// 将样本集中裁剪提取成m个样本组成的集合；
public void SubSample(Instances inst, int m) {
inst.randomize(new Random());
while (inst.numInstances() != m) {
inst.delete(0);
}
// System.out.println("subsample:=" + inst.numInstances() + " m:=" + m );
}
/**
* Buildclassifier selects a classifier from the set of classifiers by minimising error on the
* training data.
*
* @param data the training data to be used for generating the boosted classifier.
* @exception Exception if the classifier could not be built successfully
*/
public void buildClassifier(Instances data) throws Exception {
if (m_Classifiers.length == 0) {
throw new Exception("No base classifiers have been set!");
}
Instances newData = new Instances(data);
newData.deleteWithMissingClass();
newData.randomize(new Random(m_Seed));
if (newData.classAttribute().isNominal() && (m_NumXValFolds > 1))
newData.stratify(m_NumXValFolds);
Instances train = newData; // train on all data by default
Instances test = newData; // test on training data by default
Classifier bestClassifier = null;
int bestIndex = -1;
double bestPerformance = Double.NaN;
int numClassifiers = m_Classifiers.length;
for (int i = 0; i < numClassifiers; i++) {
Classifier currentClassifier = getClassifier(i);
Evaluation evaluation;
if (m_NumXValFolds > 1) {
evaluation = new Evaluation(newData);
for (int j = 0; j < m_NumXValFolds; j++) {
train = newData.trainCV(m_NumXValFolds, j);
test = newData.testCV(m_NumXValFolds, j);
currentClassifier.buildClassifier(train);
evaluation.setPriors(train);
evaluation.evaluateModel(currentClassifier, test);
}
} else {
currentClassifier.buildClassifier(train);
evaluation = new Evaluation(train);
evaluation.evaluateModel(currentClassifier, test);
}
double error = evaluation.errorRate();
if (m_Debug) {
System.err.println(
"Error rate: "
+ Utils.doubleToString(error, 6, 4)
+ " for classifier "
+ currentClassifier.getClass().getName());
}
if ((i == 0) || (error < bestPerformance)) {
bestClassifier = currentClassifier;
bestPerformance = error;
bestIndex = i;
}
}
m_ClassifierIndex = bestIndex;
m_Classifier = bestClassifier;
if (m_NumXValFolds > 1) {
m_Classifier.buildClassifier(newData);
}
}
// Create 70% training data set
public void generateTrainingDataSet() {
trainingDataSet = new Instances(instances);
int size = trainingDataSet.numInstances();
// Remove closing prize "close" attribute
trainingDataSet.deleteAttributeAt(0);
// Randomize data set
trainingDataSet.randomize(trainingDataSet.getRandomNumberGenerator(1));
}
public void split() throws IOException {
FileSystem fs = FileSystem.get(new Configuration());
fs.delete(splitsDir, true);
instances.randomize(new Random(1));
instances.stratify(numberOfSplits);
for (int i = 0; i < numberOfSplits; i++) {
BufferedWriter bw =
new BufferedWriter(
new OutputStreamWriter(fs.create(new Path(splitsDir, "train_split_" + i + ".arff"))));
bw.write(instances.testCV(numberOfSplits, i).toString());
bw.close();
}
}
/**
* Generates the classifier.
*
* @param instances set of instances serving as training data
* @throws Exception if the classifier has not been generated successfully
*/
public void buildClassifier(Instances instances) throws Exception {
// can classifier handle the data?
getCapabilities().testWithFail(instances);
// remove instances with missing class
Instances trainData = new Instances(instances);
trainData.deleteWithMissingClass();
if (!(m_Classifier instanceof OptionHandler)) {
throw new IllegalArgumentException("Base classifier should be OptionHandler.");
}
m_InitOptions = ((OptionHandler) m_Classifier).getOptions();
m_BestPerformance = -99;
m_NumAttributes = trainData.numAttributes();
Random random = new Random(m_Seed);
trainData.randomize(random);
m_TrainFoldSize = trainData.trainCV(m_NumFolds, 0).numInstances();
// Check whether there are any parameters to optimize
if (m_CVParams.size() == 0) {
m_Classifier.buildClassifier(trainData);
m_BestClassifierOptions = m_InitOptions;
return;
}
if (trainData.classAttribute().isNominal()) {
trainData.stratify(m_NumFolds);
}
m_BestClassifierOptions = null;
// Set up m_ClassifierOptions -- take getOptions() and remove
// those being optimised.
m_ClassifierOptions = ((OptionHandler) m_Classifier).getOptions();
for (int i = 0; i < m_CVParams.size(); i++) {
Utils.getOption(((CVParameter) m_CVParams.elementAt(i)).m_ParamChar, m_ClassifierOptions);
}
findParamsByCrossValidation(0, trainData, random);
String[] options = (String[]) m_BestClassifierOptions.clone();
((OptionHandler) m_Classifier).setOptions(options);
m_Classifier.buildClassifier(trainData);
}
public static void main(String[] args) throws Exception {
BufferedReader reader = new BufferedReader(new FileReader("spambase.arff"));
Instances data = new Instances(reader);
reader.close();
// setting class attribute
data.setClassIndex(data.numAttributes() - 1);
int i = data.numInstances();
int j = data.numAttributes() - 1;
File file = new File("tablelog.csv");
Writer output = null;
output = new BufferedWriter(new FileWriter(file));
output.write(
"%missing,auc1,correct1,fmeasure1,auc2,correct2,fmeasure2,auc3,correct3,fmeasure3\n");
Random randomGenerator = new Random();
data.randomize(randomGenerator);
int numBlock = data.numInstances() / 2;
double num0 = 0, num1 = 0, num2 = 0;
/*mdata.instance(0).setMissing(0);
mdata.deleteWithMissing(0);
System.out.println(mdata.numInstances()+","+data.numInstances());*/
// Instances traindata=null;
// Instances testdata=null;
// System.out.println(data.instance(3).stringValue(1));
for (int perc = 10; perc < 101; perc = perc + 10) {
Instances mdata = new Instances(data);
int numMissing = perc * numBlock / 100;
double y11[] = new double[2];
double y21[] = new double[2];
double y31[] = new double[2];
double y12[] = new double[2];
double y22[] = new double[2];
double y32[] = new double[2];
double y13[] = new double[2];
double y23[] = new double[2];
double y33[] = new double[2];
for (int p = 0; p < 2; p++) {
Instances traindata = mdata.trainCV(2, p);
Instances testdata = mdata.testCV(2, p);
num0 = 0;
num1 = 0;
num2 = 0;
for (int t = 0; t < numBlock; t++) {
if (traindata.instance(t).classValue() == 0) num0++;
if (traindata.instance(t).classValue() == 1) num1++;
// if (traindata.instance(t).classValue()==2) num2++;
}
// System.out.println(mdata.instance(0).classValue());
Instances trainwithmissing = new Instances(traindata);
Instances testwithmissing = new Instances(testdata);
for (int q = 0; q < j; q++) {
int r = randomGenerator.nextInt((int) i / 2);
for (int k = 0; k < numMissing; k++) {
// int r = randomGenerator.nextInt((int) i/2);
// int c = randomGenerator.nextInt(j);
trainwithmissing.instance((r + k) % numBlock).setMissing(q);
testwithmissing.instance((r + k) % numBlock).setMissing(q);
}
}
// trainwithmissing.deleteWithMissing(0);System.out.println(traindata.numInstances()+","+trainwithmissing.numInstances());
Classifier cModel =
(Classifier) new Logistic(); // try for different classifiers and datasets
cModel.buildClassifier(trainwithmissing);
Evaluation eTest1 = new Evaluation(trainwithmissing);
eTest1.evaluateModel(cModel, testdata);
// eTest.crossValidateModel(cModel,mdata,10,mdata.getRandomNumberGenerator(1));
y11[p] =
num0 / numBlock * eTest1.areaUnderROC(0)
+ num1
/ numBlock
* eTest1.areaUnderROC(1) /*+num2/numBlock*eTest1.areaUnderROC(2)*/;
y21[p] = eTest1.correct();
y31[p] =
num0 / numBlock * eTest1.fMeasure(0)
+ num1 / numBlock * eTest1.fMeasure(1) /*+num2/numBlock*eTest1.fMeasure(2)*/;
Classifier cModel2 = (Classifier) new Logistic();
cModel2.buildClassifier(traindata);
Evaluation eTest2 = new Evaluation(traindata);
eTest2.evaluateModel(cModel2, testwithmissing);
y12[p] =
num0 / numBlock * eTest2.areaUnderROC(0)
+ num1
/ numBlock
* eTest2.areaUnderROC(1) /*+num2/numBlock*eTest2.areaUnderROC(2)*/;
y22[p] = eTest2.correct();
y32[p] =
num0 / numBlock * eTest2.fMeasure(0)
+ num1 / numBlock * eTest2.fMeasure(1) /*+num2/numBlock*eTest2.fMeasure(2)*/;
Classifier cModel3 = (Classifier) new Logistic();
cModel3.buildClassifier(trainwithmissing);
Evaluation eTest3 = new Evaluation(trainwithmissing);
eTest3.evaluateModel(cModel3, testwithmissing);
y13[p] =
num0 / numBlock * eTest3.areaUnderROC(0)
+ num1
/ numBlock
* eTest3.areaUnderROC(1) /*+num2/numBlock*eTest3.areaUnderROC(2)*/;
y23[p] = eTest3.correct();
y33[p] =
num0 / numBlock * eTest3.fMeasure(0)
+ num1 / numBlock * eTest3.fMeasure(1) /*+num2/numBlock*eTest3.fMeasure(2)*/;
// System.out.println(num0+","+num1+","+num2+"\n");
}
double auc1 = (y11[0] + y11[1]) / 2;
double auc2 = (y12[0] + y12[1]) / 2;
double auc3 = (y13[0] + y13[1]) / 2;
double corr1 = (y21[0] + y21[1]) / i;
double corr2 = (y22[0] + y22[1]) / i;
double corr3 = (y23[0] + y23[1]) / i;
double fm1 = (y31[0] + y31[1]) / 2;
double fm2 = (y32[0] + y32[1]) / 2;
double fm3 = (y33[0] + y33[1]) / 2;
output.write(
perc + "," + auc1 + "," + corr1 + "," + fm1 + "," + auc2 + "," + corr2 + "," + fm2 + ","
+ auc3 + "," + corr3 + "," + fm3 + "\n"); // System.out.println(num0);
// mdata=data;
}
output.close();
}
/**
* Carry out the bias-variance decomposition
*
* @throws Exception if the decomposition couldn't be carried out
*/
public void decompose() throws Exception {
Reader dataReader = new BufferedReader(new FileReader(m_DataFileName));
Instances data = new Instances(dataReader);
if (m_ClassIndex < 0) {
data.setClassIndex(data.numAttributes() - 1);
} else {
data.setClassIndex(m_ClassIndex);
}
if (data.classAttribute().type() != Attribute.NOMINAL) {
throw new Exception("Class attribute must be nominal");
}
int numClasses = data.numClasses();
data.deleteWithMissingClass();
if (data.checkForStringAttributes()) {
throw new Exception("Can't handle string attributes!");
}
if (data.numInstances() < 2 * m_TrainPoolSize) {
throw new Exception(
"The dataset must contain at least " + (2 * m_TrainPoolSize) + " instances");
}
Random random = new Random(m_Seed);
data.randomize(random);
Instances trainPool = new Instances(data, 0, m_TrainPoolSize);
Instances test = new Instances(data, m_TrainPoolSize, data.numInstances() - m_TrainPoolSize);
int numTest = test.numInstances();
double[][] instanceProbs = new double[numTest][numClasses];
m_Error = 0;
for (int i = 0; i < m_TrainIterations; i++) {
if (m_Debug) {
System.err.println("Iteration " + (i + 1));
}
trainPool.randomize(random);
Instances train = new Instances(trainPool, 0, m_TrainPoolSize / 2);
Classifier current = AbstractClassifier.makeCopy(m_Classifier);
current.buildClassifier(train);
//// Evaluate the classifier on test, updating BVD stats
for (int j = 0; j < numTest; j++) {
int pred = (int) current.classifyInstance(test.instance(j));
if (pred != test.instance(j).classValue()) {
m_Error++;
}
instanceProbs[j][pred]++;
}
}
m_Error /= (m_TrainIterations * numTest);
// Average the BV over each instance in test.
m_Bias = 0;
m_Variance = 0;
m_Sigma = 0;
for (int i = 0; i < numTest; i++) {
Instance current = test.instance(i);
double[] predProbs = instanceProbs[i];
double pActual, pPred;
double bsum = 0, vsum = 0, ssum = 0;
for (int j = 0; j < numClasses; j++) {
pActual = (current.classValue() == j) ? 1 : 0; // Or via 1NN from test data?
pPred = predProbs[j] / m_TrainIterations;
bsum +=
(pActual - pPred) * (pActual - pPred) - pPred * (1 - pPred) / (m_TrainIterations - 1);
vsum += pPred * pPred;
ssum += pActual * pActual;
}
m_Bias += bsum;
m_Variance += (1 - vsum);
m_Sigma += (1 - ssum);
}
m_Bias /= (2 * numTest);
m_Variance /= (2 * numTest);
m_Sigma /= (2 * numTest);
if (m_Debug) {
System.err.println("Decomposition finished");
}
}
@Override
public Void doInBackground() {
BufferedReader reader;
publish("Computing features...");
int testingSamples = p.getAllFeatures2(path, "testing_data");
try {
publish("Reading data...");
reader = new BufferedReader(new FileReader("testing_data.arff"));
final Instances testingdata = new Instances(reader);
reader.close();
// setting class attribute
testingdata.setClassIndex(13);
testingdata.randomize(new Random(1));
long startTime = System.nanoTime();
Classifier ann = (Classifier) weka.core.SerializationHelper.read("mlp.model");
publish("Evaluating ANN...");
evalANN = new Evaluation(testingdata);
startTime = System.nanoTime();
evalANN.evaluateModel(ann, testingdata);
long runningTimeANN = (System.nanoTime() - startTime) / 1000000;
// runningTimeANN /= 100;
publish("Done evaluating ANN");
publish("Evaluating SVM...");
Classifier svm = (Classifier) weka.core.SerializationHelper.read("svm.model");
evalSVM = new Evaluation(testingdata);
startTime = System.nanoTime();
evalSVM.evaluateModel(svm, testingdata);
long runningTimeSVM = (System.nanoTime() - startTime) / 1000000;
// runningTimeSVM /= 100;
publish("Done evaluating SVM");
publish("Evaluating NB...");
Classifier nb = (Classifier) weka.core.SerializationHelper.read("naivebayes.model");
evalNB = new Evaluation(testingdata);
startTime = System.nanoTime();
evalNB.evaluateModel(nb, testingdata);
long runningTimeNB = (System.nanoTime() - startTime) / 1000000;
// runningTimeNB /= 100;
publish("Done evaluating ANN");
Platform.runLater(
new Runnable() {
@Override
public void run() {
bc.getData()
.get(0)
.getData()
.get(0)
.setYValue(evalANN.correct() / testingdata.size() * 100);
bc.getData()
.get(0)
.getData()
.get(1)
.setYValue(evalSVM.correct() / testingdata.size() * 100);
bc.getData()
.get(0)
.getData()
.get(2)
.setYValue(evalNB.correct() / testingdata.size() * 100);
for (int i = 0; i < NUM_CLASSES; i++) {
lineChart.getData().get(0).getData().get(i).setYValue(evalANN.recall(i) * 100);
lineChart.getData().get(1).getData().get(i).setYValue(evalSVM.recall(i) * 100);
lineChart.getData().get(2).getData().get(i).setYValue(evalNB.recall(i) * 100);
}
}
});
panel.fillConfTable(evalSVM.confusionMatrix());
summaryTable.setValueAt(evalANN.correct() / testingdata.size() * 100., 0, 1);
summaryTable.setValueAt(evalSVM.correct() / testingdata.size() * 100, 0, 2);
summaryTable.setValueAt(evalNB.correct() / testingdata.size() * 100, 0, 3);
summaryTable.setValueAt(runningTimeANN, 1, 1);
summaryTable.setValueAt(runningTimeSVM, 1, 2);
summaryTable.setValueAt(runningTimeNB, 1, 3);
} catch (Exception e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
return null;
}
@Override
public Void doInBackground() {
BufferedReader reader;
try {
publish("Reading data...");
reader = new BufferedReader(new FileReader("cross_validation_data.arff"));
final Instances trainingdata = new Instances(reader);
reader.close();
// setting class attribute
trainingdata.setClassIndex(13);
trainingdata.randomize(new Random(1));
long startTime = System.nanoTime();
publish("Training Naive Bayes Classifier...");
NaiveBayes nb = new NaiveBayes();
startTime = System.nanoTime();
nb.buildClassifier(trainingdata);
double runningTimeNB = (System.nanoTime() - startTime) / 1000000;
runningTimeNB /= 1000;
// saving the naive bayes model
weka.core.SerializationHelper.write("naivebayes.model", nb);
System.out.println("running time" + runningTimeNB);
publish("Done training NB.\nEvaluating NB using 10-fold cross-validation...");
evalNB = new Evaluation(trainingdata);
evalNB.crossValidateModel(nb, trainingdata, 10, new Random(1));
publish("Done evaluating NB.");
// System.out.println(evalNB.toSummaryString("\nResults for Naive Bayes\n======\n", false));
MultilayerPerceptron mlp = new MultilayerPerceptron();
mlp.setOptions(Utils.splitOptions("-L 0.3 -M 0.2 -N 500 -V 0 -S 0 -E 20 -H a"));
publish("Training ANN...");
startTime = System.nanoTime();
mlp.buildClassifier(trainingdata);
long runningTimeANN = (System.nanoTime() - startTime) / 1000000;
runningTimeANN /= 1000;
// saving the MLP model
weka.core.SerializationHelper.write("mlp.model", mlp);
publish("Done training ANN.\nEvaluating ANN using 10-fold cross-validation...");
evalANN = new Evaluation(trainingdata);
evalANN.evaluateModel(mlp, trainingdata);
// evalMLP.crossValidateModel(mlp, trainingdata, 10, new Random(1));
publish("Done evaluating ANN.");
publish("Training SVM...");
SMO svm = new SMO();
startTime = System.nanoTime();
svm.buildClassifier(trainingdata);
long runningTimeSVM = (System.nanoTime() - startTime) / 1000000;
runningTimeSVM /= 1000;
weka.core.SerializationHelper.write("svm.model", svm);
publish("Done training SVM.\nEvaluating SVM using 10-fold cross-validation...");
evalSVM = new Evaluation(trainingdata);
evalSVM.evaluateModel(svm, trainingdata);
publish("Done evaluating SVM.");
Platform.runLater(
new Runnable() {
@Override
public void run() {
bc.getData()
.get(0)
.getData()
.get(0)
.setYValue(evalANN.correct() / trainingdata.size() * 100);
bc.getData()
.get(0)
.getData()
.get(1)
.setYValue(evalSVM.correct() / trainingdata.size() * 100);
bc.getData()
.get(0)
.getData()
.get(2)
.setYValue(evalNB.correct() / trainingdata.size() * 100);
for (int i = 0; i < NUM_CLASSES; i++) {
lineChart.getData().get(0).getData().get(i).setYValue(evalANN.recall(i) * 100);
lineChart.getData().get(1).getData().get(i).setYValue(evalSVM.recall(i) * 100);
lineChart.getData().get(2).getData().get(i).setYValue(evalNB.recall(i) * 100);
}
}
});
panel.fillConfTable(evalSVM.confusionMatrix());
summaryTable.setValueAt(evalANN.correct() / trainingdata.size() * 100., 0, 1);
summaryTable.setValueAt(evalSVM.correct() / trainingdata.size() * 100, 0, 2);
summaryTable.setValueAt(evalNB.correct() / trainingdata.size() * 100, 0, 3);
summaryTable.setValueAt(runningTimeANN, 1, 1);
summaryTable.setValueAt(runningTimeSVM, 1, 2);
summaryTable.setValueAt(runningTimeNB, 1, 3);
} catch (Exception e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
return null;
}
/**
* Evaluates a feature subset by cross validation
*
* @param feature_set the subset to be evaluated
* @param num_atts the number of attributes in the subset
* @return the estimated accuracy
* @throws Exception if subset can't be evaluated
*/
protected double estimatePerformance(BitSet feature_set, int num_atts) throws Exception {
m_evaluation = new Evaluation(m_theInstances);
int i;
int[] fs = new int[num_atts];
double[] instA = new double[num_atts];
int classI = m_theInstances.classIndex();
int index = 0;
for (i = 0; i < m_numAttributes; i++) {
if (feature_set.get(i)) {
fs[index++] = i;
}
}
// create new hash table
m_entries = new Hashtable((int) (m_theInstances.numInstances() * 1.5));
// insert instances into the hash table
for (i = 0; i < m_numInstances; i++) {
Instance inst = m_theInstances.instance(i);
for (int j = 0; j < fs.length; j++) {
if (fs[j] == classI) {
instA[j] = Double.MAX_VALUE; // missing for the class
} else if (inst.isMissing(fs[j])) {
instA[j] = Double.MAX_VALUE;
} else {
instA[j] = inst.value(fs[j]);
}
}
insertIntoTable(inst, instA);
}
if (m_CVFolds == 1) {
// calculate leave one out error
for (i = 0; i < m_numInstances; i++) {
Instance inst = m_theInstances.instance(i);
for (int j = 0; j < fs.length; j++) {
if (fs[j] == classI) {
instA[j] = Double.MAX_VALUE; // missing for the class
} else if (inst.isMissing(fs[j])) {
instA[j] = Double.MAX_VALUE;
} else {
instA[j] = inst.value(fs[j]);
}
}
evaluateInstanceLeaveOneOut(inst, instA);
}
} else {
m_theInstances.randomize(m_rr);
m_theInstances.stratify(m_CVFolds);
// calculate 10 fold cross validation error
for (i = 0; i < m_CVFolds; i++) {
Instances insts = m_theInstances.testCV(m_CVFolds, i);
evaluateFoldCV(insts, fs);
}
}
switch (m_evaluationMeasure) {
case EVAL_DEFAULT:
if (m_classIsNominal) {
return m_evaluation.pctCorrect();
}
return -m_evaluation.rootMeanSquaredError();
case EVAL_ACCURACY:
return m_evaluation.pctCorrect();
case EVAL_RMSE:
return -m_evaluation.rootMeanSquaredError();
case EVAL_MAE:
return -m_evaluation.meanAbsoluteError();
case EVAL_AUC:
double[] classPriors = m_evaluation.getClassPriors();
Utils.normalize(classPriors);
double weightedAUC = 0;
for (i = 0; i < m_theInstances.classAttribute().numValues(); i++) {
double tempAUC = m_evaluation.areaUnderROC(i);
if (!Utils.isMissingValue(tempAUC)) {
weightedAUC += (classPriors[i] * tempAUC);
} else {
System.err.println("Undefined AUC!!");
}
}
return weightedAUC;
}
// shouldn't get here
return 0.0;
}