source: trunk/CrossPare/src/de/ugoe/cs/cpdp/training/GPTraining.java

package de.ugoe.cs.cpdp.training;

import java.util.LinkedList;
import java.util.List;

import org.apache.commons.collections4.list.SetUniqueList;

import weka.classifiers.AbstractClassifier;
import weka.classifiers.Classifier;
import weka.core.Instance;
import weka.core.Instances;
import org.apache.commons.lang3.ArrayUtils;
import org.jgap.Configuration;
import org.jgap.InvalidConfigurationException;
import org.jgap.gp.CommandGene;
import org.jgap.gp.GPProblem;

import org.jgap.gp.function.Add;
import org.jgap.gp.function.Multiply;
import org.jgap.gp.function.Log;
import org.jgap.gp.function.Subtract;
import org.jgap.gp.function.Divide;
import org.jgap.gp.function.Sine;
import org.jgap.gp.function.Cosine;
import org.jgap.gp.function.Max;
import org.jgap.gp.function.Exp;

import org.jgap.gp.impl.DeltaGPFitnessEvaluator;
import org.jgap.gp.impl.GPConfiguration;
import org.jgap.gp.impl.GPGenotype;
import org.jgap.gp.impl.TournamentSelector;
import org.jgap.gp.terminal.Terminal;
import org.jgap.gp.GPFitnessFunction;
import org.jgap.gp.IGPProgram;
import org.jgap.gp.terminal.Variable;
import org.jgap.gp.MathCommand;
import org.jgap.util.ICloneable;

import de.ugoe.cs.cpdp.util.WekaUtils;

import org.jgap.gp.impl.ProgramChromosome;
import org.jgap.util.CloneException;

/**
 * Genetic Programming Trainer
 * 
 * Implementation (mostly) according to Liu et al. Evolutionary Optimization of Software Quality
 * Modeling with Multiple Repositories.
 * 
 * - GPRun is a Run of a complete Genetic Programm Evolution, we want several complete runs. -
 * GPVClassifier is the Validation Classifier - GPVVClassifier is the Validation-Voting Classifier
 * 
 * config: <setwisetrainer name="GPTraining" param="populationSize:1000,numberRuns:10" />
 * 
 * @author Alexander Trautsch
 */
public class GPTraining implements ISetWiseTrainingStrategy, IWekaCompatibleTrainer {

    /**
     * the interal validation-and-voting classifier
     */
    private GPVVClassifier classifier = null;

    /**
     * size of the population of the genetic program; default from the paper is 1000
     */
    private int populationSize = 1000;

    /**
     * minimal depth of the S-expression tree at the start of the training; default from the paper
     * is 2
     */
    private int initMinDepth = 2;

    /**
     * maximal depth of the S-expression tree at the start of the training; default from the paper
     * is 6
     */
    private int initMaxDepth = 6;

    /**
     * size of the tournaments used for selection; default from the paper is 7
     */
    private int tournamentSize = 7;

    /**
     * number of genetic generations considered (i.e., number of iterations; default from the paper
     * is 50
     */
    private int maxGenerations = 50;

    /**
     * weight factor for the prediction errors for cost estimation; default from the paper is 15
     */
    private double errorType2Weight = 15;

    /**
     * number of internal replications from which the best result is picked; default from the paper
     * is 20
     */
    private int numberRuns = 20;

    /**
     * maximal depth of the S-expression tree; default from the paper is 20
     */
    private int maxDepth = 20;

    /**
     * maximal number of nodes of the S-expression tree; default from the paper is 100
     */
    private int maxNodes = 100;

    /*
     * (non-Javadoc)
     * 
     * @see de.ugoe.cs.cpdp.IParameterizable#setParameter(java.lang.String)
     */
    @Override
    public void setParameter(String parameters) {

        String[] params = parameters.split(",");
        String[] keyvalue = new String[2];

        for (int i = 0; i < params.length; i++) {
            keyvalue = params[i].split(":");

            switch (keyvalue[0])
            {
                case "populationSize":
                    this.populationSize = Integer.parseInt(keyvalue[1]);
                    break;

                case "initMinDepth":
                    this.initMinDepth = Integer.parseInt(keyvalue[1]);
                    break;

                case "tournamentSize":
                    this.tournamentSize = Integer.parseInt(keyvalue[1]);
                    break;

                case "maxGenerations":
                    this.maxGenerations = Integer.parseInt(keyvalue[1]);
                    break;

                case "errorType2Weight":
                    this.errorType2Weight = Double.parseDouble(keyvalue[1]);
                    break;

                case "numberRuns":
                    this.numberRuns = Integer.parseInt(keyvalue[1]);
                    break;

                case "maxDepth":
                    this.maxDepth = Integer.parseInt(keyvalue[1]);
                    break;

                case "maxNodes":
                    this.maxNodes = Integer.parseInt(keyvalue[1]);
                    break;
            }
        }

        this.classifier = new GPVVClassifier();
        ((GPVClassifier) this.classifier)
            .configure(populationSize, initMinDepth, initMaxDepth, tournamentSize, maxGenerations,
                       errorType2Weight, numberRuns, maxDepth, maxNodes);
    }

    /*
     * (non-Javadoc)
     * 
     * @see
     * de.ugoe.cs.cpdp.training.ISetWiseTrainingStrategy#apply(org.apache.commons.collections4.list.
     * SetUniqueList)
     */
    @Override
    public void apply(SetUniqueList<Instances> traindataSet) {
        try {
            classifier.buildClassifier(traindataSet);
        }
        catch (Exception e) {
            throw new RuntimeException(e);
        }
    }

    /*
     * (non-Javadoc)
     * 
     * @see de.ugoe.cs.cpdp.training.ISetWiseTrainingStrategy#getName()
     */
    @Override
    public String getName() {
        return "GPTraining";
    }

    /*
     * (non-Javadoc)
     * 
     * @see de.ugoe.cs.cpdp.training.IWekaCompatibleTrainer#getClassifier()
     */
    @Override
    public Classifier getClassifier() {
        return this.classifier;
    }

    /**
     * <p>
     * Internal helper class that stores the data in a format that can be used by the genetic
     * program.
     * </p>
     * 
     * @author Alexander Trautsch
     */
    public class InstanceData {

        /**
         * instances values
         */
        private double[][] instances_x;

        /**
         * class labels
         */
        private boolean[] instances_y;

        /**
         * <p>
         * Constructor. Creates the internal data representation.
         * </p>
         *
         * @param instances
         */
        public InstanceData(Instances instances) {
            this.instances_x = new double[instances.numInstances()][instances.numAttributes() - 1];
            this.instances_y = new boolean[instances.numInstances()];

            Instance current;
            for (int i = 0; i < this.instances_x.length; i++) {
                current = instances.get(i);
                this.instances_x[i] = WekaUtils.instanceValues(current);
                this.instances_y[i] = 1.0 == current.classValue();
            }
        }

        /**
         * <p>
         * returns the instance values
         * </p>
         *
         * @return the instance values
         */
        public double[][] getX() {
            return instances_x;
        }

        /**
         * <p>
         * returns the instance labels
         * </p>
         *
         * @return the instance labels
         */
        public boolean[] getY() {
            return instances_y;
        }
    }

    /**
     * One Run executed by a GP Classifier
     */
    public class GPRun extends AbstractClassifier {

        /**
         * generated serialization ID
         */
        private static final long serialVersionUID = -4250422550107888789L;

        /**
         * size of the population of the genetic program
         */
        private int populationSize;

        /**
         * minimal depth of the S-expression tree at the start of the training
         */
        private int initMinDepth;

        /**
         * maximal depth of the S-expression tree at the start of the training
         */
        private int initMaxDepth;

        /**
         * size of the tournaments used for selection
         */
        private int tournamentSize;

        /**
         * number of genetic generations considered (i.e., number of iterations
         */
        private int maxGenerations;

        /**
         * weight factor for the prediction errors for cost estimation
         */
        private double errorType2Weight;

        /**
         * maximal depth of the S-expression tree
         */
        private int maxDepth;

        /**
         * maximal number of nodes of the S-expression tree
         */
        private int maxNodes;

        /**
         * genetic program
         */
        private GPGenotype gp;

        /**
         * description of the problem to be solved by the genetic program
         */
        private GPProblem problem;

        /**
         * <p>
         * Configures the runner
         * </p>
         *
         * @param populationSize
         *            the population size
         * @param initMinDepth
         *            the initial minimal depth of the S-expression tree
         * @param initMaxDepth
         *            the initial maximal depth of the S-expression tree
         * @param tournamentSize
         *            the tournament size for selection
         * @param maxGenerations
         *            the number of generations created
         * @param errorType2Weight
         *            weigth factor for the prediction errors
         * @param maxDepth
         *            maximal depth of the S-expression tree
         * @param maxNodes
         *            maximal number of nodes of the S-expression tree
         */
        public void configure(int populationSize,
                              int initMinDepth,
                              int initMaxDepth,
                              int tournamentSize,
                              int maxGenerations,
                              double errorType2Weight,
                              int maxDepth,
                              int maxNodes)
        {
            this.populationSize = populationSize;
            this.initMinDepth = initMinDepth;
            this.initMaxDepth = initMaxDepth;
            this.tournamentSize = tournamentSize;
            this.maxGenerations = maxGenerations;
            this.errorType2Weight = errorType2Weight;
            this.maxDepth = maxDepth;
            this.maxNodes = maxNodes;
        }

        /**
         * <p>
         * returns the genetic program
         * </p>
         *
         * @return the genetic program
         */
        public GPGenotype getGp() {
            return this.gp;
        }

        /**
         * <p>
         * returns the variables of the genetic program
         * </p>
         *
         * @return the variables
         */
        public Variable[] getVariables() {
            return ((CrossPareGP) this.problem).getVariables();
        }

        /*
         * (non-Javadoc)
         * 
         * @see weka.classifiers.Classifier#buildClassifier(weka.core.Instances)
         */
        @Override
        public void buildClassifier(Instances traindata) throws Exception {
            InstanceData train = new InstanceData(traindata);
            this.problem =
                new CrossPareGP(train.getX(), train.getY(), this.populationSize, this.initMinDepth,
                                this.initMaxDepth, this.tournamentSize, this.errorType2Weight,
                                this.maxDepth, this.maxNodes);
            this.gp = problem.create();
            this.gp.evolve(this.maxGenerations);
        }

        /**
         * GPProblem implementation
         * 
         * @author Alexander Trautsch
         */
        class CrossPareGP extends GPProblem {

            /**
             * Instance values of the training data
             */
            private double[][] instances;

            /**
             * Classifications of the training data
             */
            private boolean[] output;

            /**
             * maximal depth of the S-expression tree
             */
            private int maxDepth;

            /**
             * maximal number of nodes of the S-expression tree
             */
            private int maxNodes;

            /**
             * variables of the genetic program
             */
            private Variable[] x;

            /**
             * 
             * <p>
             * Constructor. Creates a new genetic program.
             * </p>
             *
             * @param instances
             *            instance values of the training data
             * @param output
             *            classifications of the training data
             * @param populationSize
             *            the population size
             * @param minInitDept
             *            the initial minimal depth of the S-expression tree
             * @param maxInitDepth
             *            the initial maximal depth of the S-expression tree
             * @param tournamentSize
             *            the tournament size for selection
             * @param maxGenerations
             *            the number of generations created
             * @param errorType2Weight
             *            weigth factor for the prediction errors
             * @param maxDepth
             *            maximal depth of the S-expression tree
             * @param maxNodes
             *            maximal number of nodes of the S-expression tree
             * @throws InvalidConfigurationException
             *             thrown in case the problem cannot be created
             */
            public CrossPareGP(double[][] instances,
                               boolean[] output,
                               int populationSize,
                               int minInitDept,
                               int maxInitDepth,
                               int tournamentSize,
                               double errorType2Weight,
                               int maxDepth,
                               int maxNodes)
                throws InvalidConfigurationException
            {
                super(new GPConfiguration());

                this.instances = instances;
                this.output = output;
                this.maxDepth = maxDepth;
                this.maxNodes = maxNodes;

                Configuration.reset();
                GPConfiguration config = this.getGPConfiguration();

                this.x = new Variable[this.instances[0].length];

                for (int j = 0; j < this.x.length; j++) {
                    this.x[j] = Variable.create(config, "X" + j, CommandGene.DoubleClass);
                }

                config.setGPFitnessEvaluator(new DeltaGPFitnessEvaluator()); // smaller fitness is
                                                                             // better
                // config.setGPFitnessEvaluator(new DefaultGPFitnessEvaluator()); // bigger fitness
                // is better

                config.setMinInitDepth(minInitDept);
                config.setMaxInitDepth(maxInitDepth);

                config.setCrossoverProb((float) 0.60);
                config.setReproductionProb((float) 0.10);
                config.setMutationProb((float) 0.30);

                config.setSelectionMethod(new TournamentSelector(tournamentSize));

                config.setPopulationSize(populationSize);

                config.setMaxCrossoverDepth(4);
                config.setFitnessFunction(new CrossPareFitness(this.x, this.instances, this.output,
                                                               errorType2Weight));
                config.setStrictProgramCreation(true);
            }

            /**
             * <p>
             * Returns the variables of the problem. Used for running the fitness function again for
             * testing.
             * </p>
             *
             * @return the variables
             */
            public Variable[] getVariables() {
                return this.x;
            }

            /**
             * creates the genetic program
             */
            @SuppressWarnings("rawtypes")
            public GPGenotype create() throws InvalidConfigurationException {
                GPConfiguration config = this.getGPConfiguration();

                // return type
                Class[] types =
                    { CommandGene.DoubleClass };

                // Arguments of result-producing chromosome: none
                Class[][] argTypes =
                    { { } };

                // variables + functions, we set the variables with the values of the instances here
                CommandGene[] vars = new CommandGene[this.instances[0].length];
                for (int j = 0; j < this.instances[0].length; j++) {
                    vars[j] = this.x[j];
                }
                CommandGene[] funcs =
                    { new Add(config, CommandGene.DoubleClass),
                        new Subtract(config, CommandGene.DoubleClass),
                        new Multiply(config, CommandGene.DoubleClass),
                        new Divide(config, CommandGene.DoubleClass),
                        new Sine(config, CommandGene.DoubleClass),
                        new Cosine(config, CommandGene.DoubleClass),
                        new Exp(config, CommandGene.DoubleClass),
                        new Log(config, CommandGene.DoubleClass),
                        new GT(config, CommandGene.DoubleClass),
                        new Max(config, CommandGene.DoubleClass),
                        new Terminal(config, CommandGene.DoubleClass, -100.0, 100.0, true), // min,
                                                                                            // max,
                                                                                            // whole
                                                                                            // numbers
                    };

                CommandGene[] comb = (CommandGene[]) ArrayUtils.addAll(vars, funcs);
                CommandGene[][] nodeSets =
                    { comb, };

                // we only have one chromosome so this suffices
                int minDepths[] =
                    { config.getMinInitDepth() };
                int maxDepths[] =
                    { this.maxDepth };
                GPGenotype result =
                    GPGenotype.randomInitialGenotype(config, types, argTypes, nodeSets, minDepths,
                                                     maxDepths, this.maxNodes, false); // 40 =
                                                                                       // maxNodes,
                                                                                       // true =
                                                                                       // verbose
                                                                                       // output

                return result;
            }
        }

        /**
         * Internal helper class for the fitness function.
         * 
         * @author Alexander Trautsch
         */
        class CrossPareFitness extends GPFitnessFunction {

            /**
             * generated serialization ID
             */
            private static final long serialVersionUID = 75234832484387L;

            /**
             * variables of the genetic program
             */
            private Variable[] x;

            /**
             * instance values of the training data
             */
            private double[][] instances;

            /**
             * classifications of the training data
             */
            private boolean[] output;

            /**
             * weight of the error costs
             */
            private double errorType2Weight = 1.0;

            // needed in evaluate
            // private Object[] NO_ARGS = new Object[0];

            /**
             * fitness value
             */
            private double sfitness = 0.0f;

            /**
             * type I error
             */
            private int errorType1 = 0;

            /**
             * type II error
             */
            private int errorType2 = 0;

            /**
             * <p>
             * Constructor. Creates a new fitness function.
             * </p>
             *
             * @param x
             *            variables of the genetic program
             * @param instances
             *            instance values of the training data
             * @param output
             *            classification of the training data
             * @param errorType2Weight
             *            weight of the error costs
             */
            public CrossPareFitness(Variable[] x,
                                    double[][] instances,
                                    boolean[] output,
                                    double errorType2Weight)
            {
                this.x = x;
                this.instances = instances;
                this.output = output;
                this.errorType2Weight = errorType2Weight;
            }

            /**
             * <p>
             * returns the type I error
             * </p>
             *
             * @return type I error
             */
            public int getErrorType1() {
                return this.errorType1;
            }

            /**
             * <p>
             * returns the type II error
             * </p>
             *
             * @return type II error
             */
            public int getErrorType2() {
                return this.errorType2;
            }

            /**
             * <p>
             * returns the value of the secondary fitness function
             * </p>
             *
             * @return secondary fitness
             */
            public double getSecondFitness() {
                return this.sfitness;
            }

            /**
             * <p>
             * returns the number of training instances
             * </p>
             *
             * @return number of instances
             */
            public int getNumInstances() {
                return this.instances.length;
            }

            /**
             * <p>
             * The fitness function. Our fitness is best if we have the less wrong classifications,
             * this includes a weight for type2 errors.
             * </p>
             * 
             * @param program
             *            the genetic program whose fitness is evaluated.
             * 
             * @see org.jgap.gp.GPFitnessFunction#evaluate(org.jgap.gp.IGPProgram)
             */
            @Override
            protected double evaluate(final IGPProgram program) {
                double pfitness = 0.0f;
                this.sfitness = 0.0f;
                double value = 0.0f;

                // count classification errors
                this.errorType1 = 0;
                this.errorType2 = 0;

                for (int i = 0; i < this.instances.length; i++) {

                    // requires that we have a variable for each column of our dataset (attribute of
                    // instance)
                    for (int j = 0; j < this.x.length; j++) {
                        this.x[j].set(this.instances[i][j]);
                    }

                    // value gives us a double, if < 0.5 we set this instance as faulty
                    value = program.execute_double(0, this.x);

                    if (value < 0.5) {
                        if (this.output[i] != true) {
                            this.errorType1 += 1;
                        }
                    }
                    else {
                        if (this.output[i] == true) {
                            this.errorType2 += 1;
                        }
                    }
                }

                // now calc pfitness
                pfitness = (this.errorType1 + this.errorType2Weight * this.errorType2) /
                    this.instances.length;

                // number of nodes in the programm, if lower then 10 we assign sFitness of 10
                // we can set metadata with setProgramData to save this
                if (program.getChromosome(0).getSize(0) < 10) {
                    program.setApplicationData(10.0f);
                }

                return pfitness;
            }
        }

        /**
         * Custom GT implementation used in the GP Algorithm.
         * 
         * @author Alexander Trautsch
         */
        public class GT extends MathCommand implements ICloneable {

            /**
             * generated serialization ID.
             */
            private static final long serialVersionUID = 113454184817L;

            /**
             * <p>
             * Constructor. Creates a new GT.
             * </p>
             *
             * @param a_conf
             *            the configuration of the genetic program
             * @param a_returnType
             *            the return type
             * @throws InvalidConfigurationException
             *             thrown is there is a problem during the initialization of the super class
             * 
             * @see MathCommand
             */
            public GT(final GPConfiguration a_conf, @SuppressWarnings("rawtypes") java.lang.Class a_returnType)
                throws InvalidConfigurationException
            {
                super(a_conf, 2, a_returnType);
            }

            /*
             * (non-Javadoc)
             * 
             * @see org.jgap.gp.CommandGene#toString()
             */
            @Override
            public String toString() {
                return "GT(&1, &2)";
            }

            /*
             * (non-Javadoc)
             * 
             * @see org.jgap.gp.CommandGene#getName()
             */
            @Override
            public String getName() {
                return "GT";
            }

            /*
             * (non-Javadoc)
             * 
             * @see org.jgap.gp.CommandGene#execute_float(org.jgap.gp.impl.ProgramChromosome, int,
             * java.lang.Object[])
             */
            @Override
            public float execute_float(ProgramChromosome c, int n, Object[] args) {
                float f1 = c.execute_float(n, 0, args);
                float f2 = c.execute_float(n, 1, args);

                float ret = 1.0f;
                if (f1 > f2) {
                    ret = 0.0f;
                }

                return ret;
            }

            /*
             * (non-Javadoc)
             * 
             * @see org.jgap.gp.CommandGene#execute_double(org.jgap.gp.impl.ProgramChromosome, int,
             * java.lang.Object[])
             */
            @Override
            public double execute_double(ProgramChromosome c, int n, Object[] args) {
                double f1 = c.execute_double(n, 0, args);
                double f2 = c.execute_double(n, 1, args);

                double ret = 1;
                if (f1 > f2) {
                    ret = 0;
                }
                return ret;
            }

            /*
             * (non-Javadoc)
             * 
             * @see java.lang.Object#clone()
             */
            @Override
            public Object clone() {
                try {
                    GT result = new GT(getGPConfiguration(), getReturnType());
                    return result;
                }
                catch (Exception ex) {
                    throw new CloneException(ex);
                }
            }
        }
    }

    /**
     * GP Multiple Data Sets Validation-Voting Classifier
     * 
     * Basically the same as the GP Multiple Data Sets Validation Classifier. But here we do keep a
     * model candidate for each training set which may later vote
     *
     */
    public class GPVVClassifier extends GPVClassifier {

        /**
         * generated serialization ID
         */
        private static final long serialVersionUID = -654710583852839901L;

        /**
         * classifiers for each validation set
         */
        private List<Classifier> classifiers = null;

        /*
         * (non-Javadoc)
         * 
         * @see
         * de.ugoe.cs.cpdp.training.GPTraining.GPVClassifier#buildClassifier(weka.core.Instances)
         */
        @Override
        public void buildClassifier(Instances arg0) throws Exception {
            // TODO Auto-generated method stub
        }

        /**
         * Build the GP Multiple Data Sets Validation-Voting Classifier
         * 
         * This is according to Section 6 of the Paper by Liu et al. It is basically the Multiple
         * Data Sets Validation Classifier but here we keep the best models an let them vote.
         * 
         * @param traindataSet
         *            the training data
         * @throws Exception
         *             thrown in case of a problem with the training
         */
        public void buildClassifier(SetUniqueList<Instances> traindataSet) throws Exception {

            // each classifier is trained with one project from the set
            // then is evaluated on the rest
            classifiers = new LinkedList<>();
            for (int i = 0; i < traindataSet.size(); i++) {

                // candidates we get out of evaluation
                LinkedList<Classifier> candidates = new LinkedList<>();

                // number of runs, yields the best of these
                double smallest_error_count_train = Double.MAX_VALUE;
                Classifier bestTrain = null;
                for (int k = 0; k < this.numberRuns; k++) {
                    double[] errors_eval =
                        { 0.0, 0.0 };
                    Classifier classifier = new GPRun();
                    ((GPRun) classifier).configure(this.populationSize, this.initMinDepth,
                                                   this.initMaxDepth, this.tournamentSize,
                                                   this.maxGenerations, this.errorType2Weight,
                                                   this.maxDepth, this.maxNodes);

                    // one project is training data
                    classifier.buildClassifier(traindataSet.get(i));

                    double[] errors;
                    // rest of the set is evaluation data, we evaluate now
                    for (int j = 0; j < traindataSet.size(); j++) {
                        if (j != i) {
                            // if type1 and type2 errors are < 0.5 we allow the model in the
                            // candidates
                            errors = this.evaluate((GPRun) classifier, traindataSet.get(j));
                            errors_eval[0] += errors[0];
                            errors_eval[1] += errors[1];
                            if ((errors[0] < 0.5) && (errors[1] < 0.5)) {
                                candidates.add(classifier);
                            }
                        }
                    }

                    // if the candidate made fewer errors it is now the best
                    if (errors_eval[0] + errors_eval[1] < smallest_error_count_train) {
                        bestTrain = classifier;
                        smallest_error_count_train = errors_eval[0] + errors_eval[1];
                    }
                }

                // now after the evaluation we do a model selection where only one model remains for
                // the given training data
                // we select the model which is best on all evaluation data
                double smallest_error_count = Double.MAX_VALUE;
                double[] errors;
                Classifier best = null;
                for (int ii = 0; ii < candidates.size(); ii++) {
                    double[] errors_eval =
                        { 0.0, 0.0 };

                    // we add the errors the candidate makes over the evaldata
                    for (int j = 0; j < traindataSet.size(); j++) {
                        if (j != i) {
                            errors = this.evaluate((GPRun) candidates.get(ii), traindataSet.get(j));
                            errors_eval[0] += errors[0];
                            errors_eval[1] += errors[1];
                        }
                    }

                    // if the candidate made fewer errors it is now the best
                    if (errors_eval[0] + errors_eval[1] < smallest_error_count) {
                        best = candidates.get(ii);
                        smallest_error_count = errors_eval[0] + errors_eval[1];
                    }
                }

                if (best == null) {
                    best = bestTrain;
                }
                // now we have the best classifier for this training data
                classifiers.add(best);
            }
        }

        /**
         * Use the best classifiers for each training data in a majority voting
         * 
         * @param instance
         *            instance that is classified
         * 
         * @see de.ugoe.cs.cpdp.training.GPTraining.GPVClassifier#classifyInstance(weka.core.Instance)
         */
        @Override
        public double classifyInstance(Instance instance) {

            int vote_positive = 0;

            for (int i = 0; i < classifiers.size(); i++) {
                Classifier classifier = classifiers.get(i);

                GPGenotype gp = ((GPRun) classifier).getGp();
                Variable[] vars = ((GPRun) classifier).getVariables();

                IGPProgram fitest = gp.getAllTimeBest(); // all time fitest
                for (int j = 0; j < instance.numAttributes() - 1; j++) {
                    vars[j].set(instance.value(j));
                }

                if (fitest.execute_double(0, vars) < 0.5) {
                    vote_positive += 1;
                }
            }

            if (vote_positive >= (classifiers.size() / 2)) {
                return 1.0;
            }
            else {
                return 0.0;
            }
        }
    }

    /**
     * GP Multiple Data Sets Validation Classifier
     * 
     * We train a Classifier with one training project $numberRun times. Then we evaluate the
     * classifier on the rest of the training projects and keep the best classifier. After that we
     * have for each training project the best classifier as per the evaluation on the rest of the
     * data set. Then we determine the best classifier from these candidates and keep it to be used
     * later.
     * 
     * @author sherbold Alexander Trautsch
     */
    public class GPVClassifier extends AbstractClassifier {

        private List<Classifier> classifiers = null;
        private Classifier best = null;

        private static final long serialVersionUID = 3708714057579101522L;

        /**
         * size of the population of the genetic program
         */
        protected int populationSize;

        /**
         * minimal depth of the S-expression tree at the start of the training
         */
        protected int initMinDepth;

        /**
         * maximal depth of the S-expression tree at the start of the training
         */
        protected int initMaxDepth;

        /**
         * size of the tournaments used for selection
         */
        protected int tournamentSize;

        /**
         * number of genetic generations considered (i.e., number of iterations
         */
        protected int maxGenerations;

        /**
         * weight factor for the prediction errors for cost estimation
         */
        protected double errorType2Weight;

        /**
         * number of internal replications from which the best result is picked
         */
        protected int numberRuns = 20;

        /**
         * maximal depth of the S-expression tree
         */
        protected int maxDepth;

        /**
         * maximal number of nodes of the S-expression tree
         */
        protected int maxNodes;

        /**
         * 
         * <p>
         * Configure the GP Params and number of Runs
         * </p>
         * 
         * @param populationSize
         *            the population size
         * @param initMinDepth
         *            the initial minimal depth of the S-expression tree
         * @param initMaxDepth
         *            the initial maximal depth of the S-expression tree
         * @param tournamentSize
         *            the tournament size for selection
         * @param maxGenerations
         *            the number of generations created
         * @param errorType2Weight
         *            weigth factor for the prediction errors
         * @param numberRuns
         *            number of internal replications from which the best result is picked
         * @param maxDepth
         *            maximal depth of the S-expression tree
         * @param maxNodes
         *            maximal number of nodes of the S-expression tree
         */
        public void configure(int populationSize,
                              int initMinDepth,
                              int initMaxDepth,
                              int tournamentSize,
                              int maxGenerations,
                              double errorType2Weight,
                              int numberRuns,
                              int maxDepth,
                              int maxNodes)
        {
            this.populationSize = populationSize;
            this.initMinDepth = initMinDepth;
            this.initMaxDepth = initMaxDepth;
            this.tournamentSize = tournamentSize;
            this.maxGenerations = maxGenerations;
            this.errorType2Weight = errorType2Weight;
            this.numberRuns = numberRuns;
            this.maxDepth = maxDepth;
            this.maxNodes = maxNodes;
        }

        /**
         * Build the GP Multiple Data Sets Validation Classifier
         * 
         * This is according to Section 6 of the Paper by Liu et al. except for the selection of the
         * best model. Section 4 describes a slightly different approach.
         * 
         * @param traindataSet
         *            the training data
         * @throws Exception
         *             thrown in case of a problem with the training
         */
        public void buildClassifier(SetUniqueList<Instances> traindataSet) throws Exception {

            // each classifier is trained with one project from the set
            // then is evaluated on the rest
            for (int i = 0; i < traindataSet.size(); i++) {

                // candidates we get out of evaluation
                LinkedList<Classifier> candidates = new LinkedList<>();

                // numberRuns full GPRuns, we generate numberRuns models for each traindata
                for (int k = 0; k < this.numberRuns; k++) {
                    Classifier classifier = new GPRun();
                    ((GPRun) classifier).configure(this.populationSize, this.initMinDepth,
                                                   this.initMaxDepth, this.tournamentSize,
                                                   this.maxGenerations, this.errorType2Weight,
                                                   this.maxDepth, this.maxNodes);

                    classifier.buildClassifier(traindataSet.get(i));

                    double[] errors;

                    // rest of the set is evaluation data, we evaluate now
                    for (int j = 0; j < traindataSet.size(); j++) {
                        if (j != i) {
                            // if type1 and type2 errors are < 0.5 we allow the model in the
                            // candidate list
                            errors = this.evaluate((GPRun) classifier, traindataSet.get(j));
                            if ((errors[0] < 0.5) && (errors[1] < 0.5)) {
                                candidates.add(classifier);
                            }
                        }
                    }
                }

                // now after the evaluation we do a model selection where only one model remains for
                // the given training data
                // we select the model which is best on all evaluation data
                double smallest_error_count = Double.MAX_VALUE;
                double[] errors;
                Classifier best = null;
                for (int ii = 0; ii < candidates.size(); ii++) {
                    double[] errors_eval =
                        { 0.0, 0.0 };

                    // we add the errors the candidate makes over the evaldata
                    for (int j = 0; j < traindataSet.size(); j++) {
                        if (j != i) {
                            errors = this.evaluate((GPRun) candidates.get(ii), traindataSet.get(j));
                            errors_eval[0] += errors[0];
                            errors_eval[1] += errors[1];
                        }
                    }

                    // if the candidate made fewer errors it is now the best
                    if (errors_eval[0] + errors_eval[1] < smallest_error_count) {
                        best = candidates.get(ii);
                        smallest_error_count = errors_eval[0] + errors_eval[1];
                    }
                }

                // now we have the best classifier for this training data
                classifiers.add(best);

            } /* endfor trainData */

            // now we have one best classifier for each trainData
            // we evaluate again to find the best classifier of all time
            // this selection is now according to section 4 of the paper and not 6 where an average
            // of the 6 models is build
            double smallest_error_count = Double.MAX_VALUE;
            double error_count;
            double errors[];
            for (int j = 0; j < classifiers.size(); j++) {
                error_count = 0;
                Classifier current = classifiers.get(j);
                for (int i = 0; i < traindataSet.size(); i++) {
                    errors = this.evaluate((GPRun) current, traindataSet.get(i));
                    error_count = errors[0] + errors[1];
                }

                if (error_count < smallest_error_count) {
                    best = current;
                }
            }
        }

        /*
         * (non-Javadoc)
         * 
         * @see weka.classifiers.Classifier#buildClassifier(weka.core.Instances)
         */
        @Override
        public void buildClassifier(Instances traindata) throws Exception {
            final Classifier classifier = new GPRun();
            ((GPRun) classifier).configure(populationSize, initMinDepth, initMaxDepth,
                                           tournamentSize, maxGenerations, errorType2Weight,
                                           this.maxDepth, this.maxNodes);
            classifier.buildClassifier(traindata);
            classifiers.add(classifier);
        }

        /**
         * <p>
         * Evaluation of the Classifier.
         * </p>
         * <p>
         * We evaluate the classifier with the Instances of the evalData. It basically assigns the
         * instance attribute values to the variables of the s-expression-tree and then counts the
         * missclassifications.
         * </p>
         * 
         * @param classifier
         *            the classifier that is evaluated
         * @param evalData
         *            the validation data
         * @return the type I and type II error rates
         */
        public double[] evaluate(GPRun classifier, Instances evalData) {
            GPGenotype gp = classifier.getGp();
            Variable[] vars = classifier.getVariables();

            IGPProgram fitest = gp.getAllTimeBest(); // selects the fitest of all not just the last
                                                     // generation

            double classification;
            int error_type1 = 0;
            int error_type2 = 0;
            int positive = 0;
            int negative = 0;

            for (Instance instance : evalData) {

                // assign instance attribute values to the variables of the s-expression-tree
                double[] tmp = WekaUtils.instanceValues(instance);
                for (int i = 0; i < tmp.length; i++) {
                    vars[i].set(tmp[i]);
                }

                classification = fitest.execute_double(0, vars);

                // we need to count the absolutes of positives for percentage
                if (instance.classValue() == 1.0) {
                    positive += 1;
                }
                else {
                    negative += 1;
                }

                // classification < 0.5 we say defective
                if (classification < 0.5) {
                    if (instance.classValue() != 1.0) {
                        error_type1 += 1;
                    }
                }
                else {
                    if (instance.classValue() == 1.0) {
                        error_type2 += 1;
                    }
                }
            }

            // return error types percentages for the types
            double et1_per = error_type1 / negative;
            double et2_per = error_type2 / positive;
            return new double[]
                { et1_per, et2_per };
        }

        /**
         * Use only the best classifier from our evaluation phase
         * 
         * @param instance
         *            instance that is classified
         * 
         * @see weka.classifiers.AbstractClassifier#classifyInstance(weka.core.Instance)
         */
        @Override
        public double classifyInstance(Instance instance) {
            GPGenotype gp = ((GPRun) best).getGp();
            Variable[] vars = ((GPRun) best).getVariables();

            IGPProgram fitest = gp.getAllTimeBest(); // all time fitest
            for (int i = 0; i < instance.numAttributes() - 1; i++) {
                vars[i].set(instance.value(i));
            }

            double classification = fitest.execute_double(0, vars);

            if (classification < 0.5) {
                return 1.0;
            }
            else {
                return 0.0;
            }
        }
    }
}