Class SVMAttributeEval

  • All Implemented Interfaces:
    java.io.Serializable, AttributeEvaluator, CapabilitiesHandler, OptionHandler, RevisionHandler, TechnicalInformationHandler

    public class SVMAttributeEval
    extends ASEvaluation
    implements AttributeEvaluator, OptionHandler, TechnicalInformationHandler
    SVMAttributeEval :

    Evaluates the worth of an attribute by using an SVM classifier. Attributes are ranked by the square of the weight assigned by the SVM. Attribute selection for multiclass problems is handled by ranking attributes for each class seperately using a one-vs-all method and then "dealing" from the top of each pile to give a final ranking.

    For more information see:

    I. Guyon, J. Weston, S. Barnhill, V. Vapnik (2002). Gene selection for cancer classification using support vector machines. Machine Learning. 46:389-422.

    BibTeX:

     @article{Guyon2002,
        author = {I. Guyon and J. Weston and S. Barnhill and V. Vapnik},
        journal = {Machine Learning},
        pages = {389-422},
        title = {Gene selection for cancer classification using support vector machines},
        volume = {46},
        year = {2002}
     }
     

    Valid options are:

     -X <constant rate of elimination>
      Specify the constant rate of attribute
      elimination per invocation of
      the support vector machine.
      Default = 1.
     -Y <percent rate of elimination>
      Specify the percentage rate of attributes to
      elimination per invocation of
      the support vector machine.
      Trumps constant rate (above threshold).
      Default = 0.
     -Z <threshold for percent elimination>
      Specify the threshold below which 
      percentage attribute elimination
      reverts to the constant method.
     -P <epsilon>
      Specify the value of P (epsilon
      parameter) to pass on to the
      support vector machine.
      Default = 1.0e-25
     -T <tolerance>
      Specify the value of T (tolerance
      parameter) to pass on to the
      support vector machine.
      Default = 1.0e-10
     -C <complexity>
      Specify the value of C (complexity
      parameter) to pass on to the
      support vector machine.
      Default = 1.0
     -N
      Whether the SVM should 0=normalize/1=standardize/2=neither.
      (default 0=normalize)
    Version:
    $Revision: 1.28 $
    Author:
    Eibe Frank (eibe@cs.waikato.ac.nz), Mark Hall (mhall@cs.waikato.ac.nz), Kieran Holland
    See Also:
    Serialized Form
    • Constructor Detail

      • SVMAttributeEval

        public SVMAttributeEval()
        Constructor
    • Method Detail

      • globalInfo

        public java.lang.String globalInfo()
        Returns a string describing this attribute evaluator
        Returns:
        a description of the evaluator suitable for displaying in the explorer/experimenter gui
      • getTechnicalInformation

        public TechnicalInformation getTechnicalInformation()
        Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
        Specified by:
        getTechnicalInformation in interface TechnicalInformationHandler
        Returns:
        the technical information about this class
      • listOptions

        public java.util.Enumeration listOptions()
        Returns an enumeration describing all the available options
        Specified by:
        listOptions in interface OptionHandler
        Returns:
        an enumeration of options
      • setOptions

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

        Valid options are:

         -X <constant rate of elimination>
          Specify the constant rate of attribute
          elimination per invocation of
          the support vector machine.
          Default = 1.
         -Y <percent rate of elimination>
          Specify the percentage rate of attributes to
          elimination per invocation of
          the support vector machine.
          Trumps constant rate (above threshold).
          Default = 0.
         -Z <threshold for percent elimination>
          Specify the threshold below which 
          percentage attribute elimination
          reverts to the constant method.
         -P <epsilon>
          Specify the value of P (epsilon
          parameter) to pass on to the
          support vector machine.
          Default = 1.0e-25
         -T <tolerance>
          Specify the value of T (tolerance
          parameter) to pass on to the
          support vector machine.
          Default = 1.0e-10
         -C <complexity>
          Specify the value of C (complexity
          parameter) to pass on to the
          support vector machine.
          Default = 1.0
         -N
          Whether the SVM should 0=normalize/1=standardize/2=neither.
          (default 0=normalize)
        Specified by:
        setOptions in interface OptionHandler
        Parameters:
        options - the list of options as an array of strings
        Throws:
        java.lang.Exception - if an error occurs
      • getOptions

        public java.lang.String[] getOptions()
        Gets the current settings of SVMAttributeEval
        Specified by:
        getOptions in interface OptionHandler
        Returns:
        an array of strings suitable for passing to setOptions()
      • attsToEliminatePerIterationTipText

        public java.lang.String attsToEliminatePerIterationTipText()
        Returns a tip text for this property suitable for display in the GUI
        Returns:
        tip text string describing this property
      • percentToEliminatePerIterationTipText

        public java.lang.String percentToEliminatePerIterationTipText()
        Returns a tip text for this property suitable for display in the GUI
        Returns:
        tip text string describing this property
      • percentThresholdTipText

        public java.lang.String percentThresholdTipText()
        Returns a tip text for this property suitable for display in the GUI
        Returns:
        tip text string describing this property
      • epsilonParameterTipText

        public java.lang.String epsilonParameterTipText()
        Returns a tip text for this property suitable for display in the GUI
        Returns:
        tip text string describing this property
      • toleranceParameterTipText

        public java.lang.String toleranceParameterTipText()
        Returns a tip text for this property suitable for display in the GUI
        Returns:
        tip text string describing this property
      • complexityParameterTipText

        public java.lang.String complexityParameterTipText()
        Returns a tip text for this property suitable for display in the GUI
        Returns:
        tip text string describing this property
      • filterTypeTipText

        public java.lang.String filterTypeTipText()
        Returns a tip text for this property suitable for display in the GUI
        Returns:
        tip text string describing this property
      • setAttsToEliminatePerIteration

        public void setAttsToEliminatePerIteration​(int cRate)
        Set the constant rate of attribute elimination per iteration
        Parameters:
        cRate - the constant rate of attribute elimination per iteration
      • getAttsToEliminatePerIteration

        public int getAttsToEliminatePerIteration()
        Get the constant rate of attribute elimination per iteration
        Returns:
        the constant rate of attribute elimination per iteration
      • setPercentToEliminatePerIteration

        public void setPercentToEliminatePerIteration​(int pRate)
        Set the percentage of attributes to eliminate per iteration
        Parameters:
        pRate - percent of attributes to eliminate per iteration
      • getPercentToEliminatePerIteration

        public int getPercentToEliminatePerIteration()
        Get the percentage rate of attribute elimination per iteration
        Returns:
        the percentage rate of attribute elimination per iteration
      • setPercentThreshold

        public void setPercentThreshold​(int pThresh)
        Set the threshold below which percentage elimination reverts to constant elimination.
        Parameters:
        pThresh - percent of attributes to eliminate per iteration
      • getPercentThreshold

        public int getPercentThreshold()
        Get the threshold below which percentage elimination reverts to constant elimination.
        Returns:
        the threshold below which percentage elimination stops
      • setEpsilonParameter

        public void setEpsilonParameter​(double svmP)
        Set the value of P for SMO
        Parameters:
        svmP - the value of P
      • getEpsilonParameter

        public double getEpsilonParameter()
        Get the value of P used with SMO
        Returns:
        the value of P
      • setToleranceParameter

        public void setToleranceParameter​(double svmT)
        Set the value of T for SMO
        Parameters:
        svmT - the value of T
      • getToleranceParameter

        public double getToleranceParameter()
        Get the value of T used with SMO
        Returns:
        the value of T
      • setComplexityParameter

        public void setComplexityParameter​(double svmC)
        Set the value of C for SMO
        Parameters:
        svmC - the value of C
      • getComplexityParameter

        public double getComplexityParameter()
        Get the value of C used with SMO
        Returns:
        the value of C
      • setFilterType

        public void setFilterType​(SelectedTag newType)
        The filtering mode to pass to SMO
        Parameters:
        newType - the new filtering mode
      • getFilterType

        public SelectedTag getFilterType()
        Get the filtering mode passed to SMO
        Returns:
        the filtering mode
      • buildEvaluator

        public void buildEvaluator​(Instances data)
                            throws java.lang.Exception
        Initializes the evaluator.
        Specified by:
        buildEvaluator in class ASEvaluation
        Parameters:
        data - set of instances serving as training data
        Throws:
        java.lang.Exception - if the evaluator has not been generated successfully
      • evaluateAttribute

        public double evaluateAttribute​(int attribute)
                                 throws java.lang.Exception
        Evaluates an attribute by returning the rank of the square of its coefficient in a linear support vector machine.
        Specified by:
        evaluateAttribute in interface AttributeEvaluator
        Parameters:
        attribute - the index of the attribute to be evaluated
        Returns:
        the "merit" of the attribute
        Throws:
        java.lang.Exception - if the attribute could not be evaluated
      • toString

        public java.lang.String toString()
        Return a description of the evaluator
        Overrides:
        toString in class java.lang.Object
        Returns:
        description as a string
      • main

        public static void main​(java.lang.String[] args)
        Main method for testing this class.
        Parameters:
        args - the options