/**
* It generates the output file from a given dataset and stores it in a file
*
* @param dataset myDataset input dataset
* @param filename String the name of the file
*/
private double doOutput(myDataset dataset, String filename, boolean test) {
String output = new String("");
confusionMatrix = new int[dataset.getnClasses()][dataset.getnClasses()];
output = dataset.copyHeader(); // we insert the header in the output file
// We write the output for each example
for (int i = 0; i < dataset.getnData(); i++) {
String clReal = dataset.getOutputAsString(i);
String clPred = classificationOutput(i, test);
confusionMatrix[dataset.getOutputAsInteger(i)][dataset.numericClass(clPred)]++;
output += clReal + " " + clPred + "\n";
}
double acc = 0;
int nClasses = 0;
for (int i = 0; i < confusionMatrix.length; i++) {
int count = 0;
for (int j = 0; j < confusionMatrix[i].length; j++) {
count += confusionMatrix[i][j];
}
if (count > 0) {
acc += 1.0 * confusionMatrix[i][i] / count;
nClasses++;
}
}
Files.writeFile(filename, output);
return acc / nClasses;
// return 1.0*hits/dataset.size();
}
private String printConfusionMatrix() {
String salida = new String("");
for (int i = 0; i < train.getnClasses(); i++) {
salida += "\n";
for (int j = 0; j < train.getnClasses(); j++) {
salida += confusionMatrix[i][j] + "\t";
}
}
salida += "\n";
return salida;
}
/** It launches the algorithm */
public void execute() {
if (this.somethingWrong) { // We do not execute the program
System.err.println("An error was found, either the data-set has missing values.");
System.err.println(
"Please remove the examples with missing data or apply a MV preprocessing.");
System.err.println("Aborting the program");
// We should not use the statement: System.exit(-1);
} else {
// We do here the algorithm's operations
int nClasses = train.getnClasses();
aprioriClassDistribution = new double[nClasses];
for (int i = 0; i < nClasses; i++) {
aprioriClassDistribution[i] = 1.0 * val.numberInstances(i) / val.size();
}
if (model) { // el modelo no esta generado en fichero previamente
NSGA2 search =
new NSGA2(
train, seed, populationSize, maxTrials, crossover, mutation, instances, fitness);
try {
search.execute();
} catch (Exception e) {
e.printStackTrace(System.err);
}
}
// Finally we should fill the training and test output files
this.generateModel();
double avgTr = this.doOutput(val, this.outputTr, false);
double aucTr = getAUC(val);
double avgTst = this.doOutput(test, this.outputTst, true);
double aucTst = getAUC(test);
System.out.print("AUC Train: " + aucTr);
System.out.println("; AvgAcc Train: " + avgTr);
System.out.print("AUC Test: " + aucTst);
System.out.println("; AvgAcc Test: " + avgTst);
totalTime = System.currentTimeMillis() - startTime;
System.out.println("Algorithm Finished: " + totalTime);
}
}
/** It launches the algorithm */
public void execute() {
if (somethingWrong) { // We do not execute the program
System.err.println("An error was found, either the data-set has missing values.");
System.err.println(
"Please remove the examples with missing data or apply a MV preprocessing.");
System.err.println("Aborting the program");
// We should not use the statement: System.exit(-1);
} else {
// We do here the algorithm's operations
nClasses = train.getnClasses();
dataBase =
new DataBase(
train.getnInputs(), train.getRanges(), train.varNames(), train.getNominals());
Population pobl =
new Population(
train,
dataBase,
populationSize,
nRules,
crossProb,
ruleWeight,
combinationType,
inferenceType,
p_DC,
michProb);
pobl.Generation(this.nGenerations);
dataBase.writeFile(this.fileDB);
ruleBase = pobl.bestRB();
ruleBase.writeFile(this.fileBR);
// Finally we should fill the training and test output files
double accTra = doOutput(this.val, this.outputTr);
double accTst = doOutput(this.test, this.outputTst);
System.out.println("Accuracy obtained in training: " + accTra);
System.out.println("Accuracy obtained in test: " + accTst);
System.out.println("Algorithm Finished");
}
}
/**
* It returns the algorithm classification output given an input example
*
* @param example double[] The input example
* @return String the output generated by the algorithm
*/
private String classificationOutput(int index, boolean test) {
String output = new String("?");
/**
* Here we should include the algorithm directives to generate the classification output from
* the input example
*/
double votos[] = new double[train.getnClasses()];
// System.err.print("\nClassifying new example: ");
// boolean ENSEMBLE = true;
if (ensemble == this.NONE) { // best solution
// double [] probs = new double[train.getnClasses()];
if (test) {
// probs = models.get(i).probsTest(index);
votos[models.get(indexBest).classifyTest(index)]++;
} else {
// probs = models.get(i).probsTrain(index);
votos[models.get(indexBest).classifyTrain(index)]++;
}
} else { // ensemble
for (int i = 0; i < models.size(); i++) {
double[] probs = new double[train.getnClasses()];
if (test) {
probs = models.get(i).probsTest(index);
// votos[models.get(i).classifyTest(index)]++;
} else {
probs = models.get(i).probsTrain(index);
// votos[models.get(i).classifyTrain(index)]++;
}
// 0 = binary, 1 = weighted, 2 = winner_takes_all
if (ensemble == this.VOTE) {
int maxIndex = 0;
double max = probs[0];
for (int j = 1; j < votos.length; j++) {
// votos[j] += probs[j];
if (probs[j] > probs[maxIndex]) {
maxIndex = j;
max = probs[j];
}
}
votos[maxIndex] += 1;
} else if (ensemble == this.WV) {
for (int j = 0; j < votos.length; j++) {
votos[j] += probs[j];
}
} else {
int maxIndex = 0;
double max = probs[0];
for (int j = 1; j < votos.length; j++) {
// votos[j] += probs[j];
if (probs[j] > probs[maxIndex]) {
maxIndex = j;
max = probs[j];
}
}
votos[maxIndex] += max;
}
if (this.weighting) {
for (int j = 0; j < votos.length; j++) {
votos[j] *= this.weightsAUC[i];
}
}
}
}
// System.err.println("A clasificar");
return getOutputTies(votos);
}
/** It launches the algorithm */
public void execute() {
int i, j, k, l;
int t;
int ele;
double prob[];
double aux;
double NUmax = 1.5; // used for lineal ranking
double NUmin = 0.5; // used for lineal ranking
double pos1, pos2;
int sel1, sel2;
int data[][];
int infoAttr[];
int classData[];
Vector<Rule> contenedor = new Vector<Rule>();
Vector<Rule> conjR = new Vector<Rule>();
Rule tmpRule;
Condition tmpCondition[] = new Condition[1];
RuleSet population[];
RuleSet hijo1, hijo2;
if (somethingWrong) { // We do not execute the program
System.err.println("An error was found, the data-set has numerical values.");
System.err.println("Aborting the program");
// We should not use the statement: System.exit(-1);
} else {
Randomize.setSeed(seed);
nClasses = train.getnClasses();
/*Build the nominal data information*/
infoAttr = new int[train.getnInputs()];
for (i = 0; i < infoAttr.length; i++) {
infoAttr[i] = train.numberValues(i);
}
data = new int[train.getnData()][train.getnInputs()];
for (i = 0; i < data.length; i++) {
for (j = 0; j < data[i].length; j++) {
if (train.isMissing(i, j)) data[i][j] = -1;
else data[i][j] = train.valueExample(i, j);
}
}
classData = new int[train.getnData()];
for (i = 0; i < classData.length; i++) {
classData[i] = train.getOutputAsInteger(i);
}
/*Find first-order rules which result interesting*/
for (i = 0; i < nClasses; i++) {
for (j = 0; j < infoAttr.length; j++) {
for (k = 0; k < infoAttr[j]; k++) {
tmpCondition[0] = new Condition(j, k);
tmpRule = new Rule(tmpCondition);
if (Math.abs(computeAdjustedResidual(data, classData, tmpRule, i)) > 1.96) {
if (!contenedor.contains(tmpRule)) {
contenedor.add(tmpRule);
conjR.add(tmpRule);
}
}
}
}
}
// Construct the Baker selection roulette
prob = new double[popSize];
for (j = 0; j < popSize; j++) {
aux = (double) (NUmax - NUmin) * ((double) j / (popSize - 1));
prob[j] = (double) (1.0 / (popSize)) * (NUmax - aux);
}
for (j = 1; j < popSize; j++) prob[j] = prob[j] + prob[j - 1];
/*Steady-State Genetic Algorithm*/
ele = 2;
population = new RuleSet[popSize];
while (conjR.size() >= 2) {
t = 0;
System.out.println("Producing rules of level " + ele);
for (i = 0; i < population.length; i++) {
population[i] = new RuleSet(conjR);
population[i].computeFitness(data, classData, infoAttr, contenedor, nClasses);
}
Arrays.sort(population);
while (t < numGenerations && !population[0].equals(population[popSize - 1])) {
System.out.println("Generation " + t);
t++;
/*Baker's selection*/
pos1 = Randomize.Rand();
pos2 = Randomize.Rand();
for (l = 0; l < popSize && prob[l] < pos1; l++) ;
sel1 = l;
for (l = 0; l < popSize && prob[l] < pos2; l++) ;
sel2 = l;
hijo1 = new RuleSet(population[sel1]);
hijo2 = new RuleSet(population[sel2]);
if (Randomize.Rand() < pCross) {
RuleSet.crossover1(hijo1, hijo2);
} else {
RuleSet.crossover2(hijo1, hijo2);
}
RuleSet.mutation(hijo1, conjR, pMut, data, classData, infoAttr, contenedor, nClasses);
RuleSet.mutation(hijo2, conjR, pMut, data, classData, infoAttr, contenedor, nClasses);
hijo1.computeFitness(data, classData, infoAttr, contenedor, nClasses);
hijo2.computeFitness(data, classData, infoAttr, contenedor, nClasses);
population[popSize - 2] = new RuleSet(hijo1);
population[popSize - 1] = new RuleSet(hijo2);
Arrays.sort(population);
}
/*Decode function*/
ele++;
conjR.removeAllElements();
System.out.println(
"Fitness of the best chromosome in rule level " + ele + ": " + population[0].fitness);
for (i = 0; i < population[0].getRuleSet().length; i++) {
if (Math.abs(computeAdjustedResidual(data, classData, population[0].getRule(i), i))
> 1.96) {
if (validarRegla(population[0].getRule(i))
&& !contenedor.contains(population[0].getRule(i))) {
contenedor.add(population[0].getRule(i));
conjR.add(population[0].getRule(i));
}
}
}
}
// Finally we should fill the training and test output files
doOutput(this.val, this.outputTr, data, classData, infoAttr, contenedor, nClasses);
doOutput(this.test, this.outputTst, data, classData, infoAttr, contenedor, nClasses);
/*Print the rule obtained*/
for (i = contenedor.size() - 1; i >= 0; i--) {
if (reglaPositiva(
this.train, data, classData, infoAttr, nClasses, contenedor.elementAt(i))) {
Fichero.AnadirtoFichero(outputRule, contenedor.elementAt(i).toString(train));
Fichero.AnadirtoFichero(
outputRule,
" -> "
+ consecuente(
this.train, data, classData, infoAttr, nClasses, contenedor.elementAt(i))
+ "\n");
}
}
System.out.println("Algorithm Finished");
}
}