de.jstacs.classifiers

Class MappingClassifier

java.lang.Object

de.jstacs.classifiers.AbstractClassifier

de.jstacs.classifiers.AbstractScoreBasedClassifier

de.jstacs.classifiers.MappingClassifier

All Implemented Interfaces:

Storable, Cloneable

public class MappingClassifier
extends AbstractScoreBasedClassifier

This class allows the user to train the classifier on a given number of classes and to evaluate the classifier on a smaller number of classes by mapping classes together. For instance the user has a classifier for 3 classes, but likes to evaluate whether the classifier is able to discriminate between class 1 and class 2 and 3. This is a good example where to use this class. The user has to create its 3-class-classifier, create an instance of this class using its classifier, map the test data sets together ( mapDataSet(DataSet[])) and invoke AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet, boolean, DataSet...) with these mapped DataSet. Alternatively, the method AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet, boolean, DataSet...) can be used directly and the DataSets will be mapped internally (i.e. inside the evaluate method).

Author:

Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.classifiers.AbstractScoreBasedClassifier

AbstractScoreBasedClassifier.DoubleTableResult

Constructor Summary

Constructors

Constructor and Description
MappingClassifier(AbstractScoreBasedClassifier classifier, int... mapping) Creates a new MappingClassifier from a given classifier and a class mapping.
MappingClassifier(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	extractFurtherClassifierInfosFromXML(StringBuffer xml) Extracts further information of a classifier from an XML representation.
CategoricalResult[]	getClassifierAnnotation() Returns an array of Results of dimension AbstractClassifier.getNumberOfClasses() that contains information about the classifier and for each class. res[0] = new CategoricalResult( "classifier", "the kind of classifier", getInstanceName() ); res[1] = new CategoricalResult( "class info 0", "some information about the class", "info0" ); res[2] = new CategoricalResult( "class info 1", "some information about the class", "info1" ); ...
protected StringBuffer	getFurtherClassifierInfos() This method returns further information of a classifier as a StringBuffer.
String	getInstanceName() Returns a short description of the classifier.
NumericalResultSet	getNumericalCharacteristics() Returns the subset of numerical values that are also returned by AbstractClassifier.getCharacteristics().
protected boolean	getResults(LinkedList list, DataSet[] s, double[][] weights, AbstractPerformanceMeasureParameterSet<? extends PerformanceMeasure> params, boolean exceptionIfNotComputeable) This method computes the results for any evaluation of the classifier.
protected double	getScore(Sequence seq, int i, boolean check) This method returns the score for a given Sequence and a given class.
protected String	getXMLTag() Returns the String that is used as tag for the XML representation of the classifier.
boolean	isInitialized() This method gives information about the state of the classifier.
DataSet[]	mapDataSet(DataSet[] s) This method maps the given DataSets to the internal classes.
double[][]	mapWeights(double[][] w) This method maps the given Sequence weights to the internal classes.
void	train(DataSet[] s, double[][] weights) This method trains a classifier over an array of weighted DataSet s.

Methods inherited from class de.jstacs.classifiers.AbstractScoreBasedClassifier

check, check, classify, classify, clone, createDefaultClassWeights, getClassWeight, getClassWeights, getMultiClassScores, getNumberOfClasses, getPValue, getPValue, getScore, getScores, setClassWeights, setClassWeights, setThresholdClassWeights

Methods inherited from class de.jstacs.classifiers.AbstractClassifier

classify, evaluate, evaluate, getAlphabetContainer, getCharacteristics, getLength, toXML, train

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MappingClassifier

public MappingClassifier(AbstractScoreBasedClassifier classifier,
                         int... mapping)
                  throws CloneNotSupportedException

Creates a new MappingClassifier from a given classifier and a class mapping.

Parameters:

classifier - the internal used classifier

mapping - the mapping from the classes of the internal classifier to the classes of this classifier

Throws:

CloneNotSupportedException - if something went wrong while cloning the classifier

MappingClassifier

public MappingClassifier(StringBuffer representation)
                  throws NonParsableException

The standard constructor for the interface Storable. Creates a new MappingClassifier out of its XML representation.

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the MappingClassifier could not be reconstructed out of the XML representation (the StringBuffer representation could not be parsed)

See Also:

AbstractScoreBasedClassifier.AbstractScoreBasedClassifier(StringBuffer), Storable

Method Detail

extractFurtherClassifierInfosFromXML

protected void extractFurtherClassifierInfosFromXML(StringBuffer xml)
                                             throws NonParsableException

Description copied from class: AbstractClassifier

Extracts further information of a classifier from an XML representation. This method is used by the method AbstractClassifier.fromXML(StringBuffer) and should not be made public.

Overrides:

extractFurtherClassifierInfosFromXML in class AbstractScoreBasedClassifier

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the information could not be parsed out of the XML representation (the StringBuffer could not be parsed)

See Also:

AbstractClassifier.fromXML(StringBuffer)

getFurtherClassifierInfos

protected StringBuffer getFurtherClassifierInfos()

Description copied from class: AbstractClassifier

This method returns further information of a classifier as a StringBuffer. This method is used by the method AbstractClassifier.toXML() and should not be made public.

Overrides:

getFurtherClassifierInfos in class AbstractScoreBasedClassifier

Returns:

further information of a classifier as a StringBuffer

See Also:

AbstractClassifier.toXML()

getScore

protected double getScore(Sequence seq,
                          int i,
                          boolean check)
                   throws IllegalArgumentException,
                          NotTrainedException,
                          Exception

Description copied from class: AbstractScoreBasedClassifier

This method returns the score for a given Sequence and a given class.

Specified by:

getScore in class AbstractScoreBasedClassifier

Parameters:

seq - the Sequence

i - the index of the class

check - the switch to decide whether to check AlphabetContainer and the length of the Sequence or not

Returns:

the score for a given Sequence and a given class

Throws:

IllegalArgumentException - if something is wrong with the Sequence seq

NotTrainedException - if the classifier is not trained

Exception - if something went wrong

getClassifierAnnotation

public CategoricalResult[] getClassifierAnnotation()

Description copied from class: AbstractClassifier

Returns an array of Results of dimension AbstractClassifier.getNumberOfClasses() that contains information about the classifier and for each class.

res[0] = new CategoricalResult( "classifier", "the kind of classifier", getInstanceName() );
res[1] = new CategoricalResult( "class info 0", "some information about the class", "info0" );
res[2] = new CategoricalResult( "class info 1", "some information about the class", "info1" );
...

Specified by:

getClassifierAnnotation in class AbstractClassifier

Returns:

an array of Results that contains information about the classifier

getInstanceName

public String getInstanceName()

Description copied from class: AbstractClassifier

Returns a short description of the classifier.

Specified by:

getInstanceName in class AbstractClassifier

Returns:

a short description of the classifier

getNumericalCharacteristics

public NumericalResultSet getNumericalCharacteristics()
                                               throws Exception

Description copied from class: AbstractClassifier

Returns the subset of numerical values that are also returned by AbstractClassifier.getCharacteristics().

Specified by:

getNumericalCharacteristics in class AbstractClassifier

Returns:

the numerical characteristics

Throws:

Exception - if some of the characteristics could not be defined

getXMLTag

protected String getXMLTag()

Description copied from class: AbstractClassifier

Returns the String that is used as tag for the XML representation of the classifier. This method is used by the methods AbstractClassifier.fromXML(StringBuffer) and AbstractClassifier.toXML().

Specified by:

getXMLTag in class AbstractClassifier

Returns:

the String that is used as tag for the XML representation of the classifier

isInitialized

public boolean isInitialized()

Description copied from class: AbstractClassifier

This method gives information about the state of the classifier.

Specified by:

isInitialized in class AbstractClassifier

Returns:

true if the classifier is initialized and therefore able to classify sequences, otherwise false

train

public void train(DataSet[] s,
                  double[][] weights)
           throws Exception

Description copied from class: AbstractClassifier

This method trains a classifier over an array of weighted DataSet s. That is why the following has to be fulfilled:

• s.length == weights.length
• and for all i: weights[i] == null || s[i].getNumberOfElements() == weights[i].length.

This method should work non-incrementally as the method AbstractClassifier.train(DataSet...).

This method should check that the DataSets are defined over the underlying alphabet and length.

Specified by:

train in class AbstractClassifier

Parameters:

s - an array of DataSets

weights - the weights for the DataSets

Throws:

Exception - if the weights are incorrect or the training did not succeed

See Also:

AbstractClassifier.train(DataSet...)

getResults

protected boolean getResults(LinkedList list,
                             DataSet[] s,
                             double[][] weights,
                             AbstractPerformanceMeasureParameterSet<? extends PerformanceMeasure> params,
                             boolean exceptionIfNotComputeable)
                      throws Exception

Description copied from class: AbstractClassifier

This method computes the results for any evaluation of the classifier.

Overrides:

getResults in class AbstractScoreBasedClassifier

Parameters:

list - a list adding the results

s - the array of DataSets

weights - the weights of the sequences for each data set

params - the current parameters

exceptionIfNotComputeable - indicates the method throws an Exception if a measure could not be computed

Returns:

a boolean indicating if all results are numerical

Throws:

Exception - if something went wrong

See Also:

AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet, boolean, DataSet[], double[][]), NumericalResult, Result

mapDataSet

public DataSet[] mapDataSet(DataSet[] s)

This method maps the given DataSets to the internal classes.

Parameters:

s - the array of DataSets

Returns:

the array of data sets corresponding to the classes

mapWeights

public double[][] mapWeights(double[][] w)

This method maps the given Sequence weights to the internal classes.

Parameters:

w - the array of weights

Returns:

the array of weights corresponding to the classes