/**
* Generates a clusterer by the mean of spectral clustering algorithm.
*
* @param data set of instances serving as training data
* @exception Exception if the clusterer has not been generated successfully
*/
public void buildClusterer(Instances data) throws java.lang.Exception {
m_Sequences = new Instances(data);
int n = data.numInstances();
int k = data.numAttributes();
DoubleMatrix2D w;
if (useSparseMatrix) w = DoubleFactory2D.sparse.make(n, n);
else w = DoubleFactory2D.dense.make(n, n);
double[][] v1 = new double[n][];
for (int i = 0; i < n; i++) v1[i] = data.instance(i).toDoubleArray();
v = DoubleFactory2D.dense.make(v1);
double sigma_sq = sigma * sigma;
// Sets up similarity matrix
for (int i = 0; i < n; i++)
for (int j = i; j < n; j++) {
/*double dist = distnorm2(v.viewRow(i), v.viewRow(j));
if((r == -1) || (dist < r)) {
double sim = Math.exp(- (dist * dist) / (2 * sigma_sq));
w.set(i, j, sim);
w.set(j, i, sim);
}*/
/* String [] key = {data.instance(i).stringValue(0), data.instance(j).stringValue(0)};
System.out.println(key[0]);
System.out.println(key[1]);
System.out.println(simScoreMap.containsKey(key));
Double simValue = simScoreMap.get(key);*/
double sim = sim_matrix[i][j];
w.set(i, j, sim);
w.set(j, i, sim);
}
// Partitions points
int[][] p = partition(w, alpha_star);
// Deploys results
numOfClusters = p.length;
cluster = new int[n];
for (int i = 0; i < p.length; i++) for (int j = 0; j < p[i].length; j++) cluster[p[i][j]] = i;
// System.out.println("Final partition:");
// UtilsJS.printMatrix(p);
// System.out.println("Cluster:\n");
// UtilsJS.printArray(cluster);
this.numOfClusters = cluster[Utils.maxIndex(cluster)] + 1;
// System.out.println("Num clusters:\t"+this.numOfClusters);
}
/**
* Classifies an instance for internal leave one out cross validation of feature sets
*
* @param instance instance to be "left out" and classified
* @param instA feature values of the selected features for the instance
* @return the classification of the instance
* @throws Exception if something goes wrong
*/
double evaluateInstanceLeaveOneOut(Instance instance, double[] instA) throws Exception {
DecisionTableHashKey thekey;
double[] tempDist;
double[] normDist;
thekey = new DecisionTableHashKey(instA);
if (m_classIsNominal) {
// if this one is not in the table
if ((tempDist = (double[]) m_entries.get(thekey)) == null) {
throw new Error("This should never happen!");
} else {
normDist = new double[tempDist.length];
System.arraycopy(tempDist, 0, normDist, 0, tempDist.length);
normDist[(int) instance.classValue()] -= instance.weight();
// update the table
// first check to see if the class counts are all zero now
boolean ok = false;
for (int i = 0; i < normDist.length; i++) {
if (Utils.gr(normDist[i], 1.0)) {
ok = true;
break;
}
}
// downdate the class prior counts
m_classPriorCounts[(int) instance.classValue()] -= instance.weight();
double[] classPriors = m_classPriorCounts.clone();
Utils.normalize(classPriors);
if (!ok) { // majority class
normDist = classPriors;
}
m_classPriorCounts[(int) instance.classValue()] += instance.weight();
// if (ok) {
Utils.normalize(normDist);
if (m_evaluationMeasure == EVAL_AUC) {
m_evaluation.evaluateModelOnceAndRecordPrediction(normDist, instance);
} else {
m_evaluation.evaluateModelOnce(normDist, instance);
}
return Utils.maxIndex(normDist);
/*} else {
normDist = new double [normDist.length];
normDist[(int)m_majority] = 1.0;
if (m_evaluationMeasure == EVAL_AUC) {
m_evaluation.evaluateModelOnceAndRecordPrediction(normDist, instance);
} else {
m_evaluation.evaluateModelOnce(normDist, instance);
}
return m_majority;
} */
}
// return Utils.maxIndex(tempDist);
} else {
// see if this one is already in the table
if ((tempDist = (double[]) m_entries.get(thekey)) != null) {
normDist = new double[tempDist.length];
System.arraycopy(tempDist, 0, normDist, 0, tempDist.length);
normDist[0] -= (instance.classValue() * instance.weight());
normDist[1] -= instance.weight();
if (Utils.eq(normDist[1], 0.0)) {
double[] temp = new double[1];
temp[0] = m_majority;
m_evaluation.evaluateModelOnce(temp, instance);
return m_majority;
} else {
double[] temp = new double[1];
temp[0] = normDist[0] / normDist[1];
m_evaluation.evaluateModelOnce(temp, instance);
return temp[0];
}
} else {
throw new Error("This should never happen!");
}
}
// shouldn't get here
// return 0.0;
}
/**
* Returns a description of the classifier.
*
* @return a description of the classifier as a string.
*/
public String toString() {
if (m_entries == null) {
return "Decision Table: No model built yet.";
} else {
StringBuffer text = new StringBuffer();
text.append(
"Decision Table:"
+ "\n\nNumber of training instances: "
+ m_numInstances
+ "\nNumber of Rules : "
+ m_entries.size()
+ "\n");
if (m_useIBk) {
text.append("Non matches covered by IB1.\n");
} else {
text.append("Non matches covered by Majority class.\n");
}
text.append(m_search.toString());
/*text.append("Best first search for feature set,\nterminated after "+
m_maxStale+" non improving subsets.\n"); */
text.append("Evaluation (for feature selection): CV ");
if (m_CVFolds > 1) {
text.append("(" + m_CVFolds + " fold) ");
} else {
text.append("(leave one out) ");
}
text.append("\nFeature set: " + printFeatures());
if (m_displayRules) {
// find out the max column width
int maxColWidth = 0;
for (int i = 0; i < m_dtInstances.numAttributes(); i++) {
if (m_dtInstances.attribute(i).name().length() > maxColWidth) {
maxColWidth = m_dtInstances.attribute(i).name().length();
}
if (m_classIsNominal || (i != m_dtInstances.classIndex())) {
Enumeration e = m_dtInstances.attribute(i).enumerateValues();
while (e.hasMoreElements()) {
String ss = (String) e.nextElement();
if (ss.length() > maxColWidth) {
maxColWidth = ss.length();
}
}
}
}
text.append("\n\nRules:\n");
StringBuffer tm = new StringBuffer();
for (int i = 0; i < m_dtInstances.numAttributes(); i++) {
if (m_dtInstances.classIndex() != i) {
int d = maxColWidth - m_dtInstances.attribute(i).name().length();
tm.append(m_dtInstances.attribute(i).name());
for (int j = 0; j < d + 1; j++) {
tm.append(" ");
}
}
}
tm.append(m_dtInstances.attribute(m_dtInstances.classIndex()).name() + " ");
for (int i = 0; i < tm.length() + 10; i++) {
text.append("=");
}
text.append("\n");
text.append(tm);
text.append("\n");
for (int i = 0; i < tm.length() + 10; i++) {
text.append("=");
}
text.append("\n");
Enumeration e = m_entries.keys();
while (e.hasMoreElements()) {
DecisionTableHashKey tt = (DecisionTableHashKey) e.nextElement();
text.append(tt.toString(m_dtInstances, maxColWidth));
double[] ClassDist = (double[]) m_entries.get(tt);
if (m_classIsNominal) {
int m = Utils.maxIndex(ClassDist);
try {
text.append(m_dtInstances.classAttribute().value(m) + "\n");
} catch (Exception ee) {
System.out.println(ee.getMessage());
}
} else {
text.append((ClassDist[0] / ClassDist[1]) + "\n");
}
}
for (int i = 0; i < tm.length() + 10; i++) {
text.append("=");
}
text.append("\n");
text.append("\n");
}
return text.toString();
}
}