Package weka.attributeSelection
Class PrincipalComponents
- java.lang.Object
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- weka.attributeSelection.ASEvaluation
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- weka.attributeSelection.UnsupervisedAttributeEvaluator
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- weka.attributeSelection.PrincipalComponents
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- 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: 6690 $
- Author:
- Mark Hall (mhall@cs.waikato.ac.nz), Gabi Schmidberger (gabi@cs.waikato.ac.nz)
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description PrincipalComponents()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
buildEvaluator(Instances data)
Initializes principal components and performs the analysisjava.lang.String
centerDataTipText()
Returns the tip text for this propertyInstance
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.java.lang.String[]
getOptions()
Gets the current settings of PrincipalComponentsjava.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 componentsjava.lang.String
globalInfo()
Returns a string describing this attribute transformerjava.util.Enumeration
listOptions()
Returns an enumeration describing the available options.static void
main(java.lang.String[] argv)
Main method for testing this classjava.lang.String
maximumAttributeNamesTipText()
Returns the tip text for this propertyvoid
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(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 spacevoid
setVarianceCovered(double vc)
Sets the amount of variance to account for when retaining principal componentsjava.lang.String
toString()
Returns a description of this attribute transformerjava.lang.String
transformBackToOriginalTipText()
Returns the tip text for this propertyInstances
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
clean, forName, makeCopies, postProcess
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Method Detail
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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
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listOptions
public java.util.Enumeration listOptions()
Returns an enumeration describing the available options.- Specified by:
listOptions
in interfaceOptionHandler
- Returns:
- an enumeration of all the available options.
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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 interfaceOptionHandler
- Parameters:
options
- the list of options as an array of strings- Throws:
java.lang.Exception
- if an option is not supported
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centerDataTipText
public java.lang.String centerDataTipText()
Returns the tip text for this property- Returns:
- tip text for this property suitable for displaying in the explorer/experimenter gui
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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
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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.
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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
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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
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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
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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
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setMaximumAttributeNames
public void setMaximumAttributeNames(int m)
Sets maximum number of attributes to include in transformed attribute names.- Parameters:
m
- the maximum number of attributes
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getMaximumAttributeNames
public int getMaximumAttributeNames()
Gets maximum number of attributes to include in transformed attribute names.- Returns:
- the maximum number of attributes
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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
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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
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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
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getOptions
public java.lang.String[] getOptions()
Gets the current settings of PrincipalComponents- Specified by:
getOptions
in interfaceOptionHandler
- Returns:
- an array of strings suitable for passing to setOptions()
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getCapabilities
public Capabilities getCapabilities()
Returns the capabilities of this evaluator.- Specified by:
getCapabilities
in interfaceCapabilitiesHandler
- Overrides:
getCapabilities
in classASEvaluation
- Returns:
- the capabilities of this evaluator
- See Also:
Capabilities
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buildEvaluator
public void buildEvaluator(Instances data) throws java.lang.Exception
Initializes principal components and performs the analysis- Specified by:
buildEvaluator
in classASEvaluation
- Parameters:
data
- the instances to analyse/transform- Throws:
java.lang.Exception
- if analysis fails
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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 interfaceAttributeTransformer
- Returns:
- the header of the transformed data.
- Throws:
java.lang.Exception
- if the header of the transformed data can't be determined.
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transformedData
public Instances transformedData(Instances data) throws java.lang.Exception
Gets the transformed training data.- Specified by:
transformedData
in interfaceAttributeTransformer
- Returns:
- the transformed training data
- Throws:
java.lang.Exception
- if transformed data can't be returned
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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 interfaceAttributeEvaluator
- Parameters:
att
- the attribute to be evaluated- Returns:
- the merit of a transformed attribute
- Throws:
java.lang.Exception
- if attribute can't be evaluated
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toString
public java.lang.String toString()
Returns a description of this attribute transformer- Overrides:
toString
in classjava.lang.Object
- Returns:
- a String describing this attribute transformer
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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 interfaceAttributeTransformer
- Parameters:
instance
- an instance in the original (unormalized) format- Returns:
- a transformed instance
- Throws:
java.lang.Exception
- if instance cant be transformed
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getRevision
public java.lang.String getRevision()
Returns the revision string.- Specified by:
getRevision
in interfaceRevisionHandler
- Overrides:
getRevision
in classASEvaluation
- Returns:
- the revision
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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)
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