public static void main(String[] args) throws Exception {
/*
* First we load the test data from our ARFF file
*/
ArffLoader testLoader = new ArffLoader();
testLoader.setSource(new File("data/titanic/test.arff"));
testLoader.setRetrieval(Loader.BATCH);
Instances testDataSet = testLoader.getDataSet();
/*
* Now we tell the data set which attribute we want to classify, in our
* case, we want to classify the first column: survived
*/
Attribute testAttribute = testDataSet.attribute(0);
testDataSet.setClass(testAttribute);
testDataSet.deleteStringAttributes();
/*
* Now we read in the serialized model from disk
*/
Classifier classifier = (Classifier) SerializationHelper.read("data/titanic/titanic.model");
/*
* This part may be a little confusing. We load up the test data again
* so we have a prediction data set to populate. As we iterate over the
* first data set we also iterate over the second data set. After an
* instance is classified, we set the value of the prediction data set
* to be the value of the classification
*/
ArffLoader test1Loader = new ArffLoader();
test1Loader.setSource(new File("data/titanic/test.arff"));
Instances test1DataSet = test1Loader.getDataSet();
Attribute test1Attribute = test1DataSet.attribute(0);
test1DataSet.setClass(test1Attribute);
/*
* Now we iterate over the test data and classify each entry and set the
* value of the 'survived' column to the result of the classification
*/
Enumeration testInstances = testDataSet.enumerateInstances();
Enumeration test1Instances = test1DataSet.enumerateInstances();
while (testInstances.hasMoreElements()) {
Instance instance = (Instance) testInstances.nextElement();
Instance instance1 = (Instance) test1Instances.nextElement();
double classification = classifier.classifyInstance(instance);
instance1.setClassValue(classification);
}
/*
* Now we want to write out our predictions. The resulting file is in a
* format suitable to submit to Kaggle.
*/
CSVSaver predictedCsvSaver = new CSVSaver();
predictedCsvSaver.setFile(new File("data/titanic/predict.csv"));
predictedCsvSaver.setInstances(test1DataSet);
predictedCsvSaver.writeBatch();
System.out.println("Prediciton saved to predict.csv");
}
private double calcNodeScorePlain(int nNode) {
Instances instances = m_BayesNet.m_Instances;
ParentSet oParentSet = m_BayesNet.getParentSet(nNode);
// determine cardinality of parent set & reserve space for frequency counts
int nCardinality = oParentSet.getCardinalityOfParents();
int numValues = instances.attribute(nNode).numValues();
int[] nCounts = new int[nCardinality * numValues];
// initialize (don't need this?)
for (int iParent = 0; iParent < nCardinality * numValues; iParent++) {
nCounts[iParent] = 0;
}
// estimate distributions
Enumeration enumInsts = instances.enumerateInstances();
while (enumInsts.hasMoreElements()) {
Instance instance = (Instance) enumInsts.nextElement();
// updateClassifier;
double iCPT = 0;
for (int iParent = 0; iParent < oParentSet.getNrOfParents(); iParent++) {
int nParent = oParentSet.getParent(iParent);
iCPT = iCPT * instances.attribute(nParent).numValues() + instance.value(nParent);
}
nCounts[numValues * ((int) iCPT) + (int) instance.value(nNode)]++;
}
return calcScoreOfCounts(nCounts, nCardinality, numValues, instances);
} // CalcNodeScore
public double ExpectedClassificationError(Instances pool, int attr_i) {
// initialize alpha's to one
int alpha[][][];
int NumberOfFeatures = pool.numAttributes() - 1;
int NumberOfLabels = pool.numClasses();
alpha = new int[NumberOfFeatures][NumberOfLabels][];
for (int i = 0; i < NumberOfFeatures; i++)
for (int j = 0; j < NumberOfLabels; j++) alpha[i][j] = new int[pool.attribute(i).numValues()];
for (int i = 0; i < NumberOfFeatures; i++)
for (int j = 0; j < NumberOfLabels; j++)
for (int k = 0; k < alpha[i][j].length; k++) alpha[i][j][k] = 1;
// construct alpha's
for (int i = 0; i < NumberOfFeatures; i++) // for each attribute
{
if (i == pool.classIndex()) // skip the class attribute
i++;
for (Enumeration<Instance> e = pool.enumerateInstances();
e.hasMoreElements(); ) // for each instance
{
Instance inst = e.nextElement();
if (!inst.isMissing(i)) // if attribute i is not missing (i.e. its been bought)
{
int j = (int) inst.classValue();
int k = (int) inst.value(i);
alpha[i][j][k]++;
}
}
}
return ExpectedClassificationError(alpha, attr_i);
}
/**
* Calculates the class membership probabilities for the given test instance.
*
* @param instance the instance to be classified
* @return predicted class probability distribution
* @throws Exception if an error occurred during the prediction
*/
public double[] distributionForInstance(Instance instance) throws Exception {
String debug = "(KStar.distributionForInstance) ";
double transProb = 0.0, temp = 0.0;
double[] classProbability = new double[m_NumClasses];
double[] predictedValue = new double[1];
// initialization ...
for (int i = 0; i < classProbability.length; i++) {
classProbability[i] = 0.0;
}
predictedValue[0] = 0.0;
if (m_InitFlag == ON) {
// need to compute them only once and will be used for all instances.
// We are doing this because the evaluation module controls the calls.
if (m_BlendMethod == B_ENTROPY) {
generateRandomClassColomns();
}
m_Cache = new KStarCache[m_NumAttributes];
for (int i = 0; i < m_NumAttributes; i++) {
m_Cache[i] = new KStarCache();
}
m_InitFlag = OFF;
// System.out.println("Computing...");
}
// init done.
Instance trainInstance;
Enumeration enu = m_Train.enumerateInstances();
while (enu.hasMoreElements()) {
trainInstance = (Instance) enu.nextElement();
transProb = instanceTransformationProbability(instance, trainInstance);
switch (m_ClassType) {
case Attribute.NOMINAL:
classProbability[(int) trainInstance.classValue()] += transProb;
break;
case Attribute.NUMERIC:
predictedValue[0] += transProb * trainInstance.classValue();
temp += transProb;
break;
}
}
if (m_ClassType == Attribute.NOMINAL) {
double sum = Utils.sum(classProbability);
if (sum <= 0.0)
for (int i = 0; i < classProbability.length; i++)
classProbability[i] = (double) 1 / (double) m_NumClasses;
else Utils.normalize(classProbability, sum);
return classProbability;
} else {
predictedValue[0] = (temp != 0) ? predictedValue[0] / temp : 0.0;
return predictedValue;
}
}
/**
* Gets the subset of instances that apply to a particluar branch of the split. If the branch
* index is -1, the subset will consist of those instances that don't apply to any branch.
*
* @param branch the index of the branch
* @param sourceInstances the instances from which to find the subset
* @return the set of instances that apply
*/
public ReferenceInstances instancesDownBranch(int branch, Instances instances) {
ReferenceInstances filteredInstances = new ReferenceInstances(instances, 1);
if (branch == -1) {
for (Enumeration e = instances.enumerateInstances(); e.hasMoreElements(); ) {
Instance inst = (Instance) e.nextElement();
if (inst.isMissing(attIndex)) filteredInstances.addReference(inst);
}
} else if (branch == 0) {
for (Enumeration e = instances.enumerateInstances(); e.hasMoreElements(); ) {
Instance inst = (Instance) e.nextElement();
if (!inst.isMissing(attIndex) && inst.value(attIndex) < splitPoint)
filteredInstances.addReference(inst);
}
} else {
for (Enumeration e = instances.enumerateInstances(); e.hasMoreElements(); ) {
Instance inst = (Instance) e.nextElement();
if (!inst.isMissing(attIndex) && inst.value(attIndex) >= splitPoint)
filteredInstances.addReference(inst);
}
}
return filteredInstances;
}
/**
* Splits a dataset according to the values of a nominal attribute.
*
* @param data the data which is to be split
* @param att the attribute to be used for splitting
* @return the sets of instances produced by the split
*/
private Instances[] splitData(Instances data, Attribute att) {
Instances[] splitData = new Instances[att.numValues()];
for (int j = 0; j < att.numValues(); j++) {
splitData[j] = new Instances(data, data.numInstances());
}
Enumeration instEnum = data.enumerateInstances();
while (instEnum.hasMoreElements()) {
Instance inst = (Instance) instEnum.nextElement();
splitData[(int) inst.value(att)].add(inst);
}
for (int i = 0; i < splitData.length; i++) {
splitData[i].compactify();
}
return splitData;
}
/**
* Computes the entropy of a dataset.
*
* @param data the data for which entropy is to be computed
* @return the entropy of the data's class distribution
* @throws Exception if computation fails
*/
private double computeEntropy(Instances data) throws Exception {
double[] classCounts = new double[data.numClasses()];
Enumeration instEnum = data.enumerateInstances();
while (instEnum.hasMoreElements()) {
Instance inst = (Instance) instEnum.nextElement();
classCounts[(int) inst.classValue()]++;
}
double entropy = 0;
for (int j = 0; j < data.numClasses(); j++) {
if (classCounts[j] > 0) {
entropy -= classCounts[j] * Utils.log2(classCounts[j]);
}
}
entropy /= (double) data.numInstances();
return entropy + Utils.log2(data.numInstances());
}
/**
* Sets split point to greatest value in given data smaller or equal to old split point. (C4.5
* does this for some strange reason).
*/
public final void setSplitPoint(Instances allInstances) {
double newSplitPoint = -Double.MAX_VALUE;
double tempValue;
Instance instance;
if ((!allInstances.attribute(m_attIndex).isNominal()) && (m_numSubsets > 1)) {
Enumeration enu = allInstances.enumerateInstances();
while (enu.hasMoreElements()) {
instance = (Instance) enu.nextElement();
if (!instance.isMissing(m_attIndex)) {
tempValue = instance.value(m_attIndex);
if (Utils.gr(tempValue, newSplitPoint) && Utils.smOrEq(tempValue, m_splitPoint))
newSplitPoint = tempValue;
}
}
m_splitPoint = newSplitPoint;
}
}
/**
* Creates split on enumerated attribute.
*
* @exception Exception if something goes wrong
*/
private void handleEnumeratedAttribute(Instances trainInstances) throws Exception {
Distribution newDistribution, secondDistribution;
int numAttValues;
double currIG, currGR;
Instance instance;
int i;
numAttValues = trainInstances.attribute(m_attIndex).numValues();
newDistribution = new Distribution(numAttValues, trainInstances.numClasses());
// Only Instances with known values are relevant.
Enumeration enu = trainInstances.enumerateInstances();
while (enu.hasMoreElements()) {
instance = (Instance) enu.nextElement();
if (!instance.isMissing(m_attIndex))
newDistribution.add((int) instance.value(m_attIndex), instance);
}
m_distribution = newDistribution;
// For all values
for (i = 0; i < numAttValues; i++) {
if (Utils.grOrEq(newDistribution.perBag(i), m_minNoObj)) {
secondDistribution = new Distribution(newDistribution, i);
// Check if minimum number of Instances in the two
// subsets.
if (secondDistribution.check(m_minNoObj)) {
m_numSubsets = 2;
currIG = m_infoGainCrit.splitCritValue(secondDistribution, m_sumOfWeights);
currGR = m_gainRatioCrit.splitCritValue(secondDistribution, m_sumOfWeights, currIG);
if ((i == 0) || Utils.gr(currGR, m_gainRatio)) {
m_gainRatio = currGR;
m_infoGain = currIG;
m_splitPoint = (double) i;
m_distribution = secondDistribution;
}
}
}
}
}
/**
* Method for building an Id3 tree.
*
* @param data the training data
* @exception Exception if decision tree can't be built successfully
*/
private void makeTree(Instances data) throws Exception {
// Check if no instances have reached this node.
if (data.numInstances() == 0) {
m_Attribute = null;
m_ClassValue = Utils.missingValue();
m_Distribution = new double[data.numClasses()];
return;
}
// Compute attribute with maximum information gain.
double[] infoGains = new double[data.numAttributes()];
Enumeration attEnum = data.enumerateAttributes();
while (attEnum.hasMoreElements()) {
Attribute att = (Attribute) attEnum.nextElement();
infoGains[att.index()] = computeInfoGain(data, att);
}
m_Attribute = data.attribute(Utils.maxIndex(infoGains));
// Make leaf if information gain is zero.
// Otherwise create successors.
if (Utils.eq(infoGains[m_Attribute.index()], 0)) {
m_Attribute = null;
m_Distribution = new double[data.numClasses()];
Enumeration instEnum = data.enumerateInstances();
while (instEnum.hasMoreElements()) {
Instance inst = (Instance) instEnum.nextElement();
m_Distribution[(int) inst.classValue()]++;
}
Utils.normalize(m_Distribution);
m_ClassValue = Utils.maxIndex(m_Distribution);
m_ClassAttribute = data.classAttribute();
} else {
Instances[] splitData = splitData(data, m_Attribute);
m_Successors = new Id3[m_Attribute.numValues()];
for (int j = 0; j < m_Attribute.numValues(); j++) {
m_Successors[j] = new Id3();
m_Successors[j].makeTree(splitData[j]);
}
}
}
@Override
protected void manipulateAttributes(Instances data) throws TaskException {
String[] attribs = this.getParameterVal(ATTRIBS).split("\\s+");
for (int i = 0; i < attribs.length; ++i) {
if (data.attribute(attribs[i]) == null) {
Logger.getInstance()
.message(
"Attribute " + attribs[i] + " not found in data set " + data.relationName(),
Logger.V_WARNING);
continue;
}
Enumeration<Instance> insts = data.enumerateInstances();
int attrIndex = data.attribute(attribs[i]).index();
while (insts.hasMoreElements()) {
Instance inst = insts.nextElement();
inst.setMissing(attrIndex);
}
}
}
/**
* Creates split on enumerated attribute.
*
* @exception Exception if something goes wrong
*/
private void handleEnumeratedAttribute(Instances trainInstances) throws Exception {
Instance instance;
m_distribution = new Distribution(m_complexityIndex, trainInstances.numClasses());
// Only Instances with known values are relevant.
Enumeration<Instance> enu = trainInstances.enumerateInstances();
while (enu.hasMoreElements()) {
instance = enu.nextElement();
if (!instance.isMissing(m_attIndex)) {
m_distribution.add((int) instance.value(m_attIndex), instance);
}
}
// Check if minimum number of Instances in at least two
// subsets.
if (m_distribution.check(m_minNoObj)) {
m_numSubsets = m_complexityIndex;
m_infoGain = infoGainCrit.splitCritValue(m_distribution, m_sumOfWeights);
m_gainRatio = gainRatioCrit.splitCritValue(m_distribution, m_sumOfWeights, m_infoGain);
}
}
public static void main(String[] args) throws Exception {
// NaiveBayesSimple nb = new NaiveBayesSimple();
// BufferedReader br_train = new BufferedReader(new FileReader("src/train.arff.txt"));
// String s = null;
// long st_time = System.currentTimeMillis();
// Instances inst_train = new Instances(br_train);
// System.out.println(inst_train.numAttributes());
// inst_train.setClassIndex(inst_train.numAttributes()-1);
// System.out.println("train time"+(System.currentTimeMillis()-st_time));
// NaiveBayes nb1 = new NaiveBayes();
// nb1.buildClassifier(inst_train);
// br_train.close();
long st_time = System.currentTimeMillis();
st_time = System.currentTimeMillis();
Classifier classifier = (Classifier) SerializationHelper.read("NaiveBayes.model");
// BufferedReader br_test = new BufferedReader(new FileReader("src/test.arff.txt"));
// Instances inst_test = new Instances(br_test);
// inst_test.setClassIndex(inst_test.numAttributes()-1);
// System.out.println("test time"+(System.currentTimeMillis()-st_time));
//
ArffLoader testLoader = new ArffLoader();
testLoader.setSource(new File("src/test.arff"));
testLoader.setRetrieval(Loader.BATCH);
Instances testDataSet = testLoader.getDataSet();
Attribute testAttribute = testDataSet.attribute("class");
testDataSet.setClass(testAttribute);
int correct = 0;
int incorrect = 0;
FastVector attInfo = new FastVector();
attInfo.addElement(new Attribute("Id"));
attInfo.addElement(new Attribute("Category"));
Instances outputInstances = new Instances("predict", attInfo, testDataSet.numInstances());
Enumeration testInstances = testDataSet.enumerateInstances();
int index = 1;
while (testInstances.hasMoreElements()) {
Instance instance = (Instance) testInstances.nextElement();
double classification = classifier.classifyInstance(instance);
Instance predictInstance = new Instance(outputInstances.numAttributes());
predictInstance.setValue(0, index++);
predictInstance.setValue(1, (int) classification + 1);
outputInstances.add(predictInstance);
}
System.out.println("Correct Instance: " + correct);
System.out.println("IncCorrect Instance: " + incorrect);
double accuracy = (double) (correct) / (double) (correct + incorrect);
System.out.println("Accuracy: " + accuracy);
CSVSaver predictedCsvSaver = new CSVSaver();
predictedCsvSaver.setFile(new File("predict.csv"));
predictedCsvSaver.setInstances(outputInstances);
predictedCsvSaver.writeBatch();
System.out.println("Prediciton saved to predict.csv");
}
/**
* Creates split on numeric attribute.
*
* @exception Exception if something goes wrong
*/
private void handleNumericAttribute(Instances trainInstances) throws Exception {
int firstMiss;
int next = 1;
int last = 0;
int index = 0;
int splitIndex = -1;
double currentInfoGain;
double defaultEnt;
double minSplit;
Instance instance;
int i;
// Current attribute is a numeric attribute.
m_distribution = new Distribution(2, trainInstances.numClasses());
// Only Instances with known values are relevant.
Enumeration enu = trainInstances.enumerateInstances();
i = 0;
while (enu.hasMoreElements()) {
instance = (Instance) enu.nextElement();
if (instance.isMissing(m_attIndex)) break;
m_distribution.add(1, instance);
i++;
}
firstMiss = i;
// Compute minimum number of Instances required in each
// subset.
minSplit = 0.1 * (m_distribution.total()) / ((double) trainInstances.numClasses());
if (Utils.smOrEq(minSplit, m_minNoObj)) minSplit = m_minNoObj;
else if (Utils.gr(minSplit, 25)) minSplit = 25;
// Enough Instances with known values?
if (Utils.sm((double) firstMiss, 2 * minSplit)) return;
// Compute values of criteria for all possible split
// indices.
defaultEnt = m_infoGainCrit.oldEnt(m_distribution);
while (next < firstMiss) {
if (trainInstances.instance(next - 1).value(m_attIndex) + 1e-5
< trainInstances.instance(next).value(m_attIndex)) {
// Move class values for all Instances up to next
// possible split point.
m_distribution.shiftRange(1, 0, trainInstances, last, next);
// Check if enough Instances in each subset and compute
// values for criteria.
if (Utils.grOrEq(m_distribution.perBag(0), minSplit)
&& Utils.grOrEq(m_distribution.perBag(1), minSplit)) {
currentInfoGain =
m_infoGainCrit.splitCritValue(m_distribution, m_sumOfWeights, defaultEnt);
if (Utils.gr(currentInfoGain, m_infoGain)) {
m_infoGain = currentInfoGain;
splitIndex = next - 1;
}
index++;
}
last = next;
}
next++;
}
// Was there any useful split?
if (index == 0) return;
// Compute modified information gain for best split.
if (m_useMDLcorrection) {
m_infoGain = m_infoGain - (Utils.log2(index) / m_sumOfWeights);
}
if (Utils.smOrEq(m_infoGain, 0)) return;
// Set instance variables' values to values for
// best split.
m_numSubsets = 2;
m_splitPoint =
(trainInstances.instance(splitIndex + 1).value(m_attIndex)
+ trainInstances.instance(splitIndex).value(m_attIndex))
/ 2;
// In case we have a numerical precision problem we need to choose the
// smaller value
if (m_splitPoint == trainInstances.instance(splitIndex + 1).value(m_attIndex)) {
m_splitPoint = trainInstances.instance(splitIndex).value(m_attIndex);
}
// Restore distributioN for best split.
m_distribution = new Distribution(2, trainInstances.numClasses());
m_distribution.addRange(0, trainInstances, 0, splitIndex + 1);
m_distribution.addRange(1, trainInstances, splitIndex + 1, firstMiss);
// Compute modified gain ratio for best split.
m_gainRatio = m_gainRatioCrit.splitCritValue(m_distribution, m_sumOfWeights, m_infoGain);
}
/**
* add noise to the dataset
*
* <p>a given percentage of the instances are changed in the way, that a set of instances are
* randomly selected using seed. The attribute given by its index is changed from its current
* value to one of the other possibly ones, also randomly. This is done with leaving the apportion
* the same. if m_UseMissing is true, missing value is used as a value of its own
*
* @param instances is the dataset
* @param seed used for random function
* @param percent percentage of instances that are changed
* @param attIndex index of the attribute changed
* @param useMissing if true missing values are treated as extra value
*/
public void addNoise(
Instances instances, int seed, int percent, int attIndex, boolean useMissing) {
int indexList[];
int partition_count[];
int partition_max[];
double splitPercent = (double) percent; // percentage used for splits
// fill array with the indexes
indexList = new int[instances.numInstances()];
for (int i = 0; i < instances.numInstances(); i++) {
indexList[i] = i;
}
// randomize list of indexes
Random random = new Random(seed);
for (int i = instances.numInstances() - 1; i >= 0; i--) {
int hValue = indexList[i];
int hIndex = (int) (random.nextDouble() * (double) i);
indexList[i] = indexList[hIndex];
indexList[hIndex] = hValue;
}
// initialize arrays that are used to count instances
// of each value and to keep the amount of instances of that value
// that has to be changed
// this is done for the missing values in the two variables
// missing_count and missing_max
int numValues = instances.attribute(attIndex).numValues();
partition_count = new int[numValues];
partition_max = new int[numValues];
int missing_count = 0;
;
int missing_max = 0;
;
for (int i = 0; i < numValues; i++) {
partition_count[i] = 0;
partition_max[i] = 0;
}
// go through the dataset and count all occurrences of values
// and all missing values using temporarily .._max arrays and
// variable missing_max
for (Enumeration e = instances.enumerateInstances(); e.hasMoreElements(); ) {
Instance instance = (Instance) e.nextElement();
if (instance.isMissing(attIndex)) {
missing_max++;
} else {
int j = (int) instance.value(attIndex);
partition_max[(int) instance.value(attIndex)]++;
}
}
// use given percentage to calculate
// how many have to be changed per split and
// how many of the missing values
if (!useMissing) {
missing_max = missing_count;
} else {
missing_max = (int) (((double) missing_max / 100) * splitPercent + 0.5);
}
int sum_max = missing_max;
for (int i = 0; i < numValues; i++) {
partition_max[i] = (int) (((double) partition_max[i] / 100) * splitPercent + 0.5);
sum_max = sum_max + partition_max[i];
}
// initialize sum_count to zero, use this variable to see if
// everything is done already
int sum_count = 0;
// add noise
// using the randomized index-array
//
Random randomValue = new Random(seed);
int numOfValues = instances.attribute(attIndex).numValues();
for (int i = 0; i < instances.numInstances(); i++) {
if (sum_count >= sum_max) {
break;
} // finished
Instance currInstance = instances.instance(indexList[i]);
// if value is missing then...
if (currInstance.isMissing(attIndex)) {
if (missing_count < missing_max) {
changeValueRandomly(randomValue, numOfValues, attIndex, currInstance, useMissing);
missing_count++;
sum_count++;
}
} else {
int vIndex = (int) currInstance.value(attIndex);
if (partition_count[vIndex] < partition_max[vIndex]) {
changeValueRandomly(randomValue, numOfValues, attIndex, currInstance, useMissing);
partition_count[vIndex]++;
sum_count++;
}
}
}
}
/**
* Generates the classifier.
*
* @param instances set of instances serving as training data
* @exception Exception if the classifier has not been generated successfully
*/
@Override
public void buildClassifier(Instances instances) throws Exception {
int attIndex = 0;
double sum;
// can classifier handle the data?
getCapabilities().testWithFail(instances);
// remove instances with missing class
instances = new Instances(instances);
instances.deleteWithMissingClass();
m_Instances = new Instances(instances, 0);
// Reserve space
m_Counts = new double[instances.numClasses()][instances.numAttributes() - 1][0];
m_Means = new double[instances.numClasses()][instances.numAttributes() - 1];
m_Devs = new double[instances.numClasses()][instances.numAttributes() - 1];
m_Priors = new double[instances.numClasses()];
Enumeration<Attribute> enu = instances.enumerateAttributes();
while (enu.hasMoreElements()) {
Attribute attribute = enu.nextElement();
if (attribute.isNominal()) {
for (int j = 0; j < instances.numClasses(); j++) {
m_Counts[j][attIndex] = new double[attribute.numValues()];
}
} else {
for (int j = 0; j < instances.numClasses(); j++) {
m_Counts[j][attIndex] = new double[1];
}
}
attIndex++;
}
// Compute counts and sums
Enumeration<Instance> enumInsts = instances.enumerateInstances();
while (enumInsts.hasMoreElements()) {
Instance instance = enumInsts.nextElement();
if (!instance.classIsMissing()) {
Enumeration<Attribute> enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (!instance.isMissing(attribute)) {
if (attribute.isNominal()) {
m_Counts[(int) instance.classValue()][attIndex][(int) instance.value(attribute)]++;
} else {
m_Means[(int) instance.classValue()][attIndex] += instance.value(attribute);
m_Counts[(int) instance.classValue()][attIndex][0]++;
}
}
attIndex++;
}
m_Priors[(int) instance.classValue()]++;
}
}
// Compute means
Enumeration<Attribute> enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (attribute.isNumeric()) {
for (int j = 0; j < instances.numClasses(); j++) {
if (m_Counts[j][attIndex][0] < 2) {
throw new Exception(
"attribute "
+ attribute.name()
+ ": less than two values for class "
+ instances.classAttribute().value(j));
}
m_Means[j][attIndex] /= m_Counts[j][attIndex][0];
}
}
attIndex++;
}
// Compute standard deviations
enumInsts = instances.enumerateInstances();
while (enumInsts.hasMoreElements()) {
Instance instance = enumInsts.nextElement();
if (!instance.classIsMissing()) {
enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (!instance.isMissing(attribute)) {
if (attribute.isNumeric()) {
m_Devs[(int) instance.classValue()][attIndex] +=
(m_Means[(int) instance.classValue()][attIndex] - instance.value(attribute))
* (m_Means[(int) instance.classValue()][attIndex]
- instance.value(attribute));
}
}
attIndex++;
}
}
}
enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (attribute.isNumeric()) {
for (int j = 0; j < instances.numClasses(); j++) {
if (m_Devs[j][attIndex] <= 0) {
throw new Exception(
"attribute "
+ attribute.name()
+ ": standard deviation is 0 for class "
+ instances.classAttribute().value(j));
} else {
m_Devs[j][attIndex] /= m_Counts[j][attIndex][0] - 1;
m_Devs[j][attIndex] = Math.sqrt(m_Devs[j][attIndex]);
}
}
}
attIndex++;
}
// Normalize counts
enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (attribute.isNominal()) {
for (int j = 0; j < instances.numClasses(); j++) {
sum = Utils.sum(m_Counts[j][attIndex]);
for (int i = 0; i < attribute.numValues(); i++) {
m_Counts[j][attIndex][i] =
(m_Counts[j][attIndex][i] + 1) / (sum + attribute.numValues());
}
}
}
attIndex++;
}
// Normalize priors
sum = Utils.sum(m_Priors);
for (int j = 0; j < instances.numClasses(); j++) {
m_Priors[j] = (m_Priors[j] + 1) / (sum + instances.numClasses());
}
}
/**
* 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 = new Instances(instances);
instances.deleteWithMissingClass();
m_headerInfo = new Instances(instances, 0);
m_numClasses = instances.numClasses();
m_numAttributes = instances.numAttributes();
m_probOfWordGivenClass = new double[m_numClasses][];
/*
initialising the matrix of word counts
NOTE: Laplace estimator introduced in case a word that does not appear for a class in the
training set does so for the test set
*/
for (int c = 0; c < m_numClasses; c++) {
m_probOfWordGivenClass[c] = new double[m_numAttributes];
for (int att = 0; att < m_numAttributes; att++) {
m_probOfWordGivenClass[c][att] = 1;
}
}
// enumerate through the instances
Instance instance;
int classIndex;
double numOccurences;
double[] docsPerClass = new double[m_numClasses];
double[] wordsPerClass = new double[m_numClasses];
java.util.Enumeration enumInsts = instances.enumerateInstances();
while (enumInsts.hasMoreElements()) {
instance = (Instance) enumInsts.nextElement();
classIndex = (int) instance.value(instance.classIndex());
docsPerClass[classIndex] += instance.weight();
for (int a = 0; a < instance.numValues(); a++)
if (instance.index(a) != instance.classIndex()) {
if (!instance.isMissing(a)) {
numOccurences = instance.valueSparse(a) * instance.weight();
if (numOccurences < 0)
throw new Exception("Numeric attribute values must all be greater or equal to zero.");
wordsPerClass[classIndex] += numOccurences;
m_probOfWordGivenClass[classIndex][instance.index(a)] += numOccurences;
}
}
}
/*
normalising probOfWordGivenClass values
and saving each value as the log of each value
*/
for (int c = 0; c < m_numClasses; c++)
for (int v = 0; v < m_numAttributes; v++)
m_probOfWordGivenClass[c][v] =
Math.log(m_probOfWordGivenClass[c][v] / (wordsPerClass[c] + m_numAttributes - 1));
/*
calculating Pr(H)
NOTE: Laplace estimator introduced in case a class does not get mentioned in the set of
training instances
*/
final double numDocs = instances.sumOfWeights() + m_numClasses;
m_probOfClass = new double[m_numClasses];
for (int h = 0; h < m_numClasses; h++)
m_probOfClass[h] = (double) (docsPerClass[h] + 1) / numDocs;
}