probabilityMachine.vpm
Class VPMBartsRMI

java.lang.Object
  |
  +--weka.classifiers.Classifier
        |
        +--probabilityMachine.VennProbabilityClassifier
              |
              +--probabilityMachine.vpm.VPMBartsRMI

All Implemented Interfaces:

java.lang.Cloneable, OptionHandler, java.io.Serializable

public class VPMBartsRMI

extends VennProbabilityClassifier

implements OptionHandler

The VPM version of the BartsRMI algorithm. (Only for use on Ovarian Cancer data)

Version:

$Revision: 1.0 $

Author:

David Lindsay (davidl@cs.rhul.ac.uk)

See Also:

Serialized Form

Constructor Summary

VPMBartsRMI()
The amazing VPMBartsRMI classifier

VPMBartsRMI(double rmit, int vennt)
The amazing VPMBartsRMI classifier, used to show how to adapt a classifer to the VPM meta learning framework!

Method Summary

void	buildClassifier(Instances instances) Generates the classifier.
double	calculateRMI(Instance instance) Calculates the Risk of Malignancy Index find ref ? (Jacobs et al)
int	getNumberVennTypes() Gets the number of Venn probability types used!
java.lang.String[]	getOptions() Gets the current settings of VPM.
double	getRMIThreshold() Gets the currently set RMI threshold
java.util.Enumeration	listOptions() Returns an enumeration describing the available options
static void	main(java.lang.String[] argv) Main method for testing this class.
void	setNumberVennTypes(int vennt) Sets the number of Venn probability types used!
void	setOptions(java.lang.String[] options) Parses a given list of options.
void	setRMIThreshold(double rmit) Sets the RMI threshold
java.lang.String	toString() Returns a description of this classifier.
Matrix	vennProbsForInstance(Instance instance) Returns the Venn probability matrix for a given test instance.

Methods inherited from class probabilityMachine.VennProbabilityClassifier

classifyInstance, computeRowOfVPMMatrix, distributionForInstance, printArray, printArray, returnDistribution, returnUpperAndLowerProbability

Methods inherited from class weka.classifiers.Classifier

debugTipText, forName, getDebug, makeCopies, setDebug

Methods inherited from class java.lang.Object

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

Constructor Detail

VPMBartsRMI

public VPMBartsRMI(double rmit,
                   int vennt)

The amazing VPMBartsRMI classifier, used to show how to adapt a classifer to the VPM meta learning framework!

The options for this wonderful algorithm are as follows:
-r threshold
Set the threshold for the RMI (default: 250)

-y num Venn types
Sets the number of types used for the VPM

Parameters:

rmit - the RMI threshold

vennt - the number of Venn probability types used

VPMBartsRMI

public VPMBartsRMI()

The amazing VPMBartsRMI classifier

Method Detail

setRMIThreshold

public void setRMIThreshold(double rmit)

Sets the RMI threshold

getRMIThreshold

public double getRMIThreshold()

Gets the currently set RMI threshold

setNumberVennTypes

public void setNumberVennTypes(int vennt)

Sets the number of Venn probability types used!

getNumberVennTypes

public int getNumberVennTypes()

Gets the number of Venn probability types used!

buildClassifier

public void buildClassifier(Instances instances)
                     throws java.lang.Exception

Generates the classifier.

Specified by:

buildClassifier in class Classifier

Parameters:

instances - set of instances serving as training data

Throws:

java.lang.Exception - if the classifier has not been generated successfully

listOptions

public java.util.Enumeration listOptions()

Returns an enumeration describing the available options

Specified by:

listOptions in interface OptionHandler

Overrides:

listOptions in class Classifier

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:

-R threshold
Set the threshold for the RMI (default: 250)

-V num Venn types
Sets the number of types used for the VPM

Specified by:

setOptions in interface OptionHandler

Overrides:

setOptions in class Classifier

Parameters:

options - the list of options as an array of strings

Throws:

java.lang.Exception - if an option is not supported

getOptions

public java.lang.String[] getOptions()

Gets the current settings of VPM.

Specified by:

getOptions in interface OptionHandler

Overrides:

getOptions in class Classifier

Returns:

an array of strings suitable for passing to setOptions()

calculateRMI

public double calculateRMI(Instance instance)

Calculates the Risk of Malignancy Index find ref ? (Jacobs et al)

vennProbsForInstance

public Matrix vennProbsForInstance(Instance instance)
                            throws java.lang.Exception

Returns the Venn probability matrix for a given test instance.

Specified by:

vennProbsForInstance in class VennProbabilityClassifier

Parameters:

instance - the instance to be classified

Returns:

the Venn probability matrix

Throws:

java.lang.Exception - no training instances

toString

public java.lang.String toString()

Returns a description of this classifier.

Overrides:

toString in class java.lang.Object

Returns:

a description of this classifier as a string.

main

public static void main(java.lang.String[] argv)

Main method for testing this class.

Parameters:

argv - should contain command line arguments for evaluation (see Evaluation).