de.jstacs.classifiers.assessment

Class KFoldCrossValidation

java.lang.Object

de.jstacs.classifiers.assessment.ClassifierAssessment<KFoldCrossValidationAssessParameterSet>

de.jstacs.classifiers.assessment.KFoldCrossValidation

public class KFoldCrossValidation
extends ClassifierAssessment<KFoldCrossValidationAssessParameterSet>

This class implements a k-fold crossvalidation. A k-fold crossvalidation assesses classifiers using the following methodology. The user supplies datasets (one for each class the classifiers are capable to distinguish). The data is randomly, mutually exclusive partitioned into k parts. Each of those parts is used once as a test dataset while the remaining k-1 parts are used as train dataset. In each of the k iterations, the train datasets are used to train the classifier and the test datasets are used to assess the classifier's performance to predict the elements therein. Additional the user has to define which assessment measures should be used.

Author:

Andre Gohr (bioinf (nospam:.) ag (nospam:@) googlemail (nospam:.) com), Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.classifiers.assessment.ClassifierAssessment

myAbstractClassifier, myModel, myTempMeanResultSets, skipLastClassifiersDuringClassifierTraining

Constructor Summary

Constructors

Modifier	Constructor and Description
	KFoldCrossValidation(AbstractClassifier... aCs) Creates a new KFoldCrossValidation from a set of AbstractClassifiers.
	KFoldCrossValidation(AbstractClassifier[] aCs, boolean buildClassifiersByCrossProduct, TrainableStatisticalModel[]... aMs) This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given TrainableStatisticalModels by a KFoldCrossValidation .
protected	KFoldCrossValidation(AbstractClassifier[] aCs, TrainableStatisticalModel[][] aMs, boolean buildClassifiersByCrossProduct, boolean checkAlphabetConsistencyAndLength) Creates a new KFoldCrossValidation from an array of AbstractClassifiers and a two-dimensional array of TrainableStatisticalModel s, which are combined to additional classifiers.
	KFoldCrossValidation(boolean buildClassifiersByCrossProduct, TrainableStatisticalModel[]... aMs) Creates a new KFoldCrossValidation from a set of TrainableStatisticalModels.

Method Summary

Modifier and Type	Method and Description
ListResult	assessWithPredefinedSplits(NumericalPerformanceMeasureParameterSet mp, ClassifierAssessmentAssessParameterSet caaps, ProgressUpdater pU, DataSet[][] splitData, double[][][] splitWeights) This method implements a k-fold crossvalidation on previously split data.
protected void	evaluateClassifier(NumericalPerformanceMeasureParameterSet mp, KFoldCrossValidationAssessParameterSet assessPS, DataSet[] s, double[][] weights, ProgressUpdater pU) Evaluates a classifier.
KFoldCrossValidationAssessParameterSet	getAssessParameterSet() This method returns an instance of ClassifierAssessmentAssessParameterSet that can be used in the assess methods.

Methods inherited from class de.jstacs.classifiers.assessment.ClassifierAssessment

assess, assess, assess, assess, getClassifier, getNameOfAssessment, prepareAssessment, test, train

Methods inherited from class java.lang.Object

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

Constructor Detail

KFoldCrossValidation

protected KFoldCrossValidation(AbstractClassifier[] aCs,
                               TrainableStatisticalModel[][] aMs,
                               boolean buildClassifiersByCrossProduct,
                               boolean checkAlphabetConsistencyAndLength)
                        throws IllegalArgumentException,
                               WrongAlphabetException,
                               CloneNotSupportedException,
                               ClassDimensionException

Creates a new KFoldCrossValidation from an array of AbstractClassifiers and a two-dimensional array of TrainableStatisticalModel s, which are combined to additional classifiers. If buildClassifiersByCrossProduct is true, the cross-product of all TrainableStatisticalModels in aMs is built to obtain these classifiers.

Parameters:

aCs - the predefined classifiers

aMs - the TrainableStatisticalModels that are used to build additional classifiers

buildClassifiersByCrossProduct - Determines how classifiers are constructed using the given models. Suppose a k-class problem. In this case, each classifier is supposed to consist of k models, one responsible for each class.
Let S_i be the set of all models in aMs[i]. Let S be the set S_1 x S_2 x ... x S_k (cross-product).

true: all possible classifiers consisting of a subset (set of k models) of S are constructed
false: one classifier consisting of the models aMs[0][i],aMs[1][i],..., aMs[k][i] for a fixed i is constructed. In this case, all second dimensions of aMs have to be equal, say m. In total m classifiers are constructed.

checkAlphabetConsistencyAndLength - indicates if alphabets and lengths shall be checked for consistency

Throws:

IllegalArgumentException - if the classifiers have different lengths

WrongAlphabetException - if the classifiers use different alphabets

CloneNotSupportedException - if something went wrong while cloning

ClassDimensionException - if there is something wrong with the class dimension of the classifier

See Also:

ClassifierAssessment.ClassifierAssessment(AbstractClassifier[], TrainableStatisticalModel[][], boolean, boolean)

KFoldCrossValidation

public KFoldCrossValidation(AbstractClassifier... aCs)
                     throws IllegalArgumentException,
                            WrongAlphabetException,
                            CloneNotSupportedException,
                            ClassDimensionException

Creates a new KFoldCrossValidation from a set of AbstractClassifiers.

Parameters:

aCs - contains the classifiers to be assessed.
If model based classifiers are trained, the order of models in classifiers determines, which model will be trained using which data set in method assess( ... ).
For a two-class problem, it is recommended

• to initiate the classifiers with models in order (foreground model (positive class), background model (negative class))
• to initiate an assessment object using models in order (foreground model (positive class), background model (negative class))
• to give data s in order (s[0] contains foreground data, s[1] contains background data)

Throws:

IllegalArgumentException - if the classifiers have different lengths

WrongAlphabetException - if not all given classifiers are defined on the same AlphabetContainer

CloneNotSupportedException - if something went wrong while cloning

ClassDimensionException - if there is something wrong with the class dimension of the classifier

See Also:

ClassifierAssessment.ClassifierAssessment(AbstractClassifier...)

KFoldCrossValidation

public KFoldCrossValidation(boolean buildClassifiersByCrossProduct,
                            TrainableStatisticalModel[]... aMs)
                     throws IllegalArgumentException,
                            WrongAlphabetException,
                            CloneNotSupportedException,
                            ClassDimensionException

Creates a new KFoldCrossValidation from a set of TrainableStatisticalModels. The argument buildClassifiersByCrossProduct determines how these TrainableStatisticalModels are combined to classifiers.

Parameters:

buildClassifiersByCrossProduct -
Determines how classifiers are constructed using the given models. Suppose a k-class problem. In this case, each classifier is supposed to consist of k models, one responsible for each class.
Let S_i be the set of all models in aMs[i]. Let S be the set S_1 x S_2 x ... x S_k (cross-product).

true: all possible classifiers consisting of a subset (set of k models) of S are constructed
false: one classifier consisting of the models aMs[0][i],aMs[1][i],..., aMs[k][i] for a fixed i is constructed. In this case, all second dimensions of aMs have to be equal, say m. In total m classifiers are constructed.

aMs -
Contains the models in the following way (suppose a k-class problem): the first dimension encodes the class (here it is k), the second dimension (aMs[i]) contains the models according to class i.
If models are trained directly (during assessment), the order of given models during initiation of this assessment object determines, which data set will be used for training which model. In general the first model will be trained using the first data set in s... .
For a two-class problem, it is recommended

• to initiate the classifiers with models in order (foreground model (positive class), background model (negative class))
• to initiate an assessment object using models in order (foreground model (positive class), background model (negative class))
• to give data s in order (s[0] contains foreground data, s[1] contains background data)

Throws:

IllegalArgumentException - if the classifiers have different lengths

WrongAlphabetException - if not all given classifiers are defined on the same AlphabetContainer

CloneNotSupportedException - if something went wrong while cloning

ClassDimensionException - if there is something wrong with the class dimension of the classifier

See Also:

ClassifierAssessment.ClassifierAssessment(boolean, TrainableStatisticalModel[][])

KFoldCrossValidation

public KFoldCrossValidation(AbstractClassifier[] aCs,
                            boolean buildClassifiersByCrossProduct,
                            TrainableStatisticalModel[]... aMs)
                     throws IllegalArgumentException,
                            WrongAlphabetException,
                            CloneNotSupportedException,
                            ClassDimensionException

This constructor allows to assess a collection of given AbstractClassifiers and those constructed using the given TrainableStatisticalModels by a KFoldCrossValidation .

Parameters:

aCs - contains some AbstractClassifiers that should be assessed in addition to the AbstractClassifier constructed using the given TrainableStatisticalModels

buildClassifiersByCrossProduct -
Determines how classifiers are constructed using the given models. Suppose a k-class problem. In this case, each classifier is supposed to consist of k models, one responsible for each class.
Let S_i be the set of all models in aMs[i]. Let S be the set S_1 x S_2 x ... x S_k (cross-product).

true: all possible classifiers consisting of a subset (set of k models) of S are constructed
false: one classifier consisting of the models aMs[0][i],aMs[1][i],..., aMs[k][i] for a fixed i is constructed. In this case, all second dimensions of aMs have to be equal, say m. In total m classifiers are constructed.

aMs -
Contains the models in the following way (suppose a k-class problem): the first dimension encodes the class (here it is k), the second dimension (aMs[i]) contains the models according to class i.
If models are trained directly (during assessment), the order of given models during initiation of this assessment object determines, which data set will be used for training which model. In general the first model will be trained using the first data set in s... .
For a two-class problem, it is recommended

• to initiate the classifiers with models in order (foreground model (positive class), background model (negative class))
• to initiate an assessment object using models in order (foreground model (positive class), background model (negative class))
• to give data s in order (s[0] contains foreground data, s[1] contains background data)

Throws:

IllegalArgumentException - if the classifiers have different lengths

WrongAlphabetException - if not all given classifiers are defined on the same AlphabetContainer

CloneNotSupportedException - if something went wrong while cloning

ClassDimensionException - if there is something wrong with the class dimension of the classifier

See Also:

ClassifierAssessment.ClassifierAssessment(AbstractClassifier[], boolean, TrainableStatisticalModel[][])

Method Detail

evaluateClassifier

protected void evaluateClassifier(NumericalPerformanceMeasureParameterSet mp,
                                  KFoldCrossValidationAssessParameterSet assessPS,
                                  DataSet[] s,
                                  double[][] weights,
                                  ProgressUpdater pU)
                           throws IllegalArgumentException,
                                  Exception

Evaluates a classifier.

Specified by:

evaluateClassifier in class ClassifierAssessment<KFoldCrossValidationAssessParameterSet>

Parameters:

mp - defines which performance measures are used to assess classifiers

pU - the progress updater which shows the progress of the k-fold crossvalidation

s - contains the data to be used for assessment. The order of data sets is important.
If model based classifiers are trained, the order of the models in the classifiers determines, which model will be trained using which data set. The first model in the classifier will be trained using the first data set in s. If the models are trained directly, the order of the given models during initiation of this assessment object determines, which data set will be used for training which model. In general the first model will be trained using the first data set in s... .
For a two-class problem, it is recommended

• to initiate the classifiers with models in order (foreground model (positive class), background model (negative class))
• to initiate an assessment object using models in order (foreground model (positive class), background model (negative class))
• to give data s in order (s[0] contains foreground data, s[1] contains background data)

assessPS - contains parameters for a run of this KFoldCrossValidation. Must be of type KFoldCrossValidationAssessParameterSet.

weights - the (non-negative) weights for the data; weight for each data set (first dimension) and each sequence (second dimension), can be null which is the same as weight 1 for all sequences in all data sets

Throws:

IllegalArgumentException - if the given assessPS is not of type KFoldCrossValidationAssessParameterSet

Exception - if something went wrong

See Also:

ClassifierAssessment.evaluateClassifier(NumericalPerformanceMeasureParameterSet, ClassifierAssessmentAssessParameterSet, DataSet[], double[][], ProgressUpdater)

assessWithPredefinedSplits

public ListResult assessWithPredefinedSplits(NumericalPerformanceMeasureParameterSet mp,
                                             ClassifierAssessmentAssessParameterSet caaps,
                                             ProgressUpdater pU,
                                             DataSet[][] splitData,
                                             double[][][] splitWeights)
                                      throws Exception

This method implements a k-fold crossvalidation on previously split data. This might be useful if you like to compare the results of your classifier(s) with those of a previous study in a paper or manuscript.

Parameters:

mp - defines which performance measures are used to assess classifiers

caaps - contains the defined element length and choice whether an exception should be thrown if a measure could not be computed

pU - the progress updater which shows the progress of the k-fold crossvalidation

splitData - the previously split data; splitData[i] contains the splits for class i; therefore the length of each subarray splitData[i] has to to be identical

splitWeights - the (non-negative) weights for the previously split data; weight for each split (first dimension) of each data set (second dimension) and each sequence (third dimension), can be null which is the same as weight 1 for all sequences in all data sets

Returns:

the result packed in a ListResult

Throws:

Exception - if something went wrong

getAssessParameterSet

public KFoldCrossValidationAssessParameterSet getAssessParameterSet()
                                                             throws Exception

Description copied from class: ClassifierAssessment

This method returns an instance of ClassifierAssessmentAssessParameterSet that can be used in the assess methods.

Specified by:

getAssessParameterSet in class ClassifierAssessment<KFoldCrossValidationAssessParameterSet>

Returns:

an instance of ClassifierAssessmentAssessParameterSet that can be used in the assess methods.

Throws:

Exception - if the parameter set could not be created properly

See Also:

ClassifierAssessment.assess(NumericalPerformanceMeasureParameterSet, ClassifierAssessmentAssessParameterSet, DataSet...), ClassifierAssessment.assess(NumericalPerformanceMeasureParameterSet, ClassifierAssessmentAssessParameterSet, ProgressUpdater, DataSet[]), ClassifierAssessment.assess(NumericalPerformanceMeasureParameterSet, ClassifierAssessmentAssessParameterSet, ProgressUpdater, DataSet[], double[][])