Schmidberger (gabi@cs.waikato.ac.nz)

See Also:

Serialized Form

Constructor Summary

PrincipalComponents()

Method Summary

void	buildEvaluator(Instances data) Initializes principal components and performs the analysis
String	centerDataTipText() Returns the tip text for this property
Instance	convertInstance(Instance instance) Transform an instance in original (unormalized) format.
double	evaluateAttribute(int att) Evaluates the merit of a transformed attribute.
Capabilities	getCapabilities() Returns the capabilities of this evaluator.
boolean	getCenterData() Get whether to center (rather than standardize) the data.
int	getMaximumAttributeNames() Gets maximum number of attributes to include in transformed attribute names.
String[]	getOptions() Gets the current settings of PrincipalComponents
String	getRevision() Returns the revision string.
boolean	getTransformBackToOriginal() Gets whether the data is to be transformed back to the original space.
double	getVarianceCovered() Gets the proportion of total variance to account for when retaining principal components
String	globalInfo() Returns a string describing this attribute transformer
Enumeration	listOptions() Returns an enumeration describing the available options.
static void	main(String[] argv) Main method for testing this class
String	maximumAttributeNamesTipText() Returns the tip text for this property
void	setCenterData(boolean center) Set whether to center (rather than standardize) the data.
void	setMaximumAttributeNames(int m) Sets maximum number of attributes to include in transformed attribute names.
void	setOptions(String[] options) Parses a given list of options.
void	setTransformBackToOriginal(boolean b) Sets whether the data should be transformed back to the original space
void	setVarianceCovered(double vc) Sets the amount of variance to account for when retaining principal components
String	toString() Returns a description of this attribute transformer
String	transformBackToOriginalTipText() Returns the tip text for this property
Instances	transformedData(Instances data) Gets the transformed training data.
Instances	transformedHeader() Returns just the header for the transformed data (ie.
String	varianceCoveredTipText() Returns the tip text for this property

Methods inherited from class weka.attributeSelection.ASEvaluation

forName, makeCopies, postProcess, runEvaluator

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

PrincipalComponents

public PrincipalComponents()

Method Detail

globalInfo

public String globalInfo()

Returns a string describing this attribute transformer

Returns:

a description of the evaluator suitable for displaying in the explorer/experimenter gui

listOptions

public Enumeration listOptions()

Returns an enumeration describing the available options.

Specified by:

listOptions in interface OptionHandler

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:

 -C
  Center (rather than standardize) the
  data and compute PCA using the covariance (rather
   than the correlation) matrix.

 -R
  Retain enough PC attributes to account 
  for this proportion of variance in the original data.
  (default = 0.95)

 -O
  Transform through the PC space and 
  back to the original space.

 -A
  Maximum number of attributes to include in 
  transformed attribute names. (-1 = include all)

Specified by:

setOptions in interface OptionHandler

Parameters:

options - the list of options as an array of strings

Throws:

Exception - if an option is not supported

centerDataTipText

public String centerDataTipText()

Returns the tip text for this property

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setCenterData

public void setCenterData(boolean center)

Set whether to center (rather than standardize) the data. If set to true then PCA is computed from the covariance rather than correlation matrix.

Parameters:

center - true if the data is to be centered rather than standardized

getCenterData

public boolean getCenterData()

Get whether to center (rather than standardize) the data. If true then PCA is computed from the covariance rather than correlation matrix.

Returns:

true if the data is to be centered rather than standardized.

varianceCoveredTipText

public String varianceCoveredTipText()

Returns the tip text for this property

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setVarianceCovered

public void setVarianceCovered(double vc)

Sets the amount of variance to account for when retaining principal components

Parameters:

vc - the proportion of total variance to account for

getVarianceCovered

public double getVarianceCovered()

Gets the proportion of total variance to account for when retaining principal components

Returns:

the proportion of variance to account for

maximumAttributeNamesTipText

public String maximumAttributeNamesTipText()

Returns the tip text for this property

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setMaximumAttributeNames

public void setMaximumAttributeNames(int m)

Sets maximum number of attributes to include in transformed attribute names.

Parameters:

m - the maximum number of attributes

getMaximumAttributeNames

public int getMaximumAttributeNames()

Gets maximum number of attributes to include in transformed attribute names.

Returns:

the maximum number of attributes

transformBackToOriginalTipText

public String transformBackToOriginalTipText()

Returns the tip text for this property

Returns:

tip text for this property suitable for displaying in the explorer/experimenter gui

setTransformBackToOriginal

public void setTransformBackToOriginal(boolean b)

Sets whether the data should be transformed back to the original space

Parameters:

b - true if the data should be transformed back to the original space

getTransformBackToOriginal

public boolean getTransformBackToOriginal()

Gets whether the data is to be transformed back to the original space.

Returns:

true if the data is to be transformed back to the original space

getOptions

public String[] getOptions()

Gets the current settings of PrincipalComponents

Specified by:

getOptions in interface OptionHandler

Returns:

an array of strings suitable for passing to setOptions()

getCapabilities

public Capabilities getCapabilities()

Returns the capabilities of this evaluator.

Specified by:

getCapabilities in interface CapabilitiesHandler

Overrides:

getCapabilities in class ASEvaluation

Returns:

the capabilities of this evaluator

See Also:

Capabilities

buildEvaluator

public void buildEvaluator(Instances data)
                    throws Exception

Initializes principal components and performs the analysis

Specified by:

buildEvaluator in class ASEvaluation

Parameters:

data - the instances to analyse/transform

Throws:

Exception - if analysis fails

transformedHeader

public Instances transformedHeader()
                            throws Exception

Returns just the header for the transformed data (ie. an empty set of instances. This is so that AttributeSelection can determine the structure of the transformed data without actually having to get all the transformed data through transformedData().

Specified by:

transformedHeader in interface AttributeTransformer

Returns:

the header of the transformed data.

Throws:

Exception - if the header of the transformed data can't be determined.

transformedData

public Instances transformedData(Instances data)
                          throws Exception

Gets the transformed training data.

Specified by:

transformedData in interface AttributeTransformer

Returns:

the transformed training data

Throws:

Exception - if transformed data can't be returned

evaluateAttribute

public double evaluateAttribute(int att)
                         throws Exception

Evaluates the merit of a transformed attribute. This is defined to be 1 minus the cumulative variance explained. Merit can't be meaningfully evaluated if the data is to be transformed back to the original space.

Specified by:

evaluateAttribute in interface AttributeEvaluator

Parameters:

att - the attribute to be evaluated

Returns:

the merit of a transformed attribute

Throws:

Exception - if attribute can't be evaluated

toString

public String toString()

Returns a description of this attribute transformer

Overrides:

toString in class Object

Returns:

a String describing this attribute transformer

convertInstance

public Instance convertInstance(Instance instance)
                         throws Exception

Transform an instance in original (unormalized) format. Convert back to the original space if requested.

Specified by:

convertInstance in interface AttributeTransformer

Parameters:

instance - an instance in the original (unormalized) format

Returns:

a transformed instance

Throws:

Exception - if instance cant be transformed

getRevision

public String getRevision()

Returns the revision string.

Specified by:

getRevision in interface RevisionHandler

Overrides:

getRevision in class ASEvaluation

Returns:

the revision

main

public static void main(String[] argv)

Main method for testing this class

Parameters:

argv - should contain the command line arguments to the evaluator/transformer (see AttributeSelection)