/*********************************************************************** This file is part of KEEL-software, the Data Mining tool for regression, classification, clustering, pattern mining and so on. Copyright (C) 2004-2010 F. Herrera (herrera@decsai.ugr.es) L. Sánchez (luciano@uniovi.es) J. Alcalá-Fdez (jalcala@decsai.ugr.es) S. García (sglopez@ujaen.es) A. Fernández (alberto.fernandez@ujaen.es) J. Luengo (julianlm@decsai.ugr.es) 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 3 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, see http://www.gnu.org/licenses/ **********************************************************************/ // // SSMA.javA HIBRIDO PSO // // Salvador Garc�a L�pez // // Created by Salvador Garc�a L�pez 3-10-2005. // Copyright (c) 2004 __MyCompanyName__. All rights reserved. // package keel.Algorithms.Instance_Generation.SSMAPSO; import keel.Algorithms.Preprocess.Basic.*; import keel.Algorithms.Instance_Generation.Basic.PrototypeGenerator; import keel.Algorithms.Instance_Generation.Basic.Prototype; import keel.Algorithms.Instance_Generation.Basic.PrototypeGenerationAlgorithm; import keel.Algorithms.Instance_Generation.Basic.PrototypeSet; import keel.Algorithms.Instance_Generation.utilities.*; //import keel.Algorithms.Instance_Generation.utilities.KNN.KNN; import keel.Dataset.Attributes; import keel.Dataset.InstanceAttributes; import keel.Dataset.InstanceSet; import org.core.*; import java.util.StringTokenizer; import java.util.Arrays; public class SSMAPSO extends Metodo { /*Own parameters of the algorithm*/ private long semilla; private int tamPoblacion; private double nEval; private double pCross; private double pMut; private int kNeigh; public String Script; // para releer par�metros.. private PrototypeSet trainingDataSet; private PrototypeGenerator generador; //Par�metros PSO private int SwarmSize; // SwarmSize == P private int ParticleSize; // ParticleSize == K (in the article) private int MaxIter; private double C1; private double C2; private double VMax; private double Wstart; private double Wend; protected int numberOfClass; protected int numberOfPrototypes; // Particle size is the percentage protected int numberOfStrategies; // number of strategies in the pool public SSMAPSO (String ficheroScript) { super (ficheroScript); } /** * Reads the prototype set from a data file. * @param nameOfFile Name of data file to be read. * @return PrototypeSet built with the data of the file. */ public static PrototypeSet readPrototypeSet(String nameOfFile) { Attributes.clearAll();//BUGBUGBUG InstanceSet training = new InstanceSet(); try { //System.out.print("PROBANDO:\n"+nameOfFile); training.readSet(nameOfFile, true); training.setAttributesAsNonStatic(); InstanceAttributes att = training.getAttributeDefinitions(); Prototype.setAttributesTypes(att); } catch(Exception e) { System.err.println("readPrototypeSet has failed!"); e.printStackTrace(); } return new PrototypeSet(training); } /** * Implements the 1NN algorithm * @param current Prototype which the algorithm will find its nearest-neighbor. * @param dataSet Prototype set in which the algorithm will search. * @return Nearest prototype to current in the prototype set dataset. */ public static Prototype _1nn(Prototype current, PrototypeSet dataSet) { Prototype nearestNeighbor = dataSet.get(0); int indexNN = 0; //double minDist = Distance.dSquared(current, nearestNeighbor); //double minDist = Distance.euclideanDistance(current, nearestNeighbor); double minDist =Double.POSITIVE_INFINITY; double currDist; int _size = dataSet.size(); // System.out.println("****************"); // current.print(); for (int i=0; i<_size; i++) { Prototype pi = dataSet.get(i); //if(!current.equals(pi)) //{ // double currDist = Distance.dSquared(current, pi); currDist = Distance.euclideanDistance(pi,current); // System.out.println(currDist); if(currDist >0){ if (currDist < minDist) { minDist = currDist; // nearestNeighbor = pi; indexNN =i; } } //} } // System.out.println("Min dist =" + minDist + " Vecino Cercano = "+ indexNN); return dataSet.get(indexNN); } public double classficationAccuracy1NN(PrototypeSet training, PrototypeSet test) { int wellClassificated = 0; for(Prototype p : test) { Prototype nearestNeighbor = _1nn(p, training); if(p.getOutput(0) == nearestNeighbor.getOutput(0)) ++wellClassificated; } return 100.0* (wellClassificated / (double)test.size()); } /** * Generate a reduced prototype set by the PSOGenerator method. * @return Reduced set by PSOGenerator's method. */ public PrototypeSet reduceSet(PrototypeSet initial) { System.out.print("\nThe algorithm is starting...\n Computing...\n"); //Algorithm // First, we create the population, with SwarmSize. // like a prototypeSet's vector. PrototypeSet population [] = new PrototypeSet [SwarmSize]; PrototypeSet mejorPosicion [] = new PrototypeSet [SwarmSize]; PrototypeSet nominalPopulation = new PrototypeSet(); double fitness[] = new double[SwarmSize]; double fitness_bestPopulation[] = new double[SwarmSize]; PrototypeSet bestParticle = new PrototypeSet(); double inertia = ((Wstart-Wend)*(MaxIter))/ (MaxIter + Wend); int mejorParticula =0; // The best particle in the population double aleatorio; //Each particle must have Particle Size % //Initialization. population[0]= new PrototypeSet(initial) ; generador = new PrototypeGenerator(trainingDataSet); nominalPopulation = new PrototypeSet(); nominalPopulation.formatear(population[0]); fitness[0] = classficationAccuracy1NN(nominalPopulation,trainingDataSet); this.numberOfClass = trainingDataSet.getPosibleValuesOfOutput().size(); System.out.println("Best initial fitness = "+ fitness[0]); fitness_bestPopulation[0] = fitness[0]; for(int i=1; i< SwarmSize; i++){ population[i] = new PrototypeSet(); for(int j=0; j< population[0].size(); j++){ Prototype aux = new Prototype(trainingDataSet.getFromClass(population[0].get(j).getOutput(0)).getRandom()); population[i].add(aux); } nominalPopulation = new PrototypeSet(); nominalPopulation.formatear(population[i]); fitness[i] = classficationAccuracy1NN(population[i],trainingDataSet); // PSOfitness fitness_bestPopulation[i] = fitness[i]; // Initially the same fitness. } //We select the best initial particle double bestFitness=fitness[0]; int bestFitnessIndex=0; for(int i=1; i< SwarmSize;i++){ if(fitness[i]>bestFitness){ bestFitness = fitness[i]; bestFitnessIndex=i; } } for(int j=0;j<SwarmSize;j++){ mejorPosicion[j] = population[j].clone(); // hard-copy.Save the best position of the particle. //Initial mejorPosicion = initial population. //Now, I establish the index of each prototype. for(int i=0; i<population[j].size(); ++i) population[j].get(i).setIndex(i); } double velocidad[][][] = new double[SwarmSize][][]; // tri-dimensional vector int num_atribs = population[0].get(0).numberOfInputs(); for(int i=0; i<SwarmSize;i++){ velocidad[i]= new double[population[0].size()][]; // velocity matrix. // Initially there is no velocity, no memory.. for(int j=0; j<population[0].size();j++){ velocidad[i][j] = new double[num_atribs]; for(int k = 0; k<num_atribs;k++){ velocidad[i][j][k] = RandomGenerator.Randdouble(-VMax, VMax)*1. ; // the initial velocity, a random number between -Vmax , Vmax // System.out.println(velocidad[i][j][k]); } } } for(int iter=0; iter< MaxIter; iter++){ // Main loop for(int i=0; i< SwarmSize; i++){ for(int k = 0; k< population[i].size();k++){ Prototype resta = mejorPosicion[i].get(k).sub(population[i].get(k)); Prototype restaBestParticle = mejorPosicion[bestFitnessIndex].get(k).sub(population[i].get(k)); for(int j=0; j< num_atribs ; j++){ velocidad[i][k][j]= inertia * velocidad[i][k][j] ; // Memory velocity. aleatorio =RandomGenerator.Randdouble(0, 1) ; velocidad[i][k][j]+= C1*aleatorio* resta.getInput(j) ; // Cognition part. aleatorio =RandomGenerator.Randdouble(0, 1) ; velocidad[i][k][j]+= C2*aleatorio * restaBestParticle.getInput(j) ; // Social part. //System.out.print(aleatorio + "\t"); // Then we do xi = xi + vi. if(velocidad[i][k][j]>VMax){ velocidad[i][k][j] = VMax; // The particles's velocities has a maximum velocity. }else if(velocidad[i][k][j]< -VMax){ velocidad[i][k][j]=-VMax; // absolute value. �? or -VMax , Vmax. ? } //System.out.print("\nVelocidad ="+ velocidad[i][k][j] + "\n"); // System.out.print("\nvalor= "+ population[i].get(k).getInput(j)+ "\n"); double suma = population[i].get(k).getInput(j) + velocidad[i][k][j]*1.; //if(suma>1) suma = 1; //else if( suma<0) suma = 0; // Establish the normalize limits [0,1] //System.out.print("\nSuma= "+ suma+ "\n"); population[i].get(k).setInput(j,suma); // We add the velocity to the attribute population[i].get(k).applyThresholds(); } } } //Now we have xi = xi + vi.for all particles. // Particles has changed, We must calculate fitness and compare all. for(int i=0; i< SwarmSize; i++){ /* if(k<=population[i].size()) fitness[i] = absoluteclassficationAccuracy1NNKNN(population[i], trainingDataSet,k); // PSO fitness else fitness[i] = absoluteclassficationAccuracy1NNKNN(population[i],trainingDataSet,population[i].size()); */ // Antes de calcular el fitness, tengo que "transformar los datos nominales.." nominalPopulation = new PrototypeSet(); nominalPopulation.formatear(population[i]); fitness[i] = classficationAccuracy1NN(nominalPopulation,trainingDataSet); //fitness[i] = classficationAccuracy1NN(population[i],trainingDataSet); } for(int i=0; i< SwarmSize;i++){ // Where is the best? if(fitness[i]>bestFitness){ bestFitness = fitness[i]; bestFitnessIndex=i; } //Save the best particles! if(fitness[i]>fitness_bestPopulation[i]){ fitness_bestPopulation[i] = fitness[i]; mejorPosicion[i] = population[i].clone(); // Hard Copy. } } //Calculate the new inertia. inertia = ((Wstart-Wend)*(MaxIter-iter))/ (MaxIter + Wend); } System.err.println("Best Fitness "+ bestFitness); nominalPopulation = new PrototypeSet(); nominalPopulation.formatear(mejorPosicion[bestFitnessIndex]); System.err.println("\n% de acierto en training Nominal " + classficationAccuracy1NN(nominalPopulation,trainingDataSet)); return nominalPopulation; } /* MEzcla de algoritmos */ public void ejecutar () { int i, j, l; double conjS[][]; double conjR[][]; int conjN[][]; boolean conjM[][]; int clasesS[]; int nSel = 0; Cromosoma poblacion[]; double ev = 0; double dMatrix[][]; int sel1, sel2, comp1, comp2; Cromosoma hijos[]; double umbralOpt; boolean veryLarge; double GAeffort=0, LSeffort=0, temporal; double fAcierto=0, fReduccion=0; int contAcierto=0, contReduccion=0; int nClases; long tiempo = System.currentTimeMillis(); /*Getting the number of different classes*/ nClases = 0; for (i=0; i<clasesTrain.length; i++) if (clasesTrain[i] > nClases) nClases = clasesTrain[i]; nClases++; if (datosTrain.length > 9000) { veryLarge = true; } else { veryLarge = false; } if (veryLarge == false) { /*Construct a distance matrix of the instances*/ dMatrix = new double[datosTrain.length][datosTrain.length]; for (i = 0; i < dMatrix.length; i++) { for (j = i + 1; j < dMatrix[i].length; j++) { dMatrix[i][j] = KNN.distancia(datosTrain[i], realTrain[i], nominalTrain[i], nulosTrain[i], datosTrain[j], realTrain[j], nominalTrain[j], nulosTrain[j], distanceEu); } } for (i = 0; i < dMatrix.length; i++) { dMatrix[i][i] = Double.POSITIVE_INFINITY; } for (i = 0; i < dMatrix.length; i++) { for (j = i - 1; j >= 0; j--) { dMatrix[i][j] = dMatrix[j][i]; } } } else { dMatrix = null; } /*Random inicialization of the population*/ Randomize.setSeed (semilla); poblacion = new Cromosoma[tamPoblacion]; for (i=0; i<tamPoblacion; i++) poblacion[i] = new Cromosoma (kNeigh, datosTrain.length, dMatrix, datosTrain, realTrain, nominalTrain, nulosTrain, distanceEu); /*Initial evaluation of the population*/ for (i=0; i<tamPoblacion; i++) { poblacion[i].evaluacionCompleta(nClases, kNeigh, clasesTrain); } umbralOpt = 0; /*Until stop condition*/ while (ev < nEval) { Arrays.sort(poblacion); if (fAcierto >= (double)poblacion[0].getFitnessAc()*100.0/(double)datosTrain.length) { contAcierto++; } else { contAcierto=0; } fAcierto = (double)poblacion[0].getFitnessAc()*100.0/(double)datosTrain.length; if (fReduccion >= (1.0-((double)poblacion[0].genesActivos()/(double)datosTrain.length))*100.0) { contReduccion++; } else { contReduccion=0; } fReduccion = (1.0-((double)poblacion[0].genesActivos()/(double)datosTrain.length))*100.0; if (contReduccion >= 10 || contAcierto >= 10){ if (Randomize.Randint(0,1)==0) { if (contAcierto >= 10) { contAcierto = 0; umbralOpt++; } else { contReduccion = 0; umbralOpt--; } } else { if (contReduccion >= 10) { contReduccion = 0; umbralOpt--; } else { contAcierto = 0; umbralOpt++; } } } /*Binary tournament selection*/ comp1 = Randomize.Randint(0,tamPoblacion-1); do { comp2 = Randomize.Randint(0,tamPoblacion-1); } while (comp2 == comp1); if (poblacion[comp1].getFitness() > poblacion[comp2].getFitness()) sel1 = comp1; else sel1 = comp2; comp1 = Randomize.Randint(0,tamPoblacion-1); do { comp2 = Randomize.Randint(0,tamPoblacion-1); } while (comp2 == comp1); if (poblacion[comp1].getFitness() > poblacion[comp2].getFitness()) sel2 = comp1; else sel2 = comp2; hijos = new Cromosoma[2]; hijos[0] = new Cromosoma (kNeigh, poblacion[sel1], poblacion[sel2], pCross,datosTrain.length); hijos[1] = new Cromosoma (kNeigh, poblacion[sel2], poblacion[sel1], pCross,datosTrain.length); hijos[0].mutation (kNeigh, pMut, dMatrix, datosTrain, realTrain, nominalTrain, nulosTrain, distanceEu); hijos[1].mutation (kNeigh, pMut, dMatrix, datosTrain, realTrain, nominalTrain, nulosTrain, distanceEu); /*Evaluation of offsprings*/ hijos[0].evaluacionCompleta(nClases, kNeigh, clasesTrain); hijos[1].evaluacionCompleta(nClases, kNeigh, clasesTrain); ev+=2; GAeffort += 2; temporal = ev; if (hijos[0].getFitness() > poblacion[tamPoblacion-1].getFitness() || Randomize.Rand() < 0.0625) { ev += hijos[0].optimizacionLocal(nClases, kNeigh, clasesTrain,dMatrix,umbralOpt, datosTrain, realTrain, nominalTrain, nulosTrain, distanceEu); } if (hijos[1].getFitness() > poblacion[tamPoblacion-1].getFitness() || Randomize.Rand() < 0.0625) { ev += hijos[1].optimizacionLocal(nClases, kNeigh, clasesTrain,dMatrix,umbralOpt, datosTrain, realTrain, nominalTrain, nulosTrain, distanceEu); } LSeffort += (ev - temporal); /*Replace the two worst*/ if (hijos[0].getFitness() > poblacion[tamPoblacion-1].getFitness()) { poblacion[tamPoblacion-1] = new Cromosoma (kNeigh, datosTrain.length, hijos[0]); } if (hijos[1].getFitness() > poblacion[tamPoblacion-2].getFitness()) { poblacion[tamPoblacion-2] = new Cromosoma (kNeigh, datosTrain.length, hijos[1]); } /* System.out.println(ev + " - (" + umbralOpt + ")" + (double)poblacion[0].getFitnessAc()*100.0/(double)datosTrain.length + " / " + (double)poblacion[tamPoblacion-1].getFitnessAc()*100.0/(double)datosTrain.length + " - " + (1.0-((double)poblacion[0].genesActivos()/(double)datosTrain.length))*100.0 + " / " + (1.0-((double)poblacion[tamPoblacion-1].genesActivos()/(double)datosTrain.length))*100.0);*/ } Arrays.sort(poblacion); nSel = poblacion[0].genesActivos(); /*Construction of S set from the best cromosome*/ conjS = new double[nSel][datosTrain[0].length]; conjR = new double[nSel][datosTrain[0].length]; conjN = new int[nSel][datosTrain[0].length]; conjM = new boolean[nSel][datosTrain[0].length]; clasesS = new int[nSel]; for (i=0, l=0; i<datosTrain.length; i++) { if (poblacion[0].getGen(i)) { //the instance must be copied to the solution for (j=0; j<datosTrain[i].length; j++) { conjS[l][j] = datosTrain[i][j]; conjR[l][j] = realTrain[i][j]; conjN[l][j] = nominalTrain[i][j]; conjM[l][j] = nulosTrain[i][j]; } clasesS[l] = clasesTrain[i]; l++; } } System.out.println("SSMA "+ relation + " " + (double)(System.currentTimeMillis()-tiempo)/1000.0 + "s"); OutputIS.escribeSalida(ficheroSalida[0], conjR, conjN, conjM, clasesS, entradas, salida, nEntradas, relation); OutputIS.escribeSalida(ficheroSalida[1], test, entradas, salida, nEntradas, relation); /** AHORA A�ADO MI DE!! **/ Parameters.assertBasicArgs(ficheroSalida); PrototypeGenerationAlgorithm.readParametersFile(this.Script); PrototypeGenerationAlgorithm.printParameters(); PrototypeSet training = readPrototypeSet(ficheroSalida[0]); training.print(); // Conjunto devuelto POR SSMA trainingDataSet = readPrototypeSet(this.ficheroTraining); // Conjunto inicial // trainingDataSet.print(); //this.numberOfPrototypes = (int)Math.floor((trainingDataSet.size())*ParticleSize/100.0); PrototypeSet SADE = reduceSet(training); // LLAMO al SADE SADE.save(ficheroSalida[0]); // Lo guardo //Copy the test input file to the output test file // KeelFile.copy(inputFilesPath.get(TEST), outputFilesPath.get(TEST)); // COn conjS me vale. int trainRealClass[][]; int trainPrediction[][]; trainRealClass = new int[datosTrain.length][1]; trainPrediction = new int[datosTrain.length][1]; //Working on training for ( i=0; i<datosTrain.length; i++) { trainRealClass[i][0] = clasesTrain[i]; trainPrediction[i][0] = KNN.evaluate(datosTrain[i],SADE.prototypeSetTodouble(), nClases, SADE.getClases(), 1); } KNN.writeOutput(ficheroSalida[0], trainRealClass, trainPrediction, entradas, salida, relation); //Working on test int realClass[][] = new int[datosTest.length][1]; int prediction[][] = new int[datosTest.length][1]; //Check time for (i=0; i<realClass.length; i++) { realClass[i][0] = clasesTest[i]; prediction[i][0]= KNN.evaluate(datosTest[i],SADE.prototypeSetTodouble(), nClases, SADE.getClases(), 1); } KNN.writeOutput(ficheroSalida[1], realClass, prediction, entradas, salida, relation); } public void leerConfiguracion (String ficheroScript) { String fichero, linea, token; StringTokenizer lineasFichero, tokens; byte line[]; int i, j; ficheroSalida = new String[2]; fichero = Fichero.leeFichero (ficheroScript); lineasFichero = new StringTokenizer (fichero,"\n\r"); lineasFichero.nextToken(); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); token = tokens.nextToken(); /*Getting the name of training and test files*/ line = token.getBytes(); for (i=0; line[i]!='\"'; i++); i++; for (j=i; line[j]!='\"'; j++); ficheroTraining = new String (line,i,j-i); for (i=j+1; line[i]!='\"'; i++); i++; for (j=i; line[j]!='\"'; j++); ficheroValidation = new String (line,i,j-i); for (i=j+1; line[i]!='\"'; i++); i++; for (j=i; line[j]!='\"'; j++); ficheroTest = new String (line,i,j-i); //Parameters.assertBasicArgs(ficheroSalida); /*Obtainin the path and the base name of the results files*/ linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); token = tokens.nextToken(); /*Getting the name of output files*/ line = token.getBytes(); for (i=0; line[i]!='\"'; i++); i++; for (j=i; line[j]!='\"'; j++); ficheroSalida[0] = new String (line,i,j-i); for (i=j+1; line[i]!='\"'; i++); i++; for (j=i; line[j]!='\"'; j++); ficheroSalida[1] = new String (line,i,j-i); /*Getting the seed*/ linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); semilla = Long.parseLong(tokens.nextToken().substring(1)); /*Getting the size of the poblation and the number of evaluations*/ linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); tamPoblacion = Integer.parseInt(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); nEval = Double.parseDouble(tokens.nextToken().substring(1)); /*Getting the probabilities of evolutionary operators*/ linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); pCross = Double.parseDouble(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); pMut = Double.parseDouble(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); kNeigh = Integer.parseInt(tokens.nextToken().substring(1)); /*Getting the type of distance function*/ linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); distanceEu = tokens.nextToken().substring(1).equalsIgnoreCase("Euclidean")?true:false; linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); this.SwarmSize = Integer.parseInt(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); this.MaxIter = Integer.parseInt(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); this.C1 = Double.parseDouble(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); this.C2 = Double.parseDouble(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); this.VMax = Double.parseDouble(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); this.Wstart = Double.parseDouble(tokens.nextToken().substring(1)); linea = lineasFichero.nextToken(); tokens = new StringTokenizer (linea, "="); tokens.nextToken(); this.Wend = Double.parseDouble(tokens.nextToken().substring(1)); System.out.print("\nIsaac dice: Swar= "+SwarmSize+ " Maxiter= "+ MaxIter+" Wend= "+this.Wend+ "\n"); } }