weka.classifiers
Class Evaluation

java.lang.Object
  |
  +--weka.classifiers.Evaluation

All Implemented Interfaces:

Summarizable

public class Evaluation

extends java.lang.Object

implements Summarizable

Class for evaluating machine learning models.

-------------------------------------------------------------------

General options when evaluating a learning scheme from the command-line:

-t filename
Name of the file with the training data. (required)

-T filename
Name of the file with the test data. If missing a cross-validation is performed.

-c index
Index of the class attribute (1, 2, ...; default: last).

-x number
The number of folds for the cross-validation (default: 10).

-s seed
Random number seed for the cross-validation (default: 1).

-m filename
The name of a file containing a cost matrix.

-l filename
Loads classifier from the given file.

-d filename
Saves classifier built from the training data into the given file.

-v
Outputs no statistics for the training data.

-o
Outputs statistics only, not the classifier.

-i
Outputs information-retrieval statistics per class.

-k
Outputs information-theoretic statistics.

-p range
Outputs predictions for test instances, along with the attributes in the specified range (and nothing else). Use '-p 0' if no attributes are desired.

-r
Outputs cumulative margin distribution (and nothing else).

-g
Only for classifiers that implement "Graphable." Outputs the graph representation of the classifier (and nothing else).

-------------------------------------------------------------------

Example usage as the main of a classifier (called FunkyClassifier):

 public static void main(String [] args) {
   try {
     Classifier scheme = new FunkyClassifier();
     System.out.println(Evaluation.evaluateModel(scheme, args));
   } catch (Exception e) {
     System.err.println(e.getMessage());
   }
 }
 

------------------------------------------------------------------

Example usage from within an application:

 Instances trainInstances = ... instances got from somewhere
 Instances testInstances = ... instances got from somewhere
 Classifier scheme = ... scheme got from somewhere

 Evaluation evaluation = new Evaluation(trainInstances);
 evaluation.evaluateModel(scheme, testInstances);
 System.out.println(evaluation.toSummaryString());
 

Version:

$Revision: 1.49 $

Author:

Eibe Frank (eibe@cs.waikato.ac.nz), Len Trigg (trigg@cs.waikato.ac.nz)

Constructor Summary

Evaluation(Instances data)
Initializes all the counters for the evaluation.

Evaluation(Instances data, CostMatrix costMatrix)
Initializes all the counters for the evaluation and also takes a cost matrix as parameter.

Method Summary

double	avgCost() Gets the average cost, that is, total cost of misclassifications (incorrect plus unclassified) over the total number of instances.
double[][]	confusionMatrix() Returns a copy of the confusion matrix.
double	correct() Gets the number of instances correctly classified (that is, for which a correct prediction was made).
double	correlationCoefficient() Returns the correlation coefficient if the class is numeric.
void	crossValidateModel(Classifier classifier, Instances data, int numFolds, java.util.Random random) Performs a (stratified if class is nominal) cross-validation for a classifier on a set of instances.
void	crossValidateModel(java.lang.String classifierString, Instances data, int numFolds, java.lang.String[] options, java.util.Random random) Performs a (stratified if class is nominal) cross-validation for a classifier on a set of instances.
boolean	equals(java.lang.Object obj) Tests whether the current evaluation object is equal to another evaluation object
double	errorRate() Returns the estimated error rate or the root mean squared error (if the class is numeric).
void	evaluateModel(Classifier classifier, Instances data) Evaluates the classifier on a given set of instances.
static java.lang.String	evaluateModel(Classifier classifier, java.lang.String[] options) Evaluates a classifier with the options given in an array of strings.
static java.lang.String	evaluateModel(java.lang.String classifierString, java.lang.String[] options) Evaluates a classifier with the options given in an array of strings.
double	evaluateModelOnce(Classifier classifier, Instance instance) Evaluates the classifier on a single instance.
double	evaluateModelOnce(double[] dist, Instance instance) Evaluates the supplied distribution on a single instance.
void	evaluateModelOnce(double prediction, Instance instance) Evaluates the supplied prediction on a single instance.
double	falseNegativeRate(int classIndex) Calculate the false negative rate with respect to a particular class.
double	falsePositiveRate(int classIndex) Calculate the false positive rate with respect to a particular class.
double	fMeasure(int classIndex) Calculate the F-Measure with respect to a particular class.
double	incorrect() Gets the number of instances incorrectly classified (that is, for which an incorrect prediction was made).
double	kappa() Returns value of kappa statistic if class is nominal.
double	KBInformation() Return the total Kononenko & Bratko Information score in bits
double	KBMeanInformation() Return the Kononenko & Bratko Information score in bits per instance.
double	KBRelativeInformation() Return the Kononenko & Bratko Relative Information score
static void	main(java.lang.String[] args) A test method for this class.
double	meanAbsoluteError() Returns the mean absolute error.
double	meanPriorAbsoluteError() Returns the mean absolute error of the prior.
double	numFalseNegatives(int classIndex) Calculate number of false negatives with respect to a particular class.
double	numFalsePositives(int classIndex) Calculate number of false positives with respect to a particular class.
double	numInstances() Gets the number of test instances that had a known class value (actually the sum of the weights of test instances with known class value).
double	numTrueNegatives(int classIndex) Calculate the number of true negatives with respect to a particular class.
double	numTruePositives(int classIndex) Calculate the number of true positives with respect to a particular class.
double	pctCorrect() Gets the percentage of instances correctly classified (that is, for which a correct prediction was made).
double	pctIncorrect() Gets the percentage of instances incorrectly classified (that is, for which an incorrect prediction was made).
double	pctUnclassified() Gets the percentage of instances not classified (that is, for which no prediction was made by the classifier).
double	precision(int classIndex) Calculate the precision with respect to a particular class.
double	priorEntropy() Calculate the entropy of the prior distribution
double	recall(int classIndex) Calculate the recall with respect to a particular class.
double	relativeAbsoluteError() Returns the relative absolute error.
double	rootMeanPriorSquaredError() Returns the root mean prior squared error.
double	rootMeanSquaredError() Returns the root mean squared error.
double	rootRelativeSquaredError() Returns the root relative squared error if the class is numeric.
void	setPriors(Instances train) Sets the class prior probabilities
double	SFEntropyGain() Returns the total SF, which is the null model entropy minus the scheme entropy.
double	SFMeanEntropyGain() Returns the SF per instance, which is the null model entropy minus the scheme entropy, per instance.
double	SFMeanPriorEntropy() Returns the entropy per instance for the null model
double	SFMeanSchemeEntropy() Returns the entropy per instance for the scheme
double	SFPriorEntropy() Returns the total entropy for the null model
double	SFSchemeEntropy() Returns the total entropy for the scheme
java.lang.String	toClassDetailsString()
java.lang.String	toClassDetailsString(java.lang.String title) Generates a breakdown of the accuracy for each class, incorporating various information-retrieval statistics, such as true/false positive rate, precision/recall/F-Measure.
java.lang.String	toCumulativeMarginDistributionString() Output the cumulative margin distribution as a string suitable for input for gnuplot or similar package.
java.lang.String	toMatrixString() Calls toMatrixString() with a default title.
java.lang.String	toMatrixString(java.lang.String title) Outputs the performance statistics as a classification confusion matrix.
java.lang.String	toSummaryString() Calls toSummaryString() with no title and no complexity stats
java.lang.String	toSummaryString(boolean printComplexityStatistics) Calls toSummaryString() with a default title.
java.lang.String	toSummaryString(java.lang.String title, boolean printComplexityStatistics) Outputs the performance statistics in summary form.
double	totalCost() Gets the total cost, that is, the cost of each prediction times the weight of the instance, summed over all instances.
double	trueNegativeRate(int classIndex) Calculate the true negative rate with respect to a particular class.
double	truePositiveRate(int classIndex) Calculate the true positive rate with respect to a particular class.
double	unclassified() Gets the number of instances not classified (that is, for which no prediction was made by the classifier).
void	updatePriors(Instance instance) Updates the class prior probabilities (when incrementally training)

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Evaluation

public Evaluation(Instances data)
           throws java.lang.Exception

Initializes all the counters for the evaluation.

Parameters:

data - set of training instances, to get some header information and prior class distribution information

Throws:

java.lang.Exception - if the class is not defined

Evaluation

public Evaluation(Instances data,
                  CostMatrix costMatrix)
           throws java.lang.Exception

Initializes all the counters for the evaluation and also takes a cost matrix as parameter.

Parameters:

data - set of instances, to get some header information

costMatrix - the cost matrix---if null, default costs will be used

Throws:

java.lang.Exception - if cost matrix is not compatible with data, the class is not defined or the class is numeric

Method Detail

confusionMatrix

public double[][] confusionMatrix()

Returns a copy of the confusion matrix.

Returns:

a copy of the confusion matrix as a two-dimensional array

crossValidateModel

public void crossValidateModel(Classifier classifier,
                               Instances data,
                               int numFolds,
                               java.util.Random random)
                        throws java.lang.Exception

Performs a (stratified if class is nominal) cross-validation for a classifier on a set of instances.

Parameters:

classifier - the classifier with any options set.

data - the data on which the cross-validation is to be performed

numFolds - the number of folds for the cross-validation

random - random number generator for randomization

Throws:

java.lang.Exception - if a classifier could not be generated successfully or the class is not defined

crossValidateModel

public void crossValidateModel(java.lang.String classifierString,
                               Instances data,
                               int numFolds,
                               java.lang.String[] options,
                               java.util.Random random)
                        throws java.lang.Exception

Performs a (stratified if class is nominal) cross-validation for a classifier on a set of instances.

Parameters:

data - the data on which the cross-validation is to be performed

numFolds - the number of folds for the cross-validation

options - the options to the classifier. Any options

random - the random number generator for randomizing the data accepted by the classifier will be removed from this array.

Throws:

java.lang.Exception - if a classifier could not be generated successfully or the class is not defined

evaluateModel

public static java.lang.String evaluateModel(java.lang.String classifierString,
                                             java.lang.String[] options)
                                      throws java.lang.Exception

Evaluates a classifier with the options given in an array of strings.

Valid options are:

-t filename
Name of the file with the training data. (required)

-T filename
Name of the file with the test data. If missing a cross-validation is performed.

-c index
Index of the class attribute (1, 2, ...; default: last).

-x number
The number of folds for the cross-validation (default: 10).

-s seed
Random number seed for the cross-validation (default: 1).

-m filename
The name of a file containing a cost matrix.

-l filename
Loads classifier from the given file.

-d filename
Saves classifier built from the training data into the given file.

-v
Outputs no statistics for the training data.

-o
Outputs statistics only, not the classifier.

-i
Outputs detailed information-retrieval statistics per class.

-k
Outputs information-theoretic statistics.

-p range
Outputs predictions for test instances, along with the attributes in the specified range (and nothing else). Use '-p 0' if no attributes are desired.

-r
Outputs cumulative margin distribution (and nothing else).

-g
Only for classifiers that implement "Graphable." Outputs the graph representation of the classifier (and nothing else).

Parameters:

classifierString - class of machine learning classifier as a string

options - the array of string containing the options

Returns:

a string describing the results

Throws:

java.lang.Exception - if model could not be evaluated successfully

main

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

A test method for this class. Just extracts the first command line argument as a classifier class name and calls evaluateModel.

Parameters:

args - an array of command line arguments, the first of which must be the class name of a classifier.

evaluateModel

public static java.lang.String evaluateModel(Classifier classifier,
                                             java.lang.String[] options)
                                      throws java.lang.Exception

Evaluates a classifier with the options given in an array of strings.

Valid options are:

-t name of training file
Name of the file with the training data. (required)

-T name of test file
Name of the file with the test data. If missing a cross-validation is performed.

-c class index
Index of the class attribute (1, 2, ...; default: last).

-x number of folds
The number of folds for the cross-validation (default: 10).

-s random number seed
Random number seed for the cross-validation (default: 1).

-m file with cost matrix
The name of a file containing a cost matrix.

-l name of model input file
Loads classifier from the given file.

-d name of model output file
Saves classifier built from the training data into the given file.

-v
Outputs no statistics for the training data.

-o
Outputs statistics only, not the classifier.

-i
Outputs detailed information-retrieval statistics per class.

-k
Outputs information-theoretic statistics.

-p
Outputs predictions for test instances (and nothing else).

-r
Outputs cumulative margin distribution (and nothing else).

-g
Only for classifiers that implement "Graphable." Outputs the graph representation of the classifier (and nothing else).

Parameters:

classifier - machine learning classifier

options - the array of string containing the options

Returns:

a string describing the results

Throws:

java.lang.Exception - if model could not be evaluated successfully

evaluateModel

public void evaluateModel(Classifier classifier,
                          Instances data)
                   throws java.lang.Exception

Evaluates the classifier on a given set of instances.

Parameters:

classifier - machine learning classifier

data - set of test instances for evaluation

Throws:

java.lang.Exception - if model could not be evaluated successfully

evaluateModelOnce

public double evaluateModelOnce(Classifier classifier,
                                Instance instance)
                         throws java.lang.Exception

Evaluates the classifier on a single instance.

Parameters:

classifier - machine learning classifier

instance - the test instance to be classified

Returns:

the prediction made by the clasifier

Throws:

java.lang.Exception - if model could not be evaluated successfully or the data contains string attributes

evaluateModelOnce

public double evaluateModelOnce(double[] dist,
                                Instance instance)
                         throws java.lang.Exception

Evaluates the supplied distribution on a single instance.

Parameters:

dist - the supplied distribution

instance - the test instance to be classified

Throws:

java.lang.Exception - if model could not be evaluated successfully

evaluateModelOnce

public void evaluateModelOnce(double prediction,
                              Instance instance)
                       throws java.lang.Exception

Evaluates the supplied prediction on a single instance.

Parameters:

prediction - the supplied prediction

instance - the test instance to be classified

Throws:

java.lang.Exception - if model could not be evaluated successfully

numInstances

public final double numInstances()

Gets the number of test instances that had a known class value (actually the sum of the weights of test instances with known class value).

Returns:

the number of test instances with known class

incorrect

public final double incorrect()

Gets the number of instances incorrectly classified (that is, for which an incorrect prediction was made). (Actually the sum of the weights of these instances)

Returns:

the number of incorrectly classified instances

pctIncorrect

public final double pctIncorrect()

Gets the percentage of instances incorrectly classified (that is, for which an incorrect prediction was made).

Returns:

the percent of incorrectly classified instances (between 0 and 100)

totalCost

public final double totalCost()

Gets the total cost, that is, the cost of each prediction times the weight of the instance, summed over all instances.

Returns:

the total cost

avgCost

public final double avgCost()

Gets the average cost, that is, total cost of misclassifications (incorrect plus unclassified) over the total number of instances.

Returns:

the average cost.

correct

public final double correct()

Gets the number of instances correctly classified (that is, for which a correct prediction was made). (Actually the sum of the weights of these instances)

Returns:

the number of correctly classified instances

pctCorrect

public final double pctCorrect()

Gets the percentage of instances correctly classified (that is, for which a correct prediction was made).

Returns:

the percent of correctly classified instances (between 0 and 100)

unclassified

public final double unclassified()

Gets the number of instances not classified (that is, for which no prediction was made by the classifier). (Actually the sum of the weights of these instances)

Returns:

the number of unclassified instances

pctUnclassified

public final double pctUnclassified()

Gets the percentage of instances not classified (that is, for which no prediction was made by the classifier).

Returns:

the percent of unclassified instances (between 0 and 100)

errorRate

public final double errorRate()

Returns the estimated error rate or the root mean squared error (if the class is numeric). If a cost matrix was given this error rate gives the average cost.

Returns:

the estimated error rate (between 0 and 1, or between 0 and maximum cost)

kappa

public final double kappa()

Returns value of kappa statistic if class is nominal.

Returns:

the value of the kappa statistic

correlationCoefficient

public final double correlationCoefficient()
                                    throws java.lang.Exception

Returns the correlation coefficient if the class is numeric.

Returns:

the correlation coefficient

Throws:

java.lang.Exception - if class is not numeric

meanAbsoluteError

public final double meanAbsoluteError()

Returns the mean absolute error. Refers to the error of the predicted values for numeric classes, and the error of the predicted probability distribution for nominal classes.

Returns:

the mean absolute error

meanPriorAbsoluteError

public final double meanPriorAbsoluteError()

Returns the mean absolute error of the prior.

Returns:

the mean absolute error

relativeAbsoluteError

public final double relativeAbsoluteError()
                                   throws java.lang.Exception

Returns the relative absolute error.

Returns:

the relative absolute error

Throws:

java.lang.Exception - if it can't be computed

rootMeanSquaredError

public final double rootMeanSquaredError()

Returns the root mean squared error.

Returns:

the root mean squared error

rootMeanPriorSquaredError

public final double rootMeanPriorSquaredError()

Returns the root mean prior squared error.

Returns:

the root mean prior squared error

rootRelativeSquaredError

public final double rootRelativeSquaredError()

Returns the root relative squared error if the class is numeric.

Returns:

the root relative squared error

priorEntropy

public final double priorEntropy()
                          throws java.lang.Exception

Calculate the entropy of the prior distribution

Returns:

the entropy of the prior distribution

Throws:

java.lang.Exception - if the class is not nominal

KBInformation

public final double KBInformation()
                           throws java.lang.Exception

Return the total Kononenko & Bratko Information score in bits

Returns:

the K&B information score

Throws:

java.lang.Exception - if the class is not nominal

KBMeanInformation

public final double KBMeanInformation()
                               throws java.lang.Exception

Return the Kononenko & Bratko Information score in bits per instance.

Returns:

the K&B information score

Throws:

java.lang.Exception - if the class is not nominal

KBRelativeInformation

public final double KBRelativeInformation()
                                   throws java.lang.Exception

Return the Kononenko & Bratko Relative Information score

Returns:

the K&B relative information score

Throws:

java.lang.Exception - if the class is not nominal

SFPriorEntropy

public final double SFPriorEntropy()

Returns the total entropy for the null model

Returns:

the total null model entropy

SFMeanPriorEntropy

public final double SFMeanPriorEntropy()

Returns the entropy per instance for the null model

Returns:

the null model entropy per instance

SFSchemeEntropy

public final double SFSchemeEntropy()

Returns the total entropy for the scheme

Returns:

the total scheme entropy

SFMeanSchemeEntropy

public final double SFMeanSchemeEntropy()

Returns the entropy per instance for the scheme

Returns:

the scheme entropy per instance

SFEntropyGain

public final double SFEntropyGain()

Returns the total SF, which is the null model entropy minus the scheme entropy.

Returns:

the total SF

SFMeanEntropyGain

public final double SFMeanEntropyGain()

Returns the SF per instance, which is the null model entropy minus the scheme entropy, per instance.

Returns:

the SF per instance

toCumulativeMarginDistributionString

public java.lang.String toCumulativeMarginDistributionString()
                                                      throws java.lang.Exception

Output the cumulative margin distribution as a string suitable for input for gnuplot or similar package.

Returns:

the cumulative margin distribution

Throws:

java.lang.Exception - if the class attribute is nominal

toSummaryString

public java.lang.String toSummaryString()

Calls toSummaryString() with no title and no complexity stats

Specified by:

toSummaryString in interface Summarizable

Returns:

a summary description of the classifier evaluation

toSummaryString

public java.lang.String toSummaryString(boolean printComplexityStatistics)

Calls toSummaryString() with a default title.

Parameters:

printComplexityStatistics - if true, complexity statistics are returned as well

toSummaryString

public java.lang.String toSummaryString(java.lang.String title,
                                        boolean printComplexityStatistics)

Outputs the performance statistics in summary form. Lists number (and percentage) of instances classified correctly, incorrectly and unclassified. Outputs the total number of instances classified, and the number of instances (if any) that had no class value provided.

Parameters:

title - the title for the statistics

printComplexityStatistics - if true, complexity statistics are returned as well

Returns:

the summary as a String

toMatrixString

public java.lang.String toMatrixString()
                                throws java.lang.Exception

Calls toMatrixString() with a default title.

Returns:

the confusion matrix as a string

Throws:

java.lang.Exception - if the class is numeric

toMatrixString

public java.lang.String toMatrixString(java.lang.String title)
                                throws java.lang.Exception

Outputs the performance statistics as a classification confusion matrix. For each class value, shows the distribution of predicted class values.

Parameters:

title - the title for the confusion matrix

Returns:

the confusion matrix as a String

Throws:

java.lang.Exception - if the class is numeric

toClassDetailsString

public java.lang.String toClassDetailsString()
                                      throws java.lang.Exception

java.lang.Exception

toClassDetailsString

public java.lang.String toClassDetailsString(java.lang.String title)
                                      throws java.lang.Exception

Generates a breakdown of the accuracy for each class, incorporating various information-retrieval statistics, such as true/false positive rate, precision/recall/F-Measure. Should be useful for ROC curves, recall/precision curves.

Parameters:

title - the title to prepend the stats string with

Returns:

the statistics presented as a string

java.lang.Exception

numTruePositives

public double numTruePositives(int classIndex)

Calculate the number of true positives with respect to a particular class. This is defined as

 correctly classified positives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the true positive rate

truePositiveRate

public double truePositiveRate(int classIndex)

Calculate the true positive rate with respect to a particular class. This is defined as

 correctly classified positives
 ------------------------------
       total positives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the true positive rate

numTrueNegatives

public double numTrueNegatives(int classIndex)

Calculate the number of true negatives with respect to a particular class. This is defined as

 correctly classified negatives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the true positive rate

trueNegativeRate

public double trueNegativeRate(int classIndex)

Calculate the true negative rate with respect to a particular class. This is defined as

 correctly classified negatives
 ------------------------------
       total negatives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the true positive rate

numFalsePositives

public double numFalsePositives(int classIndex)

Calculate number of false positives with respect to a particular class. This is defined as

 incorrectly classified negatives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the false positive rate

falsePositiveRate

public double falsePositiveRate(int classIndex)

Calculate the false positive rate with respect to a particular class. This is defined as

 incorrectly classified negatives
 --------------------------------
        total negatives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the false positive rate

numFalseNegatives

public double numFalseNegatives(int classIndex)

Calculate number of false negatives with respect to a particular class. This is defined as

 incorrectly classified positives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the false positive rate

falseNegativeRate

public double falseNegativeRate(int classIndex)

Calculate the false negative rate with respect to a particular class. This is defined as

 incorrectly classified positives
 --------------------------------
        total positives
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the false positive rate

recall

public double recall(int classIndex)

Calculate the recall with respect to a particular class. This is defined as

 correctly classified positives
 ------------------------------
       total positives
 

(Which is also the same as the truePositiveRate.)

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the recall

precision

public double precision(int classIndex)

Calculate the precision with respect to a particular class. This is defined as

 correctly classified positives
 ------------------------------
  total predicted as positive
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the precision

fMeasure

public double fMeasure(int classIndex)

Calculate the F-Measure with respect to a particular class. This is defined as

 2 * recall * precision
 ----------------------
   recall + precision
 

Parameters:

classIndex - the index of the class to consider as "positive"

Returns:

the F-Measure

setPriors

public void setPriors(Instances train)
               throws java.lang.Exception

Sets the class prior probabilities

Parameters:

train - the training instances used to determine the prior probabilities

Throws:

java.lang.Exception - if the class attribute of the instances is not set

updatePriors

public void updatePriors(Instance instance)
                  throws java.lang.Exception

Updates the class prior probabilities (when incrementally training)

Parameters:

instance - the new training instance seen

Throws:

java.lang.Exception - if the class of the instance is not set

equals

public boolean equals(java.lang.Object obj)

Tests whether the current evaluation object is equal to another evaluation object

Overrides:

equals in class java.lang.Object

Parameters:

obj - the object to compare against

Returns:

true if the two objects are equal