weka.attributeSelection
Class PrincipalComponents

java.lang.Object
  extended by weka.attributeSelection.ASEvaluation
      extended by weka.attributeSelection.UnsupervisedAttributeEvaluator
          extended by weka.attributeSelection.PrincipalComponents
All Implemented Interfaces:
java.io.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:

 -D
  Don't normalize input data.
 -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: 4615 $
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
 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.
 int getMaximumAttributeNames()
          Gets maximum number of attributes to include in transformed attribute names.
 boolean getNormalize()
          Gets whether or not input data is to be normalized
 java.lang.String[] getOptions()
          Gets the current settings of PrincipalComponents
 java.lang.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
 java.lang.String globalInfo()
          Returns a string describing this attribute transformer
 java.util.Enumeration listOptions()
          Returns an enumeration describing the available options.
static void main(java.lang.String[] argv)
          Main method for testing this class
 java.lang.String maximumAttributeNamesTipText()
          Returns the tip text for this property
 java.lang.String normalizeTipText()
          Returns the tip text for this property
 void setMaximumAttributeNames(int m)
          Sets maximum number of attributes to include in transformed attribute names.
 void setNormalize(boolean n)
          Set whether input data will be normalized.
 void setOptions(java.lang.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
 java.lang.String toString()
          Returns a description of this attribute transformer
 java.lang.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.
 java.lang.String varianceCoveredTipText()
          Returns the tip text for this property
 
Methods inherited from class weka.attributeSelection.ASEvaluation
forName, makeCopies, postProcess
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

PrincipalComponents

public PrincipalComponents()
Method Detail

globalInfo

public java.lang.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 java.util.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(java.lang.String[] options)
                throws java.lang.Exception
Parses a given list of options.

Valid options are:

 -D
  Don't normalize input data.
 -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:
java.lang.Exception - if an option is not supported

normalizeTipText

public java.lang.String normalizeTipText()
Returns the tip text for this property

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

setNormalize

public void setNormalize(boolean n)
Set whether input data will be normalized.

Parameters:
n - true if input data is to be normalized

getNormalize

public boolean getNormalize()
Gets whether or not input data is to be normalized

Returns:
true if input data is to be normalized

varianceCoveredTipText

public java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.Exception
Initializes principal components and performs the analysis

Specified by:
buildEvaluator in class ASEvaluation
Parameters:
data - the instances to analyse/transform
Throws:
java.lang.Exception - if analysis fails

transformedHeader

public Instances transformedHeader()
                            throws java.lang.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:
java.lang.Exception - if the header of the transformed data can't be determined.

transformedData

public Instances transformedData(Instances data)
                          throws java.lang.Exception
Gets the transformed training data.

Specified by:
transformedData in interface AttributeTransformer
Returns:
the transformed training data
Throws:
java.lang.Exception - if transformed data can't be returned

evaluateAttribute

public double evaluateAttribute(int att)
                         throws java.lang.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:
java.lang.Exception - if attribute can't be evaluated

toString

public java.lang.String toString()
Returns a description of this attribute transformer

Overrides:
toString in class java.lang.Object
Returns:
a String describing this attribute transformer

convertInstance

public Instance convertInstance(Instance instance)
                         throws java.lang.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:
java.lang.Exception - if instance cant be transformed

getRevision

public java.lang.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(java.lang.String[] argv)
Main method for testing this class

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