Java tutorial
/* * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. */ /* * Evaluation.java * Copyright (C) 1999 University of Waikato, Hamilton, New Zealand * */ package cotraining.copy; import weka.classifiers.Classifier; import weka.classifiers.CostMatrix; import weka.classifiers.Sourcable; import weka.classifiers.UpdateableClassifier; import weka.classifiers.evaluation.NominalPrediction; import weka.classifiers.evaluation.ThresholdCurve; //import weka.classifiers.pmml.consumer.PMMLClassifier; import weka.classifiers.xml.XMLClassifier; import weka.core.Drawable; import weka.core.FastVector; import weka.core.Instance; import weka.core.Instances; import weka.core.Option; import weka.core.OptionHandler; import weka.core.Range; import weka.core.RevisionHandler; import weka.core.RevisionUtils; import weka.core.Summarizable; import weka.core.Utils; import weka.core.Version; import weka.core.converters.ConverterUtils.DataSink; import weka.core.converters.ConverterUtils.DataSource; //import weka.core.pmml.PMMLFactory; //import weka.core.pmml.PMMLModel; import weka.core.xml.KOML; import weka.core.xml.XMLOptions; import weka.core.xml.XMLSerialization; import weka.estimators.Estimator; import weka.estimators.KernelEstimator; import java.beans.BeanInfo; import java.beans.Introspector; import java.beans.MethodDescriptor; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.BufferedReader; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.FileReader; import java.io.InputStream; import java.io.ObjectInputStream; import java.io.ObjectOutputStream; import java.io.OutputStream; import java.io.Reader; import java.lang.reflect.Method; import java.util.Date; import java.util.Enumeration; import java.util.Random; import java.util.zip.GZIPInputStream; import java.util.zip.GZIPOutputStream; /** * Class for evaluating machine learning models. <p/> * * ------------------------------------------------------------------- <p/> * * General options when evaluating a learning scheme from the command-line: <p/> * * -t filename <br/> * Name of the file with the training data. (required) <p/> * * -T filename <br/> * Name of the file with the test data. If missing a cross-validation * is performed. <p/> * * -c index <br/> * Index of the class attribute (1, 2, ...; default: last). <p/> * * -x number <br/> * The number of folds for the cross-validation (default: 10). <p/> * * -no-cv <br/> * No cross validation. If no test file is provided, no evaluation * is done. <p/> * * -split-percentage percentage <br/> * Sets the percentage for the train/test set split, e.g., 66. <p/> * * -preserve-order <br/> * Preserves the order in the percentage split instead of randomizing * the data first with the seed value ('-s'). <p/> * * -s seed <br/> * Random number seed for the cross-validation and percentage split * (default: 1). <p/> * * -m filename <br/> * The name of a file containing a cost matrix. <p/> * * -l filename <br/> * Loads classifier from the given file. In case the filename ends with ".xml", * a PMML file is loaded or, if that fails, options are loaded from XML. <p/> * * -d filename <br/> * Saves classifier built from the training data into the given file. In case * the filename ends with ".xml" the options are saved XML, not the model. <p/> * * -v <br/> * Outputs no statistics for the training data. <p/> * * -o <br/> * Outputs statistics only, not the classifier. <p/> * * -i <br/> * Outputs information-retrieval statistics per class. <p/> * * -k <br/> * Outputs information-theoretic statistics. <p/> * * -p range <br/> * Outputs predictions for test instances (or the train instances if no test * instances provided and -no-cv is used), along with the attributes in the specified range * (and nothing else). Use '-p 0' if no attributes are desired. <p/> * * -distribution <br/> * Outputs the distribution instead of only the prediction * in conjunction with the '-p' option (only nominal classes). <p/> * * -r <br/> * Outputs cumulative margin distribution (and nothing else). <p/> * * -g <br/> * Only for classifiers that implement "Graphable." Outputs * the graph representation of the classifier (and nothing * else). <p/> * * -xml filename | xml-string <br/> * Retrieves the options from the XML-data instead of the command line. <p/> * * -threshold-file file <br/> * The file to save the threshold data to. * The format is determined by the extensions, e.g., '.arff' for ARFF * format or '.csv' for CSV. <p/> * * -threshold-label label <br/> * The class label to determine the threshold data for * (default is the first label) <p/> * * ------------------------------------------------------------------- <p/> * * Example usage as the main of a classifier (called FunkyClassifier): * <code> <pre> * public static void main(String [] args) { * runClassifier(new FunkyClassifier(), args); * } * </pre> </code> * <p/> * * ------------------------------------------------------------------ <p/> * * Example usage from within an application: * <code> <pre> * 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()); * </pre> </code> * * * @author Eibe Frank (eibe@cs.waikato.ac.nz) * @author Len Trigg (trigg@cs.waikato.ac.nz) * @version $Revision: 5913 $ */ public class Evaluation_D implements Summarizable, RevisionHandler { /** The number of classes. */ protected int m_NumClasses; /** The number of folds for a cross-validation. */ protected int m_NumFolds; /** The weight of all incorrectly classified instances. */ protected double m_Incorrect; /** The weight of all correctly classified instances. */ protected double m_Correct; /** The weight of all unclassified instances. */ protected double m_Unclassified; /*** The weight of all instances that had no class assigned to them. */ protected double m_MissingClass; /** The weight of all instances that had a class assigned to them. */ protected double m_WithClass; /** Array for storing the confusion matrix. */ protected double[][] m_ConfusionMatrix; /** The names of the classes. */ protected String[] m_ClassNames; /** Is the class nominal or numeric? */ protected boolean m_ClassIsNominal; /** The prior probabilities of the classes */ protected double[] m_ClassPriors; /** The sum of counts for priors */ protected double m_ClassPriorsSum; /** The cost matrix (if given). */ protected CostMatrix m_CostMatrix; /** The total cost of predictions (includes instance weights) */ protected double m_TotalCost; /** Sum of errors. */ protected double m_SumErr; /** Sum of absolute errors. */ protected double m_SumAbsErr; /** Sum of squared errors. */ protected double m_SumSqrErr; /** Sum of class values. */ protected double m_SumClass; /** Sum of squared class values. */ protected double m_SumSqrClass; /*** Sum of predicted values. */ protected double m_SumPredicted; /** Sum of squared predicted values. */ protected double m_SumSqrPredicted; /** Sum of predicted * class values. */ protected double m_SumClassPredicted; /** Sum of absolute errors of the prior */ protected double m_SumPriorAbsErr; /** Sum of absolute errors of the prior */ protected double m_SumPriorSqrErr; /** Total Kononenko & Bratko Information */ protected double m_SumKBInfo; /*** Resolution of the margin histogram */ protected static int k_MarginResolution = 500; /** Cumulative margin distribution */ protected double m_MarginCounts[]; /** Number of non-missing class training instances seen */ protected int m_NumTrainClassVals; /** Array containing all numeric training class values seen */ protected double[] m_TrainClassVals; /** Array containing all numeric training class weights */ protected double[] m_TrainClassWeights; /** Numeric class error estimator for prior */ protected Estimator m_PriorErrorEstimator; /** Numeric class error estimator for scheme */ protected Estimator m_ErrorEstimator; /** * The minimum probablility accepted from an estimator to avoid * taking log(0) in Sf calculations. */ protected static final double MIN_SF_PROB = Double.MIN_VALUE; /** Total entropy of prior predictions */ protected double m_SumPriorEntropy; /** Total entropy of scheme predictions */ protected double m_SumSchemeEntropy; /** The list of predictions that have been generated (for computing AUC) */ private FastVector m_Predictions; /** enables/disables the use of priors, e.g., if no training set is * present in case of de-serialized schemes */ protected boolean m_NoPriors = false; /** * Initializes all the counters for the evaluation. * Use <code>useNoPriors()</code> if the dataset is the test set and you * can't initialize with the priors from the training set via * <code>setPriors(Instances)</code>. * * @param data set of training instances, to get some header * information and prior class distribution information * @throws Exception if the class is not defined * @see #useNoPriors() * @see #setPriors(Instances) */ public Evaluation_D(Instances data) throws Exception { this(data, null); } /** * Initializes all the counters for the evaluation and also takes a * cost matrix as parameter. * Use <code>useNoPriors()</code> if the dataset is the test set and you * can't initialize with the priors from the training set via * <code>setPriors(Instances)</code>. * * @param data set of training instances, to get some header * information and prior class distribution information * @param costMatrix the cost matrix---if null, default costs will be used * @throws Exception if cost matrix is not compatible with * data, the class is not defined or the class is numeric * @see #useNoPriors() * @see #setPriors(Instances) */ public Evaluation_D(Instances data, CostMatrix costMatrix) throws Exception { m_NumClasses = data.numClasses(); m_NumFolds = 1; m_ClassIsNominal = data.classAttribute().isNominal(); if (m_ClassIsNominal) { m_ConfusionMatrix = new double[m_NumClasses][m_NumClasses]; m_ClassNames = new String[m_NumClasses]; for (int i = 0; i < m_NumClasses; i++) { m_ClassNames[i] = data.classAttribute().value(i); } } m_CostMatrix = costMatrix; if (m_CostMatrix != null) { if (!m_ClassIsNominal) { throw new Exception("Class has to be nominal if cost matrix " + "given!"); } if (m_CostMatrix.size() != m_NumClasses) { throw new Exception("Cost matrix not compatible with data!"); } } m_ClassPriors = new double[m_NumClasses]; setPriors(data); m_MarginCounts = new double[k_MarginResolution + 1]; } /** * Returns the area under ROC for those predictions that have been collected * in the evaluateClassifier(Classifier, Instances) method. Returns * Instance.missingValue() if the area is not available. * * @param classIndex the index of the class to consider as "positive" * @return the area under the ROC curve or not a number */ public double areaUnderROC(int classIndex) { // Check if any predictions have been collected if (m_Predictions == null) { return Instance.missingValue(); } else { ThresholdCurve tc = new ThresholdCurve(); Instances result = tc.getCurve(m_Predictions, classIndex); return ThresholdCurve.getROCArea(result); } } /** * Calculates the weighted (by class size) AUC. * * @return the weighted AUC. */ public double weightedAreaUnderROC() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double aucTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = areaUnderROC(i); if (!Instance.isMissingValue(temp)) { aucTotal += (temp * classCounts[i]); } } return aucTotal / classCountSum; } /** * Calculates the weighted (by class size) PRC area. * * @return the weighted PRC area. * @author doina */ public double weightedAreaUnderPRC() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double aucTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = areaUnderPRC(i); if (!Instance.isMissingValue(temp)) { aucTotal += (temp * classCounts[i]); } } return aucTotal / classCountSum; } /** * Returns a copy of the confusion matrix. * * @return a copy of the confusion matrix as a two-dimensional array */ public double[][] confusionMatrix() { double[][] newMatrix = new double[m_ConfusionMatrix.length][0]; for (int i = 0; i < m_ConfusionMatrix.length; i++) { newMatrix[i] = new double[m_ConfusionMatrix[i].length]; System.arraycopy(m_ConfusionMatrix[i], 0, newMatrix[i], 0, m_ConfusionMatrix[i].length); } return newMatrix; } /** * Performs a (stratified if class is nominal) cross-validation * for a classifier on a set of instances. Now performs * a deep copy of the classifier before each call to * buildClassifier() (just in case the classifier is not * initialized properly). * * @param classifier the classifier with any options set. * @param data the data on which the cross-validation is to be * performed * @param numFolds the number of folds for the cross-validation * @param random random number generator for randomization * @param forPredictionsString varargs parameter that, if supplied, is * expected to hold a StringBuffer to print predictions to, * a Range of attributes to output and a Boolean (true if the distribution * is to be printed) * @throws Exception if a classifier could not be generated * successfully or the class is not defined */ public void crossValidateModel(Classifier classifier, Instances data, int numFolds, Random random, Object... forPredictionsPrinting) throws Exception { // Make a copy of the data we can reorder data = new Instances(data); data.randomize(random); if (data.classAttribute().isNominal()) { data.stratify(numFolds); } // We assume that the first element is a StringBuffer, the second a Range (attributes // to output) and the third a Boolean (whether or not to output a distribution instead // of just a classification) if (forPredictionsPrinting.length > 0) { // print the header first StringBuffer buff = (StringBuffer) forPredictionsPrinting[0]; Range attsToOutput = (Range) forPredictionsPrinting[1]; boolean printDist = ((Boolean) forPredictionsPrinting[2]).booleanValue(); printClassificationsHeader(data, attsToOutput, printDist, buff); } // Do the folds for (int i = 0; i < numFolds; i++) { Instances train = data.trainCV(numFolds, i, random); setPriors(train); Classifier copiedClassifier = Classifier.makeCopy(classifier); copiedClassifier.buildClassifier(train); Instances test = data.testCV(numFolds, i); evaluateModel(copiedClassifier, test, forPredictionsPrinting); } m_NumFolds = numFolds; } /** * Performs a (stratified if class is nominal) cross-validation * for a classifier on a set of instances. * * @param classifierString a string naming the class of the classifier * @param data the data on which the cross-validation is to be * performed * @param numFolds the number of folds for the cross-validation * @param options the options to the classifier. Any options * @param random the random number generator for randomizing the data * accepted by the classifier will be removed from this array. * @throws Exception if a classifier could not be generated * successfully or the class is not defined */ public void crossValidateModel(String classifierString, Instances data, int numFolds, String[] options, Random random) throws Exception { crossValidateModel(Classifier.forName(classifierString, options), data, numFolds, random); } /** * Evaluates a classifier with the options given in an array of * strings. <p/> * * Valid options are: <p/> * * -t filename <br/> * Name of the file with the training data. (required) <p/> * * -T filename <br/> * Name of the file with the test data. If missing a cross-validation * is performed. <p/> * * -c index <br/> * Index of the class attribute (1, 2, ...; default: last). <p/> * * -x number <br/> * The number of folds for the cross-validation (default: 10). <p/> * * -no-cv <br/> * No cross validation. If no test file is provided, no evaluation * is done. <p/> * * -split-percentage percentage <br/> * Sets the percentage for the train/test set split, e.g., 66. <p/> * * -preserve-order <br/> * Preserves the order in the percentage split instead of randomizing * the data first with the seed value ('-s'). <p/> * * -s seed <br/> * Random number seed for the cross-validation and percentage split * (default: 1). <p/> * * -m filename <br/> * The name of a file containing a cost matrix. <p/> * * -l filename <br/> * Loads classifier from the given file. In case the filename ends with * ".xml",a PMML file is loaded or, if that fails, options are loaded from XML. <p/> * * -d filename <br/> * Saves classifier built from the training data into the given file. In case * the filename ends with ".xml" the options are saved XML, not the model. <p/> * * -v <br/> * Outputs no statistics for the training data. <p/> * * -o <br/> * Outputs statistics only, not the classifier. <p/> * * -i <br/> * Outputs detailed information-retrieval statistics per class. <p/> * * -k <br/> * Outputs information-theoretic statistics. <p/> * * -p range <br/> * Outputs predictions for test instances (or the train instances if no test * instances provided and -no-cv is used), along with the attributes in the specified range (and * nothing else). Use '-p 0' if no attributes are desired. <p/> * * -distribution <br/> * Outputs the distribution instead of only the prediction * in conjunction with the '-p' option (only nominal classes). <p/> * * -r <br/> * Outputs cumulative margin distribution (and nothing else). <p/> * * -g <br/> * Only for classifiers that implement "Graphable." Outputs * the graph representation of the classifier (and nothing * else). <p/> * * -xml filename | xml-string <br/> * Retrieves the options from the XML-data instead of the command line. <p/> * * -threshold-file file <br/> * The file to save the threshold data to. * The format is determined by the extensions, e.g., '.arff' for ARFF * format or '.csv' for CSV. <p/> * * -threshold-label label <br/> * The class label to determine the threshold data for * (default is the first label) <p/> * * @param classifierString class of machine learning classifier as a string * @param options the array of string containing the options * @throws Exception if model could not be evaluated successfully * @return a string describing the results */ public static String evaluateModel(String classifierString, String[] options) throws Exception { Classifier classifier; // Create classifier try { classifier = (Classifier) Class.forName(classifierString).newInstance(); } catch (Exception e) { throw new Exception("Can't find class with name " + classifierString + '.'); } return evaluateModel(classifier, options); } /** * A test method for this class. Just extracts the first command line * argument as a classifier class name and calls evaluateModel. * @param args an array of command line arguments, the first of which * must be the class name of a classifier. */ public static void main(String[] args) { try { if (args.length == 0) { throw new Exception("The first argument must be the class name" + " of a classifier"); } String classifier = args[0]; args[0] = ""; System.out.println(evaluateModel(classifier, args)); } catch (Exception ex) { ex.printStackTrace(); System.err.println(ex.getMessage()); } } /** * Evaluates a classifier with the options given in an array of * strings. <p/> * * Valid options are: <p/> * * -t name of training file <br/> * Name of the file with the training data. (required) <p/> * * -T name of test file <br/> * Name of the file with the test data. If missing a cross-validation * is performed. <p/> * * -c class index <br/> * Index of the class attribute (1, 2, ...; default: last). <p/> * * -x number of folds <br/> * The number of folds for the cross-validation (default: 10). <p/> * * -no-cv <br/> * No cross validation. If no test file is provided, no evaluation * is done. <p/> * * -split-percentage percentage <br/> * Sets the percentage for the train/test set split, e.g., 66. <p/> * * -preserve-order <br/> * Preserves the order in the percentage split instead of randomizing * the data first with the seed value ('-s'). <p/> * * -s seed <br/> * Random number seed for the cross-validation and percentage split * (default: 1). <p/> * * -m file with cost matrix <br/> * The name of a file containing a cost matrix. <p/> * * -l filename <br/> * Loads classifier from the given file. In case the filename ends with * ".xml",a PMML file is loaded or, if that fails, options are loaded from XML. <p/> * * -d filename <br/> * Saves classifier built from the training data into the given file. In case * the filename ends with ".xml" the options are saved XML, not the model. <p/> * * -v <br/> * Outputs no statistics for the training data. <p/> * * -o <br/> * Outputs statistics only, not the classifier. <p/> * * -i <br/> * Outputs detailed information-retrieval statistics per class. <p/> * * -k <br/> * Outputs information-theoretic statistics. <p/> * * -p range <br/> * Outputs predictions for test instances (or the train instances if no test * instances provided and -no-cv is used), along with the attributes in the specified range * (and nothing else). Use '-p 0' if no attributes are desired. <p/> * * -distribution <br/> * Outputs the distribution instead of only the prediction * in conjunction with the '-p' option (only nominal classes). <p/> * * -r <br/> * Outputs cumulative margin distribution (and nothing else). <p/> * * -g <br/> * Only for classifiers that implement "Graphable." Outputs * the graph representation of the classifier (and nothing * else). <p/> * * -xml filename | xml-string <br/> * Retrieves the options from the XML-data instead of the command line. <p/> * * @param classifier machine learning classifier * @param options the array of string containing the options * @throws Exception if model could not be evaluated successfully * @return a string describing the results */ public static String evaluateModel(Classifier classifier, String[] options) throws Exception { Instances train = null, tempTrain, test = null, template = null; int seed = 1, folds = 10, classIndex = -1; boolean noCrossValidation = false; String trainFileName, testFileName, sourceClass, classIndexString, seedString, foldsString, objectInputFileName, objectOutputFileName, attributeRangeString; boolean noOutput = false, printClassifications = false, trainStatistics = true, printMargins = false, printComplexityStatistics = false, printGraph = false, classStatistics = false, printSource = false; StringBuffer text = new StringBuffer(); DataSource trainSource = null, testSource = null; ObjectInputStream objectInputStream = null; BufferedInputStream xmlInputStream = null; CostMatrix costMatrix = null; StringBuffer schemeOptionsText = null; Range attributesToOutput = null; long trainTimeStart = 0, trainTimeElapsed = 0, testTimeStart = 0, testTimeElapsed = 0; String xml = ""; String[] optionsTmp = null; Classifier classifierBackup; Classifier classifierClassifications = null; boolean printDistribution = false; int actualClassIndex = -1; // 0-based class index String splitPercentageString = ""; int splitPercentage = -1; boolean preserveOrder = false; boolean trainSetPresent = false; boolean testSetPresent = false; String thresholdFile; String thresholdLabel; StringBuffer predsBuff = null; // predictions from cross-validation // help requested? if (Utils.getFlag("h", options) || Utils.getFlag("help", options)) { // global info requested as well? boolean globalInfo = Utils.getFlag("synopsis", options) || Utils.getFlag("info", options); throw new Exception("\nHelp requested." + makeOptionString(classifier, globalInfo)); } try { // do we get the input from XML instead of normal parameters? xml = Utils.getOption("xml", options); if (!xml.equals("")) options = new XMLOptions(xml).toArray(); // is the input model only the XML-Options, i.e. w/o built model? optionsTmp = new String[options.length]; for (int i = 0; i < options.length; i++) optionsTmp[i] = options[i]; String tmpO = Utils.getOption('l', optionsTmp); //if (Utils.getOption('l', optionsTmp).toLowerCase().endsWith(".xml")) { if (tmpO.endsWith(".xml")) { // try to load file as PMML first boolean success = false; try { //PMMLModel pmmlModel = PMMLFactory.getPMMLModel(tmpO); //if (pmmlModel instanceof PMMLClassifier) { //classifier = ((PMMLClassifier)pmmlModel); // success = true; //} } catch (IllegalArgumentException ex) { success = false; } if (!success) { // load options from serialized data ('-l' is automatically erased!) XMLClassifier xmlserial = new XMLClassifier(); Classifier cl = (Classifier) xmlserial.read(Utils.getOption('l', options)); // merge options optionsTmp = new String[options.length + cl.getOptions().length]; System.arraycopy(cl.getOptions(), 0, optionsTmp, 0, cl.getOptions().length); System.arraycopy(options, 0, optionsTmp, cl.getOptions().length, options.length); options = optionsTmp; } } noCrossValidation = Utils.getFlag("no-cv", options); // Get basic options (options the same for all schemes) classIndexString = Utils.getOption('c', options); if (classIndexString.length() != 0) { if (classIndexString.equals("first")) classIndex = 1; else if (classIndexString.equals("last")) classIndex = -1; else classIndex = Integer.parseInt(classIndexString); } trainFileName = Utils.getOption('t', options); objectInputFileName = Utils.getOption('l', options); objectOutputFileName = Utils.getOption('d', options); testFileName = Utils.getOption('T', options); foldsString = Utils.getOption('x', options); if (foldsString.length() != 0) { folds = Integer.parseInt(foldsString); } seedString = Utils.getOption('s', options); if (seedString.length() != 0) { seed = Integer.parseInt(seedString); } if (trainFileName.length() == 0) { if (objectInputFileName.length() == 0) { throw new Exception("No training file and no object " + "input file given."); } if (testFileName.length() == 0) { throw new Exception("No training file and no test " + "file given."); } } else if ((objectInputFileName.length() != 0) && ((!(classifier instanceof UpdateableClassifier)) || (testFileName.length() == 0))) { throw new Exception("Classifier not incremental, or no " + "test file provided: can't " + "use both train and model file."); } try { if (trainFileName.length() != 0) { trainSetPresent = true; trainSource = new DataSource(trainFileName); } if (testFileName.length() != 0) { testSetPresent = true; testSource = new DataSource(testFileName); } if (objectInputFileName.length() != 0) { if (objectInputFileName.endsWith(".xml")) { // if this is the case then it means that a PMML classifier was // successfully loaded earlier in the code objectInputStream = null; xmlInputStream = null; } else { InputStream is = new FileInputStream(objectInputFileName); if (objectInputFileName.endsWith(".gz")) { is = new GZIPInputStream(is); } // load from KOML? if (!(objectInputFileName.endsWith(".koml") && KOML.isPresent())) { objectInputStream = new ObjectInputStream(is); xmlInputStream = null; } else { objectInputStream = null; xmlInputStream = new BufferedInputStream(is); } } } } catch (Exception e) { throw new Exception("Can't open file " + e.getMessage() + '.'); } if (testSetPresent) { template = test = testSource.getStructure(); if (classIndex != -1) { test.setClassIndex(classIndex - 1); } else { if ((test.classIndex() == -1) || (classIndexString.length() != 0)) test.setClassIndex(test.numAttributes() - 1); } actualClassIndex = test.classIndex(); } else { // percentage split splitPercentageString = Utils.getOption("split-percentage", options); if (splitPercentageString.length() != 0) { if (foldsString.length() != 0) throw new Exception("Percentage split cannot be used in conjunction with " + "cross-validation ('-x')."); splitPercentage = Integer.parseInt(splitPercentageString); if ((splitPercentage <= 0) || (splitPercentage >= 100)) throw new Exception("Percentage split value needs be >0 and <100."); } else { splitPercentage = -1; } preserveOrder = Utils.getFlag("preserve-order", options); if (preserveOrder) { if (splitPercentage == -1) throw new Exception("Percentage split ('-percentage-split') is missing."); } // create new train/test sources if (splitPercentage > 0) { testSetPresent = true; Instances tmpInst = trainSource.getDataSet(actualClassIndex); if (!preserveOrder) tmpInst.randomize(new Random(seed)); int trainSize = tmpInst.numInstances() * splitPercentage / 100; int testSize = tmpInst.numInstances() - trainSize; Instances trainInst = new Instances(tmpInst, 0, trainSize); Instances testInst = new Instances(tmpInst, trainSize, testSize); trainSource = new DataSource(trainInst); testSource = new DataSource(testInst); template = test = testSource.getStructure(); if (classIndex != -1) { test.setClassIndex(classIndex - 1); } else { if ((test.classIndex() == -1) || (classIndexString.length() != 0)) test.setClassIndex(test.numAttributes() - 1); } actualClassIndex = test.classIndex(); } } if (trainSetPresent) { template = train = trainSource.getStructure(); if (classIndex != -1) { train.setClassIndex(classIndex - 1); } else { if ((train.classIndex() == -1) || (classIndexString.length() != 0)) train.setClassIndex(train.numAttributes() - 1); } actualClassIndex = train.classIndex(); if ((testSetPresent) && !test.equalHeaders(train)) { throw new IllegalArgumentException("Train and test file not compatible!"); } } if (template == null) { throw new Exception("No actual dataset provided to use as template"); } costMatrix = handleCostOption(Utils.getOption('m', options), template.numClasses()); classStatistics = Utils.getFlag('i', options); noOutput = Utils.getFlag('o', options); trainStatistics = !Utils.getFlag('v', options); printComplexityStatistics = Utils.getFlag('k', options); printMargins = Utils.getFlag('r', options); printGraph = Utils.getFlag('g', options); sourceClass = Utils.getOption('z', options); printSource = (sourceClass.length() != 0); printDistribution = Utils.getFlag("distribution", options); thresholdFile = Utils.getOption("threshold-file", options); thresholdLabel = Utils.getOption("threshold-label", options); // Check -p option try { attributeRangeString = Utils.getOption('p', options); } catch (Exception e) { throw new Exception(e.getMessage() + "\nNOTE: the -p option has changed. " + "It now expects a parameter specifying a range of attributes " + "to list with the predictions. Use '-p 0' for none."); } if (attributeRangeString.length() != 0) { printClassifications = true; noOutput = true; if (!attributeRangeString.equals("0")) attributesToOutput = new Range(attributeRangeString); } if (!printClassifications && printDistribution) throw new Exception("Cannot print distribution without '-p' option!"); // if no training file given, we don't have any priors if ((!trainSetPresent) && (printComplexityStatistics)) throw new Exception("Cannot print complexity statistics ('-k') without training file ('-t')!"); // If a model file is given, we can't process // scheme-specific options if (objectInputFileName.length() != 0) { Utils.checkForRemainingOptions(options); } else { // Set options for classifier if (classifier instanceof OptionHandler) { for (int i = 0; i < options.length; i++) { if (options[i].length() != 0) { if (schemeOptionsText == null) { schemeOptionsText = new StringBuffer(); } if (options[i].indexOf(' ') != -1) { schemeOptionsText.append('"' + options[i] + "\" "); } else { schemeOptionsText.append(options[i] + " "); } } } ((OptionHandler) classifier).setOptions(options); } } Utils.checkForRemainingOptions(options); } catch (Exception e) { throw new Exception("\nWeka exception: " + e.getMessage() + makeOptionString(classifier, false)); } // Setup up evaluation objects Evaluation_D trainingEvaluation = new Evaluation_D(new Instances(template, 0), costMatrix); Evaluation_D testingEvaluation = new Evaluation_D(new Instances(template, 0), costMatrix); // disable use of priors if no training file given if (!trainSetPresent) testingEvaluation.useNoPriors(); if (objectInputFileName.length() != 0) { // Load classifier from file if (objectInputStream != null) { classifier = (Classifier) objectInputStream.readObject(); // try and read a header (if present) Instances savedStructure = null; try { savedStructure = (Instances) objectInputStream.readObject(); } catch (Exception ex) { // don't make a fuss } if (savedStructure != null) { // test for compatibility with template if (!template.equalHeaders(savedStructure)) { throw new Exception("training and test set are not compatible"); } } objectInputStream.close(); } else if (xmlInputStream != null) { // whether KOML is available has already been checked (objectInputStream would null otherwise)! classifier = (Classifier) KOML.read(xmlInputStream); xmlInputStream.close(); } } // backup of fully setup classifier for cross-validation classifierBackup = Classifier.makeCopy(classifier); // Build the classifier if no object file provided if ((classifier instanceof UpdateableClassifier) && (testSetPresent || noCrossValidation) && (costMatrix == null) && (trainSetPresent)) { // Build classifier incrementally trainingEvaluation.setPriors(train); testingEvaluation.setPriors(train); trainTimeStart = System.currentTimeMillis(); if (objectInputFileName.length() == 0) { classifier.buildClassifier(train); } Instance trainInst; while (trainSource.hasMoreElements(train)) { trainInst = trainSource.nextElement(train); trainingEvaluation.updatePriors(trainInst); testingEvaluation.updatePriors(trainInst); ((UpdateableClassifier) classifier).updateClassifier(trainInst); } trainTimeElapsed = System.currentTimeMillis() - trainTimeStart; } else if (objectInputFileName.length() == 0) { // Build classifier in one go tempTrain = trainSource.getDataSet(actualClassIndex); trainingEvaluation.setPriors(tempTrain); testingEvaluation.setPriors(tempTrain); trainTimeStart = System.currentTimeMillis(); classifier.buildClassifier(tempTrain); trainTimeElapsed = System.currentTimeMillis() - trainTimeStart; } // backup of fully trained classifier for printing the classifications if (printClassifications) classifierClassifications = Classifier.makeCopy(classifier); // Save the classifier if an object output file is provided if (objectOutputFileName.length() != 0) { OutputStream os = new FileOutputStream(objectOutputFileName); // binary if (!(objectOutputFileName.endsWith(".xml") || (objectOutputFileName.endsWith(".koml") && KOML.isPresent()))) { if (objectOutputFileName.endsWith(".gz")) { os = new GZIPOutputStream(os); } ObjectOutputStream objectOutputStream = new ObjectOutputStream(os); objectOutputStream.writeObject(classifier); if (template != null) { objectOutputStream.writeObject(template); } objectOutputStream.flush(); objectOutputStream.close(); } // KOML/XML else { BufferedOutputStream xmlOutputStream = new BufferedOutputStream(os); if (objectOutputFileName.endsWith(".xml")) { XMLSerialization xmlSerial = new XMLClassifier(); xmlSerial.write(xmlOutputStream, classifier); } else // whether KOML is present has already been checked // if not present -> ".koml" is interpreted as binary - see above if (objectOutputFileName.endsWith(".koml")) { KOML.write(xmlOutputStream, classifier); } xmlOutputStream.close(); } } // If classifier is drawable output string describing graph if ((classifier instanceof Drawable) && (printGraph)) { return ((Drawable) classifier).graph(); } // Output the classifier as equivalent source if ((classifier instanceof Sourcable) && (printSource)) { return wekaStaticWrapper((Sourcable) classifier, sourceClass); } // Output model if (!(noOutput || printMargins)) { if (classifier instanceof OptionHandler) { if (schemeOptionsText != null) { text.append("\nOptions: " + schemeOptionsText); text.append("\n"); } } text.append("\n" + classifier.toString() + "\n"); } if (!printMargins && (costMatrix != null)) { text.append("\n=== Evaluation Cost Matrix ===\n\n"); text.append(costMatrix.toString()); } // Output test instance predictions only if (printClassifications) { DataSource source = testSource; predsBuff = new StringBuffer(); // no test set -> use train set if (source == null && noCrossValidation) { source = trainSource; predsBuff.append("\n=== Predictions on training data ===\n\n"); } else { predsBuff.append("\n=== Predictions on test data ===\n\n"); } if (source != null) { /* return printClassifications(classifierClassifications, new Instances(template, 0), source, actualClassIndex + 1, attributesToOutput, printDistribution); */ printClassifications(classifierClassifications, new Instances(template, 0), source, actualClassIndex + 1, attributesToOutput, printDistribution, predsBuff); // return predsText.toString(); } } // Compute error estimate from training data if ((trainStatistics) && (trainSetPresent)) { if ((classifier instanceof UpdateableClassifier) && (testSetPresent) && (costMatrix == null)) { // Classifier was trained incrementally, so we have to // reset the source. trainSource.reset(); // Incremental testing train = trainSource.getStructure(actualClassIndex); testTimeStart = System.currentTimeMillis(); Instance trainInst; while (trainSource.hasMoreElements(train)) { trainInst = trainSource.nextElement(train); trainingEvaluation.evaluateModelOnce((Classifier) classifier, trainInst); } testTimeElapsed = System.currentTimeMillis() - testTimeStart; } else { testTimeStart = System.currentTimeMillis(); trainingEvaluation.evaluateModel(classifier, trainSource.getDataSet(actualClassIndex)); testTimeElapsed = System.currentTimeMillis() - testTimeStart; } // Print the results of the training evaluation if (printMargins) { return trainingEvaluation.toCumulativeMarginDistributionString(); } else { if (!printClassifications) { text.append("\nTime taken to build model: " + Utils.doubleToString(trainTimeElapsed / 1000.0, 2) + " seconds"); if (splitPercentage > 0) text.append("\nTime taken to test model on training split: "); else text.append("\nTime taken to test model on training data: "); text.append(Utils.doubleToString(testTimeElapsed / 1000.0, 2) + " seconds"); if (splitPercentage > 0) text.append(trainingEvaluation.toSummaryString("\n\n=== Error on training" + " split ===\n", printComplexityStatistics)); else text.append(trainingEvaluation.toSummaryString("\n\n=== Error on training" + " data ===\n", printComplexityStatistics)); if (template.classAttribute().isNominal()) { if (classStatistics) { text.append("\n\n" + trainingEvaluation.toClassDetailsString()); } if (!noCrossValidation) text.append("\n\n" + trainingEvaluation.toMatrixString()); } } } } // Compute proper error estimates if (testSource != null) { // Testing is on the supplied test data testSource.reset(); test = testSource.getStructure(test.classIndex()); Instance testInst; while (testSource.hasMoreElements(test)) { testInst = testSource.nextElement(test); testingEvaluation.evaluateModelOnceAndRecordPrediction((Classifier) classifier, testInst); } if (splitPercentage > 0) { if (!printClassifications) { text.append("\n\n" + testingEvaluation.toSummaryString("=== Error on test split ===\n", printComplexityStatistics)); } } else { if (!printClassifications) { text.append("\n\n" + testingEvaluation.toSummaryString("=== Error on test data ===\n", printComplexityStatistics)); } } } else if (trainSource != null) { if (!noCrossValidation) { // Testing is via cross-validation on training data Random random = new Random(seed); // use untrained (!) classifier for cross-validation classifier = Classifier.makeCopy(classifierBackup); if (!printClassifications) { testingEvaluation.crossValidateModel(classifier, trainSource.getDataSet(actualClassIndex), folds, random); if (template.classAttribute().isNumeric()) { text.append("\n\n\n" + testingEvaluation.toSummaryString("=== Cross-validation ===\n", printComplexityStatistics)); } else { text.append("\n\n\n" + testingEvaluation.toSummaryString( "=== Stratified " + "cross-validation ===\n", printComplexityStatistics)); } } else { predsBuff = new StringBuffer(); predsBuff.append("\n=== Predictions under cross-validation ===\n\n"); testingEvaluation.crossValidateModel(classifier, trainSource.getDataSet(actualClassIndex), folds, random, predsBuff, attributesToOutput, new Boolean(printDistribution)); /* if (template.classAttribute().isNumeric()) { text.append("\n\n\n" + testingEvaluation. toSummaryString("=== Cross-validation ===\n", printComplexityStatistics)); } else { text.append("\n\n\n" + testingEvaluation. toSummaryString("=== Stratified " + "cross-validation ===\n", printComplexityStatistics)); } */ } } } if (template.classAttribute().isNominal()) { if (classStatistics && !noCrossValidation && !printClassifications) { text.append("\n\n" + testingEvaluation.toClassDetailsString()); } if (!noCrossValidation && !printClassifications) text.append("\n\n" + testingEvaluation.toMatrixString()); } // predictions from cross-validation? if (predsBuff != null) { text.append("\n" + predsBuff); } if ((thresholdFile.length() != 0) && template.classAttribute().isNominal()) { int labelIndex = 0; if (thresholdLabel.length() != 0) labelIndex = template.classAttribute().indexOfValue(thresholdLabel); if (labelIndex == -1) throw new IllegalArgumentException("Class label '" + thresholdLabel + "' is unknown!"); ThresholdCurve tc = new ThresholdCurve(); Instances result = tc.getCurve(testingEvaluation.predictions(), labelIndex); DataSink.write(thresholdFile, result); } return text.toString(); } /** * Attempts to load a cost matrix. * * @param costFileName the filename of the cost matrix * @param numClasses the number of classes that should be in the cost matrix * (only used if the cost file is in old format). * @return a <code>CostMatrix</code> value, or null if costFileName is empty * @throws Exception if an error occurs. */ protected static CostMatrix handleCostOption(String costFileName, int numClasses) throws Exception { if ((costFileName != null) && (costFileName.length() != 0)) { System.out.println("NOTE: The behaviour of the -m option has changed between WEKA 3.0" + " and WEKA 3.1. -m now carries out cost-sensitive *evaluation*" + " only. For cost-sensitive *prediction*, use one of the" + " cost-sensitive metaschemes such as" + " weka.classifiers.meta.CostSensitiveClassifier or" + " weka.classifiers.meta.MetaCost"); Reader costReader = null; try { costReader = new BufferedReader(new FileReader(costFileName)); } catch (Exception e) { throw new Exception("Can't open file " + e.getMessage() + '.'); } try { // First try as a proper cost matrix format return new CostMatrix(costReader); } catch (Exception ex) { try { // Now try as the poxy old format :-) //System.err.println("Attempting to read old format cost file"); try { costReader.close(); // Close the old one costReader = new BufferedReader(new FileReader(costFileName)); } catch (Exception e) { throw new Exception("Can't open file " + e.getMessage() + '.'); } CostMatrix costMatrix = new CostMatrix(numClasses); //System.err.println("Created default cost matrix"); costMatrix.readOldFormat(costReader); return costMatrix; //System.err.println("Read old format"); } catch (Exception e2) { // re-throw the original exception //System.err.println("Re-throwing original exception"); throw ex; } } } else { return null; } } /** * Evaluates the classifier on a given set of instances. Note that * the data must have exactly the same format (e.g. order of * attributes) as the data used to train the classifier! Otherwise * the results will generally be meaningless. * * @param classifier machine learning classifier * @param data set of test instances for evaluation * @param forPredictionsString varargs parameter that, if supplied, is * expected to hold a StringBuffer to print predictions to, * a Range of attributes to output and a Boolean (true if the distribution * is to be printed) * @return the predictions * @throws Exception if model could not be evaluated * successfully */ public double[] evaluateModel(Classifier classifier, Instances data, Object... forPredictionsPrinting) throws Exception { // for predictions printing StringBuffer buff = null; Range attsToOutput = null; boolean printDist = false; double predictions[] = new double[data.numInstances()]; if (forPredictionsPrinting.length > 0) { buff = (StringBuffer) forPredictionsPrinting[0]; attsToOutput = (Range) forPredictionsPrinting[1]; printDist = ((Boolean) forPredictionsPrinting[2]).booleanValue(); } // Need to be able to collect predictions if appropriate (for AUC) for (int i = 0; i < data.numInstances(); i++) { predictions[i] = evaluateModelOnceAndRecordPrediction((Classifier) classifier, data.instance(i)); if (buff != null) { buff.append(predictionText(classifier, data.instance(i), i, attsToOutput, printDist)); } } return predictions; } /** * Evaluates the classifier on a single instance and records the * prediction (if the class is nominal). * * @param classifier machine learning classifier * @param instance the test instance to be classified * @return the prediction made by the clasifier * @throws Exception if model could not be evaluated * successfully or the data contains string attributes */ public double evaluateModelOnceAndRecordPrediction(Classifier classifier, Instance instance) throws Exception { Instance classMissing = (Instance) instance.copy(); double pred = 0; classMissing.setDataset(instance.dataset()); classMissing.setClassMissing(); if (m_ClassIsNominal) { if (m_Predictions == null) { m_Predictions = new FastVector(); } double[] dist = classifier.distributionForInstance(classMissing); pred = Utils.maxIndex(dist); if (dist[(int) pred] <= 0) { pred = Instance.missingValue(); } updateStatsForClassifier(dist, instance); m_Predictions.addElement(new NominalPrediction(instance.classValue(), dist, instance.weight())); } else { pred = classifier.classifyInstance(classMissing); updateStatsForPredictor(pred, instance); } return pred; } /** * Evaluates the classifier on a single instance. * * @param classifier machine learning classifier * @param instance the test instance to be classified * @return the prediction made by the clasifier * @throws Exception if model could not be evaluated * successfully or the data contains string attributes */ public double evaluateModelOnce(Classifier classifier, Instance instance) throws Exception { Instance classMissing = (Instance) instance.copy(); double pred = 0; classMissing.setDataset(instance.dataset()); classMissing.setClassMissing(); if (m_ClassIsNominal) { double[] dist = classifier.distributionForInstance(classMissing); pred = Utils.maxIndex(dist); if (dist[(int) pred] <= 0) { pred = Instance.missingValue(); } updateStatsForClassifier(dist, instance); } else { pred = classifier.classifyInstance(classMissing); updateStatsForPredictor(pred, instance); } return pred; } /** * Evaluates the supplied distribution on a single instance. * * @param dist the supplied distribution * @param instance the test instance to be classified * @return the prediction * @throws Exception if model could not be evaluated * successfully */ public double evaluateModelOnce(double[] dist, Instance instance) throws Exception { double pred; if (m_ClassIsNominal) { pred = Utils.maxIndex(dist); if (dist[(int) pred] <= 0) { pred = Instance.missingValue(); } updateStatsForClassifier(dist, instance); } else { pred = dist[0]; updateStatsForPredictor(pred, instance); } return pred; } /** * Evaluates the supplied distribution on a single instance. * * @param dist the supplied distribution * @param instance the test instance to be classified * @return the prediction * @throws Exception if model could not be evaluated * successfully */ public double evaluateModelOnceAndRecordPrediction(double[] dist, Instance instance) throws Exception { double pred; if (m_ClassIsNominal) { if (m_Predictions == null) { m_Predictions = new FastVector(); } pred = Utils.maxIndex(dist); if (dist[(int) pred] <= 0) { pred = Instance.missingValue(); } updateStatsForClassifier(dist, instance); m_Predictions.addElement(new NominalPrediction(instance.classValue(), dist, instance.weight())); } else { pred = dist[0]; updateStatsForPredictor(pred, instance); } return pred; } /** * Evaluates the supplied prediction on a single instance. * * @param prediction the supplied prediction * @param instance the test instance to be classified * @throws Exception if model could not be evaluated * successfully */ public void evaluateModelOnce(double prediction, Instance instance) throws Exception { if (m_ClassIsNominal) { updateStatsForClassifier(makeDistribution(prediction), instance); } else { updateStatsForPredictor(prediction, instance); } } /** * Returns the predictions that have been collected. * * @return a reference to the FastVector containing the predictions * that have been collected. This should be null if no predictions * have been collected (e.g. if the class is numeric). */ public FastVector predictions() { return m_Predictions; } /** * Wraps a static classifier in enough source to test using the weka * class libraries. * * @param classifier a Sourcable Classifier * @param className the name to give to the source code class * @return the source for a static classifier that can be tested with * weka libraries. * @throws Exception if code-generation fails */ public static String wekaStaticWrapper(Sourcable classifier, String className) throws Exception { StringBuffer result = new StringBuffer(); String staticClassifier = classifier.toSource(className); result.append("// Generated with Weka " + Version.VERSION + "\n"); result.append("//\n"); result.append("// This code is public domain and comes with no warranty.\n"); result.append("//\n"); result.append("// Timestamp: " + new Date() + "\n"); result.append("\n"); result.append("package weka.classifiers;\n"); result.append("\n"); result.append("import weka.core.Attribute;\n"); result.append("import weka.core.Capabilities;\n"); result.append("import weka.core.Capabilities.Capability;\n"); result.append("import weka.core.Instance;\n"); result.append("import weka.core.Instances;\n"); result.append("import weka.core.RevisionUtils;\n"); result.append("import weka.classifiers.Classifier;\n"); result.append("\n"); result.append("public class WekaWrapper\n"); result.append(" extends Classifier {\n"); // globalInfo result.append("\n"); result.append(" /**\n"); result.append(" * Returns only the toString() method.\n"); result.append(" *\n"); result.append(" * @return a string describing the classifier\n"); result.append(" */\n"); result.append(" public String globalInfo() {\n"); result.append(" return toString();\n"); result.append(" }\n"); // getCapabilities result.append("\n"); result.append(" /**\n"); result.append(" * Returns the capabilities of this classifier.\n"); result.append(" *\n"); result.append(" * @return the capabilities\n"); result.append(" */\n"); result.append(" public Capabilities getCapabilities() {\n"); result.append(((Classifier) classifier).getCapabilities().toSource("result", 4)); result.append(" return result;\n"); result.append(" }\n"); // buildClassifier result.append("\n"); result.append(" /**\n"); result.append(" * only checks the data against its capabilities.\n"); result.append(" *\n"); result.append(" * @param i the training data\n"); result.append(" */\n"); result.append(" public void buildClassifier(Instances i) throws Exception {\n"); result.append(" // can classifier handle the data?\n"); result.append(" getCapabilities().testWithFail(i);\n"); result.append(" }\n"); // classifyInstance result.append("\n"); result.append(" /**\n"); result.append(" * Classifies the given instance.\n"); result.append(" *\n"); result.append(" * @param i the instance to classify\n"); result.append(" * @return the classification result\n"); result.append(" */\n"); result.append(" public double classifyInstance(Instance i) throws Exception {\n"); result.append(" Object[] s = new Object[i.numAttributes()];\n"); result.append(" \n"); result.append(" for (int j = 0; j < s.length; j++) {\n"); result.append(" if (!i.isMissing(j)) {\n"); result.append(" if (i.attribute(j).isNominal())\n"); result.append(" s[j] = new String(i.stringValue(j));\n"); result.append(" else if (i.attribute(j).isNumeric())\n"); result.append(" s[j] = new Double(i.value(j));\n"); result.append(" }\n"); result.append(" }\n"); result.append(" \n"); result.append(" // set class value to missing\n"); result.append(" s[i.classIndex()] = null;\n"); result.append(" \n"); result.append(" return " + className + ".classify(s);\n"); result.append(" }\n"); // getRevision result.append("\n"); result.append(" /**\n"); result.append(" * Returns the revision string.\n"); result.append(" * \n"); result.append(" * @return the revision\n"); result.append(" */\n"); result.append(" public String getRevision() {\n"); result.append(" return RevisionUtils.extract(\"1.0\");\n"); result.append(" }\n"); // toString result.append("\n"); result.append(" /**\n"); result.append(" * Returns only the classnames and what classifier it is based on.\n"); result.append(" *\n"); result.append(" * @return a short description\n"); result.append(" */\n"); result.append(" public String toString() {\n"); result.append(" return \"Auto-generated classifier wrapper, based on " + classifier.getClass().getName() + " (generated with Weka " + Version.VERSION + ").\\n" + "\" + this.getClass().getName() + \"/" + className + "\";\n"); result.append(" }\n"); // main result.append("\n"); result.append(" /**\n"); result.append(" * Runs the classfier from commandline.\n"); result.append(" *\n"); result.append(" * @param args the commandline arguments\n"); result.append(" */\n"); result.append(" public static void main(String args[]) {\n"); result.append(" runClassifier(new WekaWrapper(), args);\n"); result.append(" }\n"); result.append("}\n"); // actual classifier code result.append("\n"); result.append(staticClassifier); return result.toString(); } /** * 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). * * @return the number of test instances with known class */ public final double numInstances() { return m_WithClass; } /** * 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) * * @return the number of incorrectly classified instances */ public final double incorrect() { return m_Incorrect; } /** * Gets the percentage of instances incorrectly classified (that is, for * which an incorrect prediction was made). * * @return the percent of incorrectly classified instances * (between 0 and 100) */ public final double pctIncorrect() { return 100 * m_Incorrect / m_WithClass; } /** * Gets the total cost, that is, the cost of each prediction times the * weight of the instance, summed over all instances. * * @return the total cost */ public final double totalCost() { return m_TotalCost; } /** * Gets the average cost, that is, total cost of misclassifications * (incorrect plus unclassified) over the total number of instances. * * @return the average cost. */ public final double avgCost() { return m_TotalCost / m_WithClass; } /** * 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) * * @return the number of correctly classified instances */ public final double correct() { return m_Correct; } /** * Gets the percentage of instances correctly classified (that is, for * which a correct prediction was made). * * @return the percent of correctly classified instances (between 0 and 100) */ public final double pctCorrect() { return 100 * m_Correct / m_WithClass; } /** * 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) * * @return the number of unclassified instances */ public final double unclassified() { return m_Unclassified; } /** * Gets the percentage of instances not classified (that is, for * which no prediction was made by the classifier). * * @return the percent of unclassified instances (between 0 and 100) */ public final double pctUnclassified() { return 100 * m_Unclassified / m_WithClass; } /** * 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. * * @return the estimated error rate (between 0 and 1, or between 0 and * maximum cost) */ public final double errorRate() { if (!m_ClassIsNominal) { return Math.sqrt(m_SumSqrErr / (m_WithClass - m_Unclassified)); } if (m_CostMatrix == null) { return m_Incorrect / m_WithClass; } else { return avgCost(); } } /** * Returns value of kappa statistic if class is nominal. * * @return the value of the kappa statistic */ public final double kappa() { double[] sumRows = new double[m_ConfusionMatrix.length]; double[] sumColumns = new double[m_ConfusionMatrix.length]; double sumOfWeights = 0; for (int i = 0; i < m_ConfusionMatrix.length; i++) { for (int j = 0; j < m_ConfusionMatrix.length; j++) { sumRows[i] += m_ConfusionMatrix[i][j]; sumColumns[j] += m_ConfusionMatrix[i][j]; sumOfWeights += m_ConfusionMatrix[i][j]; } } double correct = 0, chanceAgreement = 0; for (int i = 0; i < m_ConfusionMatrix.length; i++) { chanceAgreement += (sumRows[i] * sumColumns[i]); correct += m_ConfusionMatrix[i][i]; } chanceAgreement /= (sumOfWeights * sumOfWeights); correct /= sumOfWeights; if (chanceAgreement < 1) { return (correct - chanceAgreement) / (1 - chanceAgreement); } else { return 1; } } /** * Returns the correlation coefficient if the class is numeric. * * @return the correlation coefficient * @throws Exception if class is not numeric */ public final double correlationCoefficient() throws Exception { if (m_ClassIsNominal) { throw new Exception("Can't compute correlation coefficient: " + "class is nominal!"); } double correlation = 0; double varActual = m_SumSqrClass - m_SumClass * m_SumClass / (m_WithClass - m_Unclassified); double varPredicted = m_SumSqrPredicted - m_SumPredicted * m_SumPredicted / (m_WithClass - m_Unclassified); double varProd = m_SumClassPredicted - m_SumClass * m_SumPredicted / (m_WithClass - m_Unclassified); if (varActual * varPredicted <= 0) { correlation = 0.0; } else { correlation = varProd / Math.sqrt(varActual * varPredicted); } return correlation; } /** * 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. * * @return the mean absolute error */ public final double meanAbsoluteError() { return m_SumAbsErr / (m_WithClass - m_Unclassified); } /** * Returns the mean absolute error of the prior. * * @return the mean absolute error */ public final double meanPriorAbsoluteError() { if (m_NoPriors) return Double.NaN; return m_SumPriorAbsErr / m_WithClass; } /** * Returns the relative absolute error. * * @return the relative absolute error * @throws Exception if it can't be computed */ public final double relativeAbsoluteError() throws Exception { if (m_NoPriors) return Double.NaN; return 100 * meanAbsoluteError() / meanPriorAbsoluteError(); } /** * Returns the root mean squared error. * * @return the root mean squared error */ public final double rootMeanSquaredError() { return Math.sqrt(m_SumSqrErr / (m_WithClass - m_Unclassified)); } /** * Returns the root mean prior squared error. * * @return the root mean prior squared error */ public final double rootMeanPriorSquaredError() { if (m_NoPriors) return Double.NaN; return Math.sqrt(m_SumPriorSqrErr / m_WithClass); } /** * Returns the root relative squared error if the class is numeric. * * @return the root relative squared error */ public final double rootRelativeSquaredError() { if (m_NoPriors) return Double.NaN; return 100.0 * rootMeanSquaredError() / rootMeanPriorSquaredError(); } /** * Calculate the entropy of the prior distribution * * @return the entropy of the prior distribution * @throws Exception if the class is not nominal */ public final double priorEntropy() throws Exception { if (!m_ClassIsNominal) { throw new Exception("Can't compute entropy of class prior: " + "class numeric!"); } if (m_NoPriors) return Double.NaN; double entropy = 0; for (int i = 0; i < m_NumClasses; i++) { entropy -= m_ClassPriors[i] / m_ClassPriorsSum * Utils.log2(m_ClassPriors[i] / m_ClassPriorsSum); } return entropy; } /** * Return the total Kononenko & Bratko Information score in bits * * @return the K&B information score * @throws Exception if the class is not nominal */ public final double KBInformation() throws Exception { if (!m_ClassIsNominal) { throw new Exception("Can't compute K&B Info score: " + "class numeric!"); } if (m_NoPriors) return Double.NaN; return m_SumKBInfo; } /** * Return the Kononenko & Bratko Information score in bits per * instance. * * @return the K&B information score * @throws Exception if the class is not nominal */ public final double KBMeanInformation() throws Exception { if (!m_ClassIsNominal) { throw new Exception("Can't compute K&B Info score: " + "class numeric!"); } if (m_NoPriors) return Double.NaN; return m_SumKBInfo / (m_WithClass - m_Unclassified); } /** * Return the Kononenko & Bratko Relative Information score * * @return the K&B relative information score * @throws Exception if the class is not nominal */ public final double KBRelativeInformation() throws Exception { if (!m_ClassIsNominal) { throw new Exception("Can't compute K&B Info score: " + "class numeric!"); } if (m_NoPriors) return Double.NaN; return 100.0 * KBInformation() / priorEntropy(); } /** * Returns the total entropy for the null model * * @return the total null model entropy */ public final double SFPriorEntropy() { if (m_NoPriors) return Double.NaN; return m_SumPriorEntropy; } /** * Returns the entropy per instance for the null model * * @return the null model entropy per instance */ public final double SFMeanPriorEntropy() { if (m_NoPriors) return Double.NaN; return m_SumPriorEntropy / m_WithClass; } /** * Returns the total entropy for the scheme * * @return the total scheme entropy */ public final double SFSchemeEntropy() { if (m_NoPriors) return Double.NaN; return m_SumSchemeEntropy; } /** * Returns the entropy per instance for the scheme * * @return the scheme entropy per instance */ public final double SFMeanSchemeEntropy() { if (m_NoPriors) return Double.NaN; return m_SumSchemeEntropy / (m_WithClass - m_Unclassified); } /** * Returns the total SF, which is the null model entropy minus * the scheme entropy. * * @return the total SF */ public final double SFEntropyGain() { if (m_NoPriors) return Double.NaN; return m_SumPriorEntropy - m_SumSchemeEntropy; } /** * Returns the SF per instance, which is the null model entropy * minus the scheme entropy, per instance. * * @return the SF per instance */ public final double SFMeanEntropyGain() { if (m_NoPriors) return Double.NaN; return (m_SumPriorEntropy - m_SumSchemeEntropy) / (m_WithClass - m_Unclassified); } /** * Output the cumulative margin distribution as a string suitable * for input for gnuplot or similar package. * * @return the cumulative margin distribution * @throws Exception if the class attribute is nominal */ public String toCumulativeMarginDistributionString() throws Exception { if (!m_ClassIsNominal) { throw new Exception("Class must be nominal for margin distributions"); } String result = ""; double cumulativeCount = 0; double margin; for (int i = 0; i <= k_MarginResolution; i++) { if (m_MarginCounts[i] != 0) { cumulativeCount += m_MarginCounts[i]; margin = (double) i * 2.0 / k_MarginResolution - 1.0; result = result + Utils.doubleToString(margin, 7, 3) + ' ' + Utils.doubleToString(cumulativeCount * 100 / m_WithClass, 7, 3) + '\n'; } else if (i == 0) { result = Utils.doubleToString(-1.0, 7, 3) + ' ' + Utils.doubleToString(0, 7, 3) + '\n'; } } return result; } /** * Calls toSummaryString() with no title and no complexity stats * * @return a summary description of the classifier evaluation */ public String toSummaryString() { return toSummaryString("", false); } /** * Calls toSummaryString() with a default title. * * @param printComplexityStatistics if true, complexity statistics are * returned as well * @return the summary string */ public String toSummaryString(boolean printComplexityStatistics) { return toSummaryString("=== Summary ===\n", 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. * * @param title the title for the statistics * @param printComplexityStatistics if true, complexity statistics are * returned as well * @return the summary as a String */ public String toSummaryString(String title, boolean printComplexityStatistics) { StringBuffer text = new StringBuffer(); if (printComplexityStatistics && m_NoPriors) { printComplexityStatistics = false; System.err.println("Priors disabled, cannot print complexity statistics!"); } text.append(title + "\n"); try { if (m_WithClass > 0) { if (m_ClassIsNominal) { text.append("Correctly Classified Instances "); text.append(Utils.doubleToString(correct(), 12, 4) + " " + Utils.doubleToString(pctCorrect(), 12, 4) + " %\n"); text.append("Incorrectly Classified Instances "); text.append(Utils.doubleToString(incorrect(), 12, 4) + " " + Utils.doubleToString(pctIncorrect(), 12, 4) + " %\n"); text.append("Kappa statistic "); text.append(Utils.doubleToString(kappa(), 12, 4) + "\n"); if (m_CostMatrix != null) { text.append("Total Cost "); text.append(Utils.doubleToString(totalCost(), 12, 4) + "\n"); text.append("Average Cost "); text.append(Utils.doubleToString(avgCost(), 12, 4) + "\n"); } if (printComplexityStatistics) { text.append("K&B Relative Info Score "); text.append(Utils.doubleToString(KBRelativeInformation(), 12, 4) + " %\n"); text.append("K&B Information Score "); text.append(Utils.doubleToString(KBInformation(), 12, 4) + " bits"); text.append(Utils.doubleToString(KBMeanInformation(), 12, 4) + " bits/instance\n"); } } else { text.append("Correlation coefficient "); text.append(Utils.doubleToString(correlationCoefficient(), 12, 4) + "\n"); } if (printComplexityStatistics) { text.append("Class complexity | order 0 "); text.append(Utils.doubleToString(SFPriorEntropy(), 12, 4) + " bits"); text.append(Utils.doubleToString(SFMeanPriorEntropy(), 12, 4) + " bits/instance\n"); text.append("Class complexity | scheme "); text.append(Utils.doubleToString(SFSchemeEntropy(), 12, 4) + " bits"); text.append(Utils.doubleToString(SFMeanSchemeEntropy(), 12, 4) + " bits/instance\n"); text.append("Complexity improvement (Sf) "); text.append(Utils.doubleToString(SFEntropyGain(), 12, 4) + " bits"); text.append(Utils.doubleToString(SFMeanEntropyGain(), 12, 4) + " bits/instance\n"); } text.append("Mean absolute error "); text.append(Utils.doubleToString(meanAbsoluteError(), 12, 4) + "\n"); text.append("Root mean squared error "); text.append(Utils.doubleToString(rootMeanSquaredError(), 12, 4) + "\n"); if (!m_NoPriors) { text.append("Relative absolute error "); text.append(Utils.doubleToString(relativeAbsoluteError(), 12, 4) + " %\n"); text.append("Root relative squared error "); text.append(Utils.doubleToString(rootRelativeSquaredError(), 12, 4) + " %\n"); } } if (Utils.gr(unclassified(), 0)) { text.append("UnClassified Instances "); text.append(Utils.doubleToString(unclassified(), 12, 4) + " " + Utils.doubleToString(pctUnclassified(), 12, 4) + " %\n"); } text.append("Total Number of Instances "); text.append(Utils.doubleToString(m_WithClass, 12, 4) + "\n"); if (m_MissingClass > 0) { text.append("Ignored Class Unknown Instances "); text.append(Utils.doubleToString(m_MissingClass, 12, 4) + "\n"); } } catch (Exception ex) { // Should never occur since the class is known to be nominal // here System.err.println("Arggh - Must be a bug in Evaluation class"); } return text.toString(); } /** * Calls toMatrixString() with a default title. * * @return the confusion matrix as a string * @throws Exception if the class is numeric */ public String toMatrixString() throws Exception { return toMatrixString("=== Confusion Matrix ===\n"); } /** * Outputs the performance statistics as a classification confusion * matrix. For each class value, shows the distribution of * predicted class values. * * @param title the title for the confusion matrix * @return the confusion matrix as a String * @throws Exception if the class is numeric */ public String toMatrixString(String title) throws Exception { StringBuffer text = new StringBuffer(); char[] IDChars = { 'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z' }; int IDWidth; boolean fractional = false; if (!m_ClassIsNominal) { throw new Exception("Evaluation: No confusion matrix possible!"); } // Find the maximum value in the matrix // and check for fractional display requirement double maxval = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { double current = m_ConfusionMatrix[i][j]; if (current < 0) { current *= -10; } if (current > maxval) { maxval = current; } double fract = current - Math.rint(current); if (!fractional && ((Math.log(fract) / Math.log(10)) >= -2)) { fractional = true; } } } IDWidth = 1 + Math.max((int) (Math.log(maxval) / Math.log(10) + (fractional ? 3 : 0)), (int) (Math.log(m_NumClasses) / Math.log(IDChars.length))); text.append(title).append("\n"); for (int i = 0; i < m_NumClasses; i++) { if (fractional) { text.append(" ").append(num2ShortID(i, IDChars, IDWidth - 3)).append(" "); } else { text.append(" ").append(num2ShortID(i, IDChars, IDWidth)); } } text.append(" <-- classified as\n"); for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { text.append(" ") .append(Utils.doubleToString(m_ConfusionMatrix[i][j], IDWidth, (fractional ? 2 : 0))); } text.append(" | ").append(num2ShortID(i, IDChars, IDWidth)).append(" = ").append(m_ClassNames[i]) .append("\n"); } return text.toString(); } /** * Generates a breakdown of the accuracy for each class (with default title), * incorporating various information-retrieval statistics, such as * true/false positive rate, precision/recall/F-Measure. Should be * useful for ROC curves, recall/precision curves. * * @return the statistics presented as a string * @throws Exception if class is not nominal */ public String toClassDetailsString() throws Exception { return toClassDetailsString("=== Detailed Accuracy By Class ===\n"); } /** * 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. * * @param title the title to prepend the stats string with * @return the statistics presented as a string * @throws Exception if class is not nominal */ public String toClassDetailsString(String title) throws Exception { if (!m_ClassIsNominal) { throw new Exception("Evaluation: No confusion matrix possible!"); } StringBuffer text = new StringBuffer(title + "\n TP Rate FP Rate" + " Precision Recall" + " F-Measure ROC Area PRC Area Class\n"); //doina for (int i = 0; i < m_NumClasses; i++) { text.append(" " + Utils.doubleToString(truePositiveRate(i), 7, 3)).append(" "); text.append(Utils.doubleToString(falsePositiveRate(i), 7, 3)).append(" "); text.append(Utils.doubleToString(precision(i), 7, 3)).append(" "); text.append(Utils.doubleToString(recall(i), 7, 3)).append(" "); text.append(Utils.doubleToString(fMeasure(i), 7, 3)).append(" "); double rocVal = areaUnderROC(i); if (Instance.isMissingValue(rocVal)) { text.append(" ? ").append(" "); } else { text.append(Utils.doubleToString(rocVal, 7, 3)).append(" "); } //doina double prcVal = areaUnderPRC(i); if (Instance.isMissingValue(prcVal)) { text.append(" ? ").append(" "); } else { text.append(Utils.doubleToString(prcVal, 7, 3)).append(" "); } //doina text.append(m_ClassNames[i]).append('\n'); } text.append("Weighted Avg. " + Utils.doubleToString(weightedTruePositiveRate(), 7, 3)); text.append(" " + Utils.doubleToString(weightedFalsePositiveRate(), 7, 3)); text.append(" " + Utils.doubleToString(weightedPrecision(), 7, 3)); text.append(" " + Utils.doubleToString(weightedRecall(), 7, 3)); text.append(" " + Utils.doubleToString(weightedFMeasure(), 7, 3)); text.append(" " + Utils.doubleToString(weightedAreaUnderROC(), 7, 3)); text.append(" " + Utils.doubleToString(weightedAreaUnderPRC(), 7, 3)); //doina text.append("\n"); return text.toString(); } /** * Calculate the number of true positives with respect to a particular class. * This is defined as<p/> * <pre> * correctly classified positives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the true positive rate */ public double numTruePositives(int classIndex) { double correct = 0; for (int j = 0; j < m_NumClasses; j++) { if (j == classIndex) { correct += m_ConfusionMatrix[classIndex][j]; } } return correct; } /** * Calculate the true positive rate with respect to a particular class. * This is defined as<p/> * <pre> * correctly classified positives * ------------------------------ * total positives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the true positive rate */ public double truePositiveRate(int classIndex) { double correct = 0, total = 0; for (int j = 0; j < m_NumClasses; j++) { if (j == classIndex) { correct += m_ConfusionMatrix[classIndex][j]; } total += m_ConfusionMatrix[classIndex][j]; } if (total == 0) { return 0; } return correct / total; } /** * Calculates the weighted (by class size) true positive rate. * * @return the weighted true positive rate. */ public double weightedTruePositiveRate() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double truePosTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = truePositiveRate(i); truePosTotal += (temp * classCounts[i]); } return truePosTotal / classCountSum; } /** * Calculate the number of true negatives with respect to a particular class. * This is defined as<p/> * <pre> * correctly classified negatives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the true positive rate */ public double numTrueNegatives(int classIndex) { double correct = 0; for (int i = 0; i < m_NumClasses; i++) { if (i != classIndex) { for (int j = 0; j < m_NumClasses; j++) { if (j != classIndex) { correct += m_ConfusionMatrix[i][j]; } } } } return correct; } /** * Calculate the true negative rate with respect to a particular class. * This is defined as<p/> * <pre> * correctly classified negatives * ------------------------------ * total negatives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the true positive rate */ public double trueNegativeRate(int classIndex) { double correct = 0, total = 0; for (int i = 0; i < m_NumClasses; i++) { if (i != classIndex) { for (int j = 0; j < m_NumClasses; j++) { if (j != classIndex) { correct += m_ConfusionMatrix[i][j]; } total += m_ConfusionMatrix[i][j]; } } } if (total == 0) { return 0; } return correct / total; } /** * Calculates the weighted (by class size) true negative rate. * * @return the weighted true negative rate. */ public double weightedTrueNegativeRate() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double trueNegTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = trueNegativeRate(i); trueNegTotal += (temp * classCounts[i]); } return trueNegTotal / classCountSum; } /** * Calculate number of false positives with respect to a particular class. * This is defined as<p/> * <pre> * incorrectly classified negatives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the false positive rate */ public double numFalsePositives(int classIndex) { double incorrect = 0; for (int i = 0; i < m_NumClasses; i++) { if (i != classIndex) { for (int j = 0; j < m_NumClasses; j++) { if (j == classIndex) { incorrect += m_ConfusionMatrix[i][j]; } } } } return incorrect; } /** * Calculate the false positive rate with respect to a particular class. * This is defined as<p/> * <pre> * incorrectly classified negatives * -------------------------------- * total negatives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the false positive rate */ public double falsePositiveRate(int classIndex) { double incorrect = 0, total = 0; for (int i = 0; i < m_NumClasses; i++) { if (i != classIndex) { for (int j = 0; j < m_NumClasses; j++) { if (j == classIndex) { incorrect += m_ConfusionMatrix[i][j]; } total += m_ConfusionMatrix[i][j]; } } } if (total == 0) { return 0; } return incorrect / total; } /** * Calculates the weighted (by class size) false positive rate. * * @return the weighted false positive rate. */ public double weightedFalsePositiveRate() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double falsePosTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = falsePositiveRate(i); falsePosTotal += (temp * classCounts[i]); } return falsePosTotal / classCountSum; } /** * Calculate number of false negatives with respect to a particular class. * This is defined as<p/> * <pre> * incorrectly classified positives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the false positive rate */ public double numFalseNegatives(int classIndex) { double incorrect = 0; for (int i = 0; i < m_NumClasses; i++) { if (i == classIndex) { for (int j = 0; j < m_NumClasses; j++) { if (j != classIndex) { incorrect += m_ConfusionMatrix[i][j]; } } } } return incorrect; } /** * Calculate the false negative rate with respect to a particular class. * This is defined as<p/> * <pre> * incorrectly classified positives * -------------------------------- * total positives * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the false positive rate */ public double falseNegativeRate(int classIndex) { double incorrect = 0, total = 0; for (int i = 0; i < m_NumClasses; i++) { if (i == classIndex) { for (int j = 0; j < m_NumClasses; j++) { if (j != classIndex) { incorrect += m_ConfusionMatrix[i][j]; } total += m_ConfusionMatrix[i][j]; } } } if (total == 0) { return 0; } return incorrect / total; } /** * Calculates the weighted (by class size) false negative rate. * * @return the weighted false negative rate. */ public double weightedFalseNegativeRate() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double falseNegTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = falseNegativeRate(i); falseNegTotal += (temp * classCounts[i]); } return falseNegTotal / classCountSum; } /** * Calculate the recall with respect to a particular class. * This is defined as<p/> * <pre> * correctly classified positives * ------------------------------ * total positives * </pre><p/> * (Which is also the same as the truePositiveRate.) * * @param classIndex the index of the class to consider as "positive" * @return the recall */ public double recall(int classIndex) { return truePositiveRate(classIndex); } /** * Calculates the weighted (by class size) recall. * * @return the weighted recall. */ public double weightedRecall() { return weightedTruePositiveRate(); } /** * Calculate the precision with respect to a particular class. * This is defined as<p/> * <pre> * correctly classified positives * ------------------------------ * total predicted as positive * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the precision */ public double precision(int classIndex) { double correct = 0, total = 0; for (int i = 0; i < m_NumClasses; i++) { if (i == classIndex) { correct += m_ConfusionMatrix[i][classIndex]; } total += m_ConfusionMatrix[i][classIndex]; } if (total == 0) { return 0; } return correct / total; } /** * Calculates the weighted (by class size) false precision. * * @return the weighted precision. */ public double weightedPrecision() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double precisionTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = precision(i); precisionTotal += (temp * classCounts[i]); } return precisionTotal / classCountSum; } /** * Calculate the F-Measure with respect to a particular class. * This is defined as<p/> * <pre> * 2 * recall * precision * ---------------------- * recall + precision * </pre> * * @param classIndex the index of the class to consider as "positive" * @return the F-Measure */ public double fMeasure(int classIndex) { double precision = precision(classIndex); double recall = recall(classIndex); if ((precision + recall) == 0) { return 0; } return 2 * precision * recall / (precision + recall); } /** * Calculates the weighted (by class size) F-Measure. * * @return the weighted F-Measure. */ public double weightedFMeasure() { double[] classCounts = new double[m_NumClasses]; double classCountSum = 0; for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { classCounts[i] += m_ConfusionMatrix[i][j]; } classCountSum += classCounts[i]; } double fMeasureTotal = 0; for (int i = 0; i < m_NumClasses; i++) { double temp = fMeasure(i); fMeasureTotal += (temp * classCounts[i]); } return fMeasureTotal / classCountSum; } /** * Sets the class prior probabilities * * @param train the training instances used to determine * the prior probabilities * @throws Exception if the class attribute of the instances is not * set */ public void setPriors(Instances train) throws Exception { m_NoPriors = false; if (!m_ClassIsNominal) { m_NumTrainClassVals = 0; m_TrainClassVals = null; m_TrainClassWeights = null; m_PriorErrorEstimator = null; m_ErrorEstimator = null; for (int i = 0; i < train.numInstances(); i++) { Instance currentInst = train.instance(i); if (!currentInst.classIsMissing()) { addNumericTrainClass(currentInst.classValue(), currentInst.weight()); } } } else { for (int i = 0; i < m_NumClasses; i++) { m_ClassPriors[i] = 1; } m_ClassPriorsSum = m_NumClasses; for (int i = 0; i < train.numInstances(); i++) { if (!train.instance(i).classIsMissing()) { m_ClassPriors[(int) train.instance(i).classValue()] += train.instance(i).weight(); m_ClassPriorsSum += train.instance(i).weight(); } } } } /** * Get the current weighted class counts * * @return the weighted class counts */ public double[] getClassPriors() { return m_ClassPriors; } /** * Updates the class prior probabilities (when incrementally * training) * * @param instance the new training instance seen * @throws Exception if the class of the instance is not * set */ public void updatePriors(Instance instance) throws Exception { if (!instance.classIsMissing()) { if (!m_ClassIsNominal) { if (!instance.classIsMissing()) { addNumericTrainClass(instance.classValue(), instance.weight()); } } else { m_ClassPriors[(int) instance.classValue()] += instance.weight(); m_ClassPriorsSum += instance.weight(); } } } /** * disables the use of priors, e.g., in case of de-serialized schemes * that have no access to the original training set, but are evaluated * on a set set. */ public void useNoPriors() { m_NoPriors = true; } /** * Tests whether the current evaluation object is equal to another * evaluation object * * @param obj the object to compare against * @return true if the two objects are equal */ public boolean equals(Object obj) { if ((obj == null) || !(obj.getClass().equals(this.getClass()))) { return false; } Evaluation_D cmp = (Evaluation_D) obj; if (m_ClassIsNominal != cmp.m_ClassIsNominal) return false; if (m_NumClasses != cmp.m_NumClasses) return false; if (m_Incorrect != cmp.m_Incorrect) return false; if (m_Correct != cmp.m_Correct) return false; if (m_Unclassified != cmp.m_Unclassified) return false; if (m_MissingClass != cmp.m_MissingClass) return false; if (m_WithClass != cmp.m_WithClass) return false; if (m_SumErr != cmp.m_SumErr) return false; if (m_SumAbsErr != cmp.m_SumAbsErr) return false; if (m_SumSqrErr != cmp.m_SumSqrErr) return false; if (m_SumClass != cmp.m_SumClass) return false; if (m_SumSqrClass != cmp.m_SumSqrClass) return false; if (m_SumPredicted != cmp.m_SumPredicted) return false; if (m_SumSqrPredicted != cmp.m_SumSqrPredicted) return false; if (m_SumClassPredicted != cmp.m_SumClassPredicted) return false; if (m_ClassIsNominal) { for (int i = 0; i < m_NumClasses; i++) { for (int j = 0; j < m_NumClasses; j++) { if (m_ConfusionMatrix[i][j] != cmp.m_ConfusionMatrix[i][j]) { return false; } } } } return true; } /** * Prints the predictions for the given dataset into a String variable. * * @param classifier the classifier to use * @param train the training data * @param testSource the test set * @param classIndex the class index (1-based), if -1 ot does not * override the class index is stored in the data * file (by using the last attribute) * @param attributesToOutput the indices of the attributes to output * @return the generated predictions for the attribute range * @throws Exception if test file cannot be opened */ public static void printClassifications(Classifier classifier, Instances train, DataSource testSource, int classIndex, Range attributesToOutput, StringBuffer predsText) throws Exception { printClassifications(classifier, train, testSource, classIndex, attributesToOutput, false, predsText); } /** * Prints the header for the predictions output into a supplied StringBuffer * * @param test structure of the test set to print predictions for * @param attributesToOutput indices of the attributes to output * @param printDistribution prints the complete distribution for nominal * attributes, not just the predicted value * @param text the StringBuffer to print to */ protected static void printClassificationsHeader(Instances test, Range attributesToOutput, boolean printDistribution, StringBuffer text) { // print header if (test.classAttribute().isNominal()) if (printDistribution) text.append(" inst# actual predicted error distribution"); else text.append(" inst# actual predicted error prediction"); else text.append(" inst# actual predicted error"); if (attributesToOutput != null) { attributesToOutput.setUpper(test.numAttributes() - 1); text.append(" ("); boolean first = true; for (int i = 0; i < test.numAttributes(); i++) { if (i == test.classIndex()) continue; if (attributesToOutput.isInRange(i)) { if (!first) text.append(","); text.append(test.attribute(i).name()); first = false; } } text.append(")"); } text.append("\n"); } /** * Prints the predictions for the given dataset into a supplied StringBuffer * * @param classifier the classifier to use * @param train the training data * @param testSource the test set * @param classIndex the class index (1-based), if -1 ot does not * override the class index is stored in the data * file (by using the last attribute) * @param attributesToOutput the indices of the attributes to output * @param printDistribution prints the complete distribution for nominal * classes, not just the predicted value * @param text StringBuffer to hold the printed predictions * @throws Exception if test file cannot be opened */ public static void printClassifications(Classifier classifier, Instances train, DataSource testSource, int classIndex, Range attributesToOutput, boolean printDistribution, StringBuffer text) throws Exception { if (testSource != null) { Instances test = testSource.getStructure(); if (classIndex != -1) { test.setClassIndex(classIndex - 1); } else { if (test.classIndex() == -1) test.setClassIndex(test.numAttributes() - 1); } // print the header printClassificationsHeader(test, attributesToOutput, printDistribution, text); // print predictions int i = 0; testSource.reset(); test = testSource.getStructure(test.classIndex()); while (testSource.hasMoreElements(test)) { Instance inst = testSource.nextElement(test); text.append(predictionText(classifier, inst, i, attributesToOutput, printDistribution)); i++; } } // return text.toString(); } /** * store the prediction made by the classifier as a string * * @param classifier the classifier to use * @param inst the instance to generate text from * @param instNum the index in the dataset * @param attributesToOutput the indices of the attributes to output * @param printDistribution prints the complete distribution for nominal * classes, not just the predicted value * @return the prediction as a String * @throws Exception if something goes wrong * @see #printClassifications(Classifier, Instances, String, int, Range, boolean) */ protected static String predictionText(Classifier classifier, Instance inst, int instNum, Range attributesToOutput, boolean printDistribution) throws Exception { StringBuffer result = new StringBuffer(); int width = 10; int prec = 3; Instance withMissing = (Instance) inst.copy(); withMissing.setDataset(inst.dataset()); withMissing.setMissing(withMissing.classIndex()); double predValue = classifier.classifyInstance(withMissing); // index result.append(Utils.padLeft("" + (instNum + 1), 6)); if (inst.dataset().classAttribute().isNumeric()) { // actual if (inst.classIsMissing()) result.append(" " + Utils.padLeft("?", width)); else result.append(" " + Utils.doubleToString(inst.classValue(), width, prec)); // predicted if (Instance.isMissingValue(predValue)) result.append(" " + Utils.padLeft("?", width)); else result.append(" " + Utils.doubleToString(predValue, width, prec)); // error if (Instance.isMissingValue(predValue) || inst.classIsMissing()) result.append(" " + Utils.padLeft("?", width)); else result.append(" " + Utils.doubleToString(predValue - inst.classValue(), width, prec)); } else { // actual result.append(" " + Utils.padLeft(((int) inst.classValue() + 1) + ":" + inst.toString(inst.classIndex()), width)); // predicted if (Instance.isMissingValue(predValue)) result.append(" " + Utils.padLeft("?", width)); else result.append(" " + Utils.padLeft( ((int) predValue + 1) + ":" + inst.dataset().classAttribute().value((int) predValue), width)); // error? if (!Instance.isMissingValue(predValue) && !inst.classIsMissing() && ((int) predValue + 1 != (int) inst.classValue() + 1)) result.append(" " + " + "); else result.append(" " + " "); // prediction/distribution if (printDistribution) { if (Instance.isMissingValue(predValue)) { result.append(" " + "?"); } else { result.append(" "); double[] dist = classifier.distributionForInstance(withMissing); for (int n = 0; n < dist.length; n++) { if (n > 0) result.append(","); if (n == (int) predValue) result.append("*"); result.append(Utils.doubleToString(dist[n], prec)); } } } else { if (Instance.isMissingValue(predValue)) result.append(" " + "?"); else result.append(" " + Utils.doubleToString( classifier.distributionForInstance(withMissing)[(int) predValue], prec)); } } // attributes result.append(" " + attributeValuesString(withMissing, attributesToOutput) + "\n"); return result.toString(); } /** * Builds a string listing the attribute values in a specified range of indices, * separated by commas and enclosed in brackets. * * @param instance the instance to print the values from * @param attRange the range of the attributes to list * @return a string listing values of the attributes in the range */ protected static String attributeValuesString(Instance instance, Range attRange) { StringBuffer text = new StringBuffer(); if (attRange != null) { boolean firstOutput = true; attRange.setUpper(instance.numAttributes() - 1); for (int i = 0; i < instance.numAttributes(); i++) if (attRange.isInRange(i) && i != instance.classIndex()) { if (firstOutput) text.append("("); else text.append(","); text.append(instance.toString(i)); firstOutput = false; } if (!firstOutput) text.append(")"); } return text.toString(); } /** * Make up the help string giving all the command line options * * @param classifier the classifier to include options for * @param globalInfo include the global information string * for the classifier (if available). * @return a string detailing the valid command line options */ protected static String makeOptionString(Classifier classifier, boolean globalInfo) { StringBuffer optionsText = new StringBuffer(""); // General options optionsText.append("\n\nGeneral options:\n\n"); optionsText.append("-h or -help\n"); optionsText.append("\tOutput help information.\n"); optionsText.append("-synopsis or -info\n"); optionsText.append("\tOutput synopsis for classifier (use in conjunction " + " with -h)\n"); optionsText.append("-t <name of training file>\n"); optionsText.append("\tSets training file.\n"); optionsText.append("-T <name of test file>\n"); optionsText.append("\tSets test file. If missing, a cross-validation will be performed\n"); optionsText.append("\ton the training data.\n"); optionsText.append("-c <class index>\n"); optionsText.append("\tSets index of class attribute (default: last).\n"); optionsText.append("-x <number of folds>\n"); optionsText.append("\tSets number of folds for cross-validation (default: 10).\n"); optionsText.append("-no-cv\n"); optionsText.append("\tDo not perform any cross validation.\n"); optionsText.append("-split-percentage <percentage>\n"); optionsText.append("\tSets the percentage for the train/test set split, e.g., 66.\n"); optionsText.append("-preserve-order\n"); optionsText.append("\tPreserves the order in the percentage split.\n"); optionsText.append("-s <random number seed>\n"); optionsText.append("\tSets random number seed for cross-validation or percentage split\n"); optionsText.append("\t(default: 1).\n"); optionsText.append("-m <name of file with cost matrix>\n"); optionsText.append("\tSets file with cost matrix.\n"); optionsText.append("-l <name of input file>\n"); optionsText.append("\tSets model input file. In case the filename ends with '.xml',\n"); optionsText.append("\ta PMML file is loaded or, if that fails, options are loaded\n"); optionsText.append("\tfrom the XML file.\n"); optionsText.append("-d <name of output file>\n"); optionsText.append("\tSets model output file. In case the filename ends with '.xml',\n"); optionsText.append("\tonly the options are saved to the XML file, not the model.\n"); optionsText.append("-v\n"); optionsText.append("\tOutputs no statistics for training data.\n"); optionsText.append("-o\n"); optionsText.append("\tOutputs statistics only, not the classifier.\n"); optionsText.append("-i\n"); optionsText.append("\tOutputs detailed information-retrieval"); optionsText.append(" statistics for each class.\n"); optionsText.append("-k\n"); optionsText.append("\tOutputs information-theoretic statistics.\n"); optionsText.append("-p <attribute range>\n"); optionsText.append("\tOnly outputs predictions for test instances (or the train\n" + "\tinstances if no test instances provided and -no-cv is used),\n" + "\talong with attributes (0 for none).\n"); optionsText.append("-distribution\n"); optionsText.append("\tOutputs the distribution instead of only the prediction\n"); optionsText.append("\tin conjunction with the '-p' option (only nominal classes).\n"); optionsText.append("-r\n"); optionsText.append("\tOnly outputs cumulative margin distribution.\n"); if (classifier instanceof Sourcable) { optionsText.append("-z <class name>\n"); optionsText.append("\tOnly outputs the source representation" + " of the classifier,\n\tgiving it the supplied" + " name.\n"); } if (classifier instanceof Drawable) { optionsText.append("-g\n"); optionsText.append("\tOnly outputs the graph representation" + " of the classifier.\n"); } optionsText.append("-xml filename | xml-string\n"); optionsText.append("\tRetrieves the options from the XML-data instead of the " + "command line.\n"); optionsText.append("-threshold-file <file>\n"); optionsText.append("\tThe file to save the threshold data to.\n" + "\tThe format is determined by the extensions, e.g., '.arff' for ARFF \n" + "\tformat or '.csv' for CSV.\n"); optionsText.append("-threshold-label <label>\n"); optionsText.append( "\tThe class label to determine the threshold data for\n" + "\t(default is the first label)\n"); // Get scheme-specific options if (classifier instanceof OptionHandler) { optionsText.append("\nOptions specific to " + classifier.getClass().getName() + ":\n\n"); Enumeration enu = ((OptionHandler) classifier).listOptions(); while (enu.hasMoreElements()) { Option option = (Option) enu.nextElement(); optionsText.append(option.synopsis() + '\n'); optionsText.append(option.description() + "\n"); } } // Get global information (if available) if (globalInfo) { try { String gi = getGlobalInfo(classifier); optionsText.append(gi); } catch (Exception ex) { // quietly ignore } } return optionsText.toString(); } /** * Return the global info (if it exists) for the supplied classifier * * @param classifier the classifier to get the global info for * @return the global info (synopsis) for the classifier * @throws Exception if there is a problem reflecting on the classifier */ protected static String getGlobalInfo(Classifier classifier) throws Exception { BeanInfo bi = Introspector.getBeanInfo(classifier.getClass()); MethodDescriptor[] methods; methods = bi.getMethodDescriptors(); Object[] args = {}; String result = "\nSynopsis for " + classifier.getClass().getName() + ":\n\n"; for (int i = 0; i < methods.length; i++) { String name = methods[i].getDisplayName(); Method meth = methods[i].getMethod(); if (name.equals("globalInfo")) { String globalInfo = (String) (meth.invoke(classifier, args)); result += globalInfo; break; } } return result; } /** * Method for generating indices for the confusion matrix. * * @param num integer to format * @param IDChars the characters to use * @param IDWidth the width of the entry * @return the formatted integer as a string */ protected String num2ShortID(int num, char[] IDChars, int IDWidth) { char ID[] = new char[IDWidth]; int i; for (i = IDWidth - 1; i >= 0; i--) { ID[i] = IDChars[num % IDChars.length]; num = num / IDChars.length - 1; if (num < 0) { break; } } for (i--; i >= 0; i--) { ID[i] = ' '; } return new String(ID); } /** * Convert a single prediction into a probability distribution * with all zero probabilities except the predicted value which * has probability 1.0; * * @param predictedClass the index of the predicted class * @return the probability distribution */ protected double[] makeDistribution(double predictedClass) { double[] result = new double[m_NumClasses]; if (Instance.isMissingValue(predictedClass)) { return result; } if (m_ClassIsNominal) { result[(int) predictedClass] = 1.0; } else { result[0] = predictedClass; } return result; } /** * Updates all the statistics about a classifiers performance for * the current test instance. * * @param predictedDistribution the probabilities assigned to * each class * @param instance the instance to be classified * @throws Exception if the class of the instance is not * set */ protected void updateStatsForClassifier(double[] predictedDistribution, Instance instance) throws Exception { int actualClass = (int) instance.classValue(); if (!instance.classIsMissing()) { updateMargins(predictedDistribution, actualClass, instance.weight()); // Determine the predicted class (doesn't detect multiple // classifications) int predictedClass = -1; double bestProb = 0.0; for (int i = 0; i < m_NumClasses; i++) { if (predictedDistribution[i] > bestProb) { predictedClass = i; bestProb = predictedDistribution[i]; } } m_WithClass += instance.weight(); // Determine misclassification cost if (m_CostMatrix != null) { if (predictedClass < 0) { // For missing predictions, we assume the worst possible cost. // This is pretty harsh. // Perhaps we could take the negative of the cost of a correct // prediction (-m_CostMatrix.getElement(actualClass,actualClass)), // although often this will be zero m_TotalCost += instance.weight() * m_CostMatrix.getMaxCost(actualClass, instance); } else { m_TotalCost += instance.weight() * m_CostMatrix.getElement(actualClass, predictedClass, instance); } } // Update counts when no class was predicted if (predictedClass < 0) { m_Unclassified += instance.weight(); return; } double predictedProb = Math.max(MIN_SF_PROB, predictedDistribution[actualClass]); double priorProb = Math.max(MIN_SF_PROB, m_ClassPriors[actualClass] / m_ClassPriorsSum); if (predictedProb >= priorProb) { m_SumKBInfo += (Utils.log2(predictedProb) - Utils.log2(priorProb)) * instance.weight(); } else { m_SumKBInfo -= (Utils.log2(1.0 - predictedProb) - Utils.log2(1.0 - priorProb)) * instance.weight(); } m_SumSchemeEntropy -= Utils.log2(predictedProb) * instance.weight(); m_SumPriorEntropy -= Utils.log2(priorProb) * instance.weight(); updateNumericScores(predictedDistribution, makeDistribution(instance.classValue()), instance.weight()); // Update other stats m_ConfusionMatrix[actualClass][predictedClass] += instance.weight(); if (predictedClass != actualClass) { m_Incorrect += instance.weight(); } else { m_Correct += instance.weight(); } } else { m_MissingClass += instance.weight(); } } /** * Updates all the statistics about a predictors performance for * the current test instance. * * @param predictedValue the numeric value the classifier predicts * @param instance the instance to be classified * @throws Exception if the class of the instance is not * set */ protected void updateStatsForPredictor(double predictedValue, Instance instance) throws Exception { if (!instance.classIsMissing()) { // Update stats m_WithClass += instance.weight(); if (Instance.isMissingValue(predictedValue)) { m_Unclassified += instance.weight(); return; } m_SumClass += instance.weight() * instance.classValue(); m_SumSqrClass += instance.weight() * instance.classValue() * instance.classValue(); m_SumClassPredicted += instance.weight() * instance.classValue() * predictedValue; m_SumPredicted += instance.weight() * predictedValue; m_SumSqrPredicted += instance.weight() * predictedValue * predictedValue; if (m_ErrorEstimator == null) { setNumericPriorsFromBuffer(); } double predictedProb = Math.max(m_ErrorEstimator.getProbability(predictedValue - instance.classValue()), MIN_SF_PROB); double priorProb = Math.max(m_PriorErrorEstimator.getProbability(instance.classValue()), MIN_SF_PROB); m_SumSchemeEntropy -= Utils.log2(predictedProb) * instance.weight(); m_SumPriorEntropy -= Utils.log2(priorProb) * instance.weight(); m_ErrorEstimator.addValue(predictedValue - instance.classValue(), instance.weight()); updateNumericScores(makeDistribution(predictedValue), makeDistribution(instance.classValue()), instance.weight()); } else m_MissingClass += instance.weight(); } /** * Update the cumulative record of classification margins * * @param predictedDistribution the probability distribution predicted for * the current instance * @param actualClass the index of the actual instance class * @param weight the weight assigned to the instance */ protected void updateMargins(double[] predictedDistribution, int actualClass, double weight) { double probActual = predictedDistribution[actualClass]; double probNext = 0; for (int i = 0; i < m_NumClasses; i++) if ((i != actualClass) && (predictedDistribution[i] > probNext)) probNext = predictedDistribution[i]; double margin = probActual - probNext; int bin = (int) ((margin + 1.0) / 2.0 * k_MarginResolution); m_MarginCounts[bin] += weight; } /** * Update the numeric accuracy measures. For numeric classes, the * accuracy is between the actual and predicted class values. For * nominal classes, the accuracy is between the actual and * predicted class probabilities. * * @param predicted the predicted values * @param actual the actual value * @param weight the weight associated with this prediction */ protected void updateNumericScores(double[] predicted, double[] actual, double weight) { double diff; double sumErr = 0, sumAbsErr = 0, sumSqrErr = 0; double sumPriorAbsErr = 0, sumPriorSqrErr = 0; for (int i = 0; i < m_NumClasses; i++) { diff = predicted[i] - actual[i]; sumErr += diff; sumAbsErr += Math.abs(diff); sumSqrErr += diff * diff; diff = (m_ClassPriors[i] / m_ClassPriorsSum) - actual[i]; sumPriorAbsErr += Math.abs(diff); sumPriorSqrErr += diff * diff; } m_SumErr += weight * sumErr / m_NumClasses; m_SumAbsErr += weight * sumAbsErr / m_NumClasses; m_SumSqrErr += weight * sumSqrErr / m_NumClasses; m_SumPriorAbsErr += weight * sumPriorAbsErr / m_NumClasses; m_SumPriorSqrErr += weight * sumPriorSqrErr / m_NumClasses; } /** * Adds a numeric (non-missing) training class value and weight to * the buffer of stored values. * * @param classValue the class value * @param weight the instance weight */ protected void addNumericTrainClass(double classValue, double weight) { if (m_TrainClassVals == null) { m_TrainClassVals = new double[100]; m_TrainClassWeights = new double[100]; } if (m_NumTrainClassVals == m_TrainClassVals.length) { double[] temp = new double[m_TrainClassVals.length * 2]; System.arraycopy(m_TrainClassVals, 0, temp, 0, m_TrainClassVals.length); m_TrainClassVals = temp; temp = new double[m_TrainClassWeights.length * 2]; System.arraycopy(m_TrainClassWeights, 0, temp, 0, m_TrainClassWeights.length); m_TrainClassWeights = temp; } m_TrainClassVals[m_NumTrainClassVals] = classValue; m_TrainClassWeights[m_NumTrainClassVals] = weight; m_NumTrainClassVals++; } /** * Sets up the priors for numeric class attributes from the * training class values that have been seen so far. */ protected void setNumericPriorsFromBuffer() { double numPrecision = 0.01; // Default value if (m_NumTrainClassVals > 1) { double[] temp = new double[m_NumTrainClassVals]; System.arraycopy(m_TrainClassVals, 0, temp, 0, m_NumTrainClassVals); int[] index = Utils.sort(temp); double lastVal = temp[index[0]]; double deltaSum = 0; int distinct = 0; for (int i = 1; i < temp.length; i++) { double current = temp[index[i]]; if (current != lastVal) { deltaSum += current - lastVal; lastVal = current; distinct++; } } if (distinct > 0) { numPrecision = deltaSum / distinct; } } m_PriorErrorEstimator = new KernelEstimator(numPrecision); m_ErrorEstimator = new KernelEstimator(numPrecision); m_ClassPriors[0] = m_ClassPriorsSum = 0; for (int i = 0; i < m_NumTrainClassVals; i++) { m_ClassPriors[0] += m_TrainClassVals[i] * m_TrainClassWeights[i]; m_ClassPriorsSum += m_TrainClassWeights[i]; m_PriorErrorEstimator.addValue(m_TrainClassVals[i], m_TrainClassWeights[i]); } } //doina,cornelia's change public void setPredictions(FastVector predictions) { m_Predictions = predictions; } /** * Returns the area under PRC for those predictions that have been collected * in the evaluateClassifier(Classifier, Instances) method. Returns * Instance.missingValue() if the area is not available. * * @param classIndex the index of the class to consider as "positive" * @return the area under the PRC curve or not a number * @author doina */ public double areaUnderPRC(int classIndex) { // Check if any predictions have been collected if (m_Predictions == null) { return Instance.missingValue(); } else { ThresholdCurve tc = new ThresholdCurve(); Instances result = tc.getCurve(m_Predictions, classIndex); return ThresholdCurve.getNPointPrecision(result, 11); } } /** * Returns the revision string. * * @return the revision */ public String getRevision() { return RevisionUtils.extract("$Revision: 5913 $"); } }