/**
   * 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();
  }
Example #2
0
  /**
   * In this method, all possible post hoc statistical test between more than three algorithms
   * results are executed, according to the configuration file
   *
   * @param code A double that identifies which methods will be applied
   * @param nfold A vector of int with fold number by algorithm
   * @param algorithms A vector of String with the names of the algorithms
   * @param fileName A String with the name of the output file
   */
  public static void doMultiple(double data[][], String algorithms[]) {

    String outputFileName = Configuration.getPath();

    String outputString = new String("");
    outputString = header();

    outputString += runMultiple(data, algorithms);

    Files.writeFile(outputFileName, outputString);
  } // end-method
  private void generateModel() {
    String salida = new String("");
    double max_auc = 0;
    ArrayList<String> solutions = this.getAllSolutions();
    models = new ArrayList<Farchd>();

    int nEjemplos = train.getnData();
    if (this.instances == this.MAJ) {
      nEjemplos = train.getMajority();
    }
    boolean[] variables = new boolean[train.getnInputs()];
    boolean[] ejemplos = new boolean[nEjemplos];
    this.weightsAUC = new double[solutions.size() / 2]; // Hay 2 soluciones FS e IS

    for (int i = 0, j = 0; i < solutions.size(); i += 2, j++) {
      int vars, ejs;
      vars = ejs = 0;
      variables = decode(solutions.get(i));
      ejemplos = decode(solutions.get(i + 1));
      for (int l = 0; l < variables.length; l++) {
        // variables[j] = solution[j];
        if (variables[l]) vars++;
      }
      for (int l = 0; l < ejemplos.length; l++) {
        if (ejemplos[l]) ejs++;
      }
      try {
        Farchd model = new Farchd(train, val, test, variables, ejemplos);

        /** ******** */
        // double fit = model.getAUCTr();
        double auc_tr = model.execute(true);
        double auc_tst = model.getAUCTst();
        if (auc_tr > max_auc) {
          max_auc = auc_tr;
          indexBest = j;
        }
        this.weightsAUC[j] = auc_tr;

        salida +=
            "Solution[" + j + "]:\t" + vars + "\t" + ejs + "\t" + auc_tr + "\t" + auc_tst + "\n";

        /** ******** */
        models.add(model);
      } catch (Exception e) {
        System.err.println("Liada maxima al generar modelo ");
        e.printStackTrace(System.err);
        System.exit(-1);
      }
    }
    System.out.print(salida);
    Files.writeFile(header + "_AUC.txt", salida);
  }
Example #4
0
  /**
   * Save network weights to a file
   *
   * @param file_name Output file name
   * @param header header of the data set for which the network has been adjusted to
   */
  protected void printNetworkToFile(String file_name, String header) {
    // write the header to the file
    Files.writeFile(file_name, header);

    Files.addToFile(file_name, "Number of neurons: " + nSel + "\n");
    for (int i = 0; i < nSel; i++) {
      Files.addToFile(file_name, "\nNeuron " + i + "\n");
      for (int j = 0; j < conjS[i].length; j++) {
        Files.addToFile(file_name, Double.toString(conjS[i][j]) + " ");
      }
      Files.addToFile(file_name, " Class = " + clasesS[i] + "\n");
    }
  }
Example #5
0
  /**
   * 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 void doOutput(myDataset dataset, String filename) {
    int i;
    double fuerza;
    String output = new String("");

    output = dataset.copyHeader(); // we insert the header in the output file

    for (i = 0; i < dataset.getnData(); i++) {
      fuerza = Output_fuzzy_system(dataset.getExample(i));
      output += (dataset.getOutputAsReal(i) + " " + fuerza + " " + "\n");
    }

    Files.writeFile(filename, output);
  }
Example #6
0
  /** Method interface for Automatic Branch and Bound */
  public void ejecutar() {
    String resultado;
    int i, numFeatures;
    Date d;

    d = new Date();
    resultado =
        "RESULTS generated at "
            + String.valueOf((Date) d)
            + " \n--------------------------------------------------\n";
    resultado += "Algorithm Name: " + params.nameAlgorithm + "\n";

    /* call of ABB algorithm */
    runABB();

    resultado += "\nPARTITION Filename: " + params.trainFileNameInput + "\n---------------\n\n";
    resultado += "Features selected: \n";

    for (i = numFeatures = 0; i < features.length; i++)
      if (features[i] == true) {
        resultado += Attributes.getInputAttribute(i).getName() + " - ";
        numFeatures++;
      }

    resultado +=
        "\n\n"
            + String.valueOf(numFeatures)
            + " features of "
            + Attributes.getInputNumAttributes()
            + "\n\n";

    resultado +=
        "Error in test (using train for prediction): "
            + String.valueOf(data.validacionCruzada(features))
            + "\n";
    resultado +=
        "Error in test (using test for prediction): "
            + String.valueOf(data.LVOTest(features))
            + "\n";

    resultado += "---------------\n";

    System.out.println("Experiment completed successfully");

    /* creates the new training and test datasets only with the selected features */
    Files.writeFile(params.extraFileNameOutput, resultado);
    data.generarFicherosSalida(params.trainFileNameOutput, params.testFileNameOutput, features);
  }
Example #7
0
 /**
  * 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
  * @return The classification accuracy
  */
 private double doOutput(myDataset dataset, String filename) {
   String output = new String("");
   int hits = 0;
   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++) {
     // for classification:
     String classOut = this.classificationOutput(dataset.getExample(i));
     output += dataset.getOutputAsString(i) + " " + classOut + "\n";
     if (dataset.getOutputAsString(i).equalsIgnoreCase(classOut)) {
       hits++;
     }
   }
   Files.writeFile(filename, output);
   return (1.0 * hits / dataset.size());
 }
Example #8
0
  /**
   * Save ensemble at file_name
   *
   * @param file_name File name
   * @param header header of the data set for which the network has been adjusted to
   */
  public void SaveEnsemble(String file_name, String header) {
    String name;

    // header of KEEL dataset
    Files.writeFile(file_name, header);
    // Save networks
    for (int i = 0; i < Nnetworks; i++) {
      Files.addToFile(file_name, "\n>>>>>>>>>>>>>>Network " + i + "\n");
      nets[i].SaveNetwork(file_name, header, true);
    }

    Files.addToFile(file_name, "\n\n********* Output weights:\n");
    // Save weigths
    // Save weights
    for (int i = 0; i < Noutputs; i++) {
      Files.addToFile(file_name, "Output: " + i + "\n");
      for (int j = 0; j < Nnetworks; j++) {
        Files.addToFile(file_name, Double.toString(weights[i][j]) + " ");
      }
    }
  }
Example #9
0
 /**
  * It stores the data base in a given file
  *
  * @param filename Name for the database file
  */
 public void saveFile(String filename) {
   String stringOut = new String("");
   stringOut = printString();
   Files.writeFile(filename, stringOut);
 }
Example #10
0
  /** It launches the algorithm */
  public void execute() {
    int i, j, num;
    double fitness, fitness2;

    if (somethingWrong) { // We do not execute the program
      System.err.println(
          "An error was found, either the data-set have numerical values or missing values.");
      System.err.println("Aborting the program");
      // We should not use the statement: System.exit(-1);
    } else {
      // We do here the algorithm's operations
      Randomize.setSeed(semilla);

      /* Generation of the initial population */
      System.out.println("Creating the initial population.");
      initializePopulation();
      Gen = 0;
      GenSincambio = 0;
      Bestperformance = -1.0;

      /* Main of the genetic algorithm */
      System.out.println("Starting the evolutionary process.");
      do {
        /* First, all rules' fitness is set to 0 */
        for (i = 0; i < tamPoblacion; i++) {
          Poblacion.get(i).fitness = 0.0;
          Poblacion.get(i).n_SistemasDifusos = 0;
        }

        /* Then Nf fuzzy system are created */
        for (i = 0; i < Nf; i++) {
          /* A fuzzy system containing Nr rules from the population is created */
          Create_fuzzy_system();

          /* The fitness asociated to this fuzzy system is calculated */
          fitness = Evaluate_fuzzy_system();

          /* The fitness value is accumulated among the rules in the fuzzy system */
          Accumulate_fitness_fuzzy_system(fitness);

          /* If the fitness of the current fuzzy system outperforms the best evolved one,
          we update this last one */
          if (fitness > Bestperformance) {
            Bestperformance = fitness;
            GenSincambio = -1;

            BestSistemaDifuso.clear();
            for (j = 0; j < Nr; j++) {
              Individual indi = new Individual(Poblacion.get(vectorNr[j]));
              BestSistemaDifuso.add(indi);
            }
          }
        }

        /* The accumulated fitness value of each individual in the population is divided
        by the number of times it has been selected */
        for (i = 0; i < tamPoblacion; i++) {
          if (Poblacion.get(i).n_SistemasDifusos != 0) {
            Poblacion.get(i).fitness /= Poblacion.get(i).n_SistemasDifusos;
          } else {
            Poblacion.get(i).fitness = 0.0;
          }

          /* Now we count the number of parameter used in the consequent, in order to
          give a better fitness to those rules with a lower number of parameters */
          num = 0;
          for (j = 0; j < entradas; j++) {
            if (Poblacion.get(i).consecuente[j] != 0.0) {
              num++;
            }
          }
          if (Poblacion.get(i).consecuente[entradas] != 0.0) {
            num++;
          }

          Poblacion.get(i).fitness /= (K + num);
        }

        /* we increment the counter of the number of generations */
        Gen++;
        GenSincambio++;

        if (GenSincambio == numGenMigration) {
          /* Migration stage: half of the population (the worst one) is radomly generated again
          to increase the searching ability of the genetic process */
          System.out.println(
              "Migrating half of the population in order to restart the evolutionary process.");
          Migration();
          GenSincambio = 0;
        } else {
          /* Reproduction stage (includes crossover) */
          Reproduction();

          /* Mutation */
          Mutation();
        }
        System.out.println("Iteration: " + Gen + ". Best fitness: " + (1.0 / Bestperformance));
      } while (Gen <= numGeneraciones);

      String salida = new String("");
      salida += Print_Population();

      SistemaDifuso.clear();
      for (i = 0; i < Nr; i++) {
        Individual indi = new Individual(BestSistemaDifuso.get(i));
        SistemaDifuso.add(indi);
      }

      salida += "MSE Training:\t" + (1.0 / Bestperformance) + "%\n";
      salida += "MSE Test:\t\t" + Evaluate_best_fuzzy_system_in_test() + "%\n\n";

      Files.writeFile(outputBC, salida);

      doOutput(this.val, this.outputTr);
      doOutput(this.test, this.outputTst);

      System.out.println("Algorithm Finished.");
    }
  }
Example #11
0
 /** Outputs contents of CMAR rule linked list (if any) */
 public void outputCMARrules(String filename) {
   String stringOut = new String("");
   stringOut = outputRules(startCMARrulelist);
   Files.writeFile(filename, stringOut);
 }