weka.classifiers.functions.LibSVM.java Source code

Java tutorial

Introduction

Here is the source code for weka.classifiers.functions.LibSVM.java

Source

/*
 *   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/>.
 */

/*
 * LibSVM.java
 * Copyright (C) 2005 Yasser EL-Manzalawy (original code)
 * Copyright (C) 2005-16 University of Waikato, Hamilton, NZ (adapted code)
 * 
 */

package weka.classifiers.functions;

import libsvm.*;
import weka.classifiers.RandomizableClassifier;
import weka.core.*;
import weka.core.Capabilities.Capability;
import weka.core.TechnicalInformation.Type;
import weka.filters.Filter;
import weka.filters.unsupervised.attribute.NominalToBinary;
import weka.filters.unsupervised.attribute.Normalize;
import weka.filters.unsupervised.attribute.ReplaceMissingValues;

import java.io.File;
import java.util.*;

/** 
 <!-- globalinfo-start -->
 * A wrapper class for the libsvm library. This wrapper supports the classifiers implemented in the libsvm
 * library, including one-class SVMs.<br>
 * Note: To be consistent with other SVMs in WEKA, the target attribute is now normalized before "
 * SVM regression is performed, if normalization is turned on.<br>
 * <br>
 * Yasser EL-Manzalawy (2005). WLSVM. URL http://www.cs.iastate.edu/~yasser/wlsvm/.<br/>
 * <br>
 * Chih-Chung Chang, Chih-Jen Lin (2001). LIBSVM - A Library for Support Vector Machines. URL http://www.csie.ntu.edu.tw/~cjlin/libsvm/.
 * <p>
 <!-- globalinfo-end -->
 *
 <!-- technical-bibtex-start -->
 * BibTeX:
 * <pre>
 * &#64;misc{EL-Manzalawy2005,
 *    author = {Yasser EL-Manzalawy},
 *    note = {You don't need to include the WLSVM package in the CLASSPATH},
 *    title = {WLSVM},
 *    year = {2005},
 *    URL = {http://www.cs.iastate.edu/\~yasser/wlsvm/}
 * }
 * 
 * &#64;misc{Chang2001,
 *    author = {Chih-Chung Chang and Chih-Jen Lin},
 *    note = {The Weka classifier works with version 2.82 of LIBSVM},
 *    title = {LIBSVM - A Library for Support Vector Machines},
 *    year = {2001},
 *    URL = {http://www.csie.ntu.edu.tw/\~cjlin/libsvm/}
 * }
 * </pre>
 * <p/>
 <!-- technical-bibtex-end -->
 *
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -S &lt;int&gt;
 *  Set type of SVM (default: 0)
 *    0 = C-SVC
 *    1 = nu-SVC
 *    2 = one-class SVM
 *    3 = epsilon-SVR
 *    4 = nu-SVR</pre>
 * 
 * <pre> -K &lt;int&gt;
 *  Set type of kernel function (default: 2)
 *    0 = linear: u'*v
 *    1 = polynomial: (gamma*u'*v + coef0)^degree
 *    2 = radial basis function: exp(-gamma*|u-v|^2)
 *    3 = sigmoid: tanh(gamma*u'*v + coef0)</pre>
 * 
 * <pre> -D &lt;int&gt;
 *  Set degree in kernel function (default: 3)</pre>
 * 
 * <pre> -G &lt;double&gt;
 *  Set gamma in kernel function (default: 1/k)</pre>
 * 
 * <pre> -R &lt;double&gt;
 *  Set coef0 in kernel function (default: 0)</pre>
 * 
 * <pre> -C &lt;double&gt;
 *  Set the parameter C of C-SVC, epsilon-SVR, and nu-SVR
 *   (default: 1)</pre>
 * 
 * <pre> -N &lt;double&gt;
 *  Set the parameter nu of nu-SVC, one-class SVM, and nu-SVR
 *   (default: 0.5)</pre>
 * 
 * <pre> -Z
 *  Turns on normalization of input data (default: off)</pre>
 * 
 * <pre> -J
 *  Turn off nominal to binary conversion.
 *  WARNING: use only if your data is all numeric!</pre>
 * 
 * <pre> -V
 *  Turn off missing value replacement.
 *  WARNING: use only if your data has no missing values.</pre>
 * 
 * <pre> -P &lt;double&gt;
 *  Set the epsilon in loss function of epsilon-SVR (default: 0.1)</pre>
 * 
 * <pre> -M &lt;double&gt;
 *  Set cache memory size in MB (default: 40)</pre>
 * 
 * <pre> -E &lt;double&gt;
 *  Set tolerance of termination criterion (default: 0.001)</pre>
 * 
 * <pre> -H
 *  Turns the shrinking heuristics off (default: on)</pre>
 * 
 * <pre> -W &lt;double&gt;
 *  Set the parameters C of class i to weight[i]*C, for C-SVC.
 *  E.g., for a 3-class problem, you could use "1 1 1" for equally
 *  weighted classes.
 *  (default: 1 for all classes)</pre>
 * 
 * <pre> -B
 *  Trains a SVC model instead of a SVR one (default: SVR)</pre>
 * 
 * <pre> -model &lt;file&gt;
 *  Specifies the filename to save the libsvm-internal model to.
 *  Gets ignored if a directory is provided.</pre>
 * 
 * <pre> -D
 *  If set, classifier is run in debug mode and
 *  may output additional info to the console</pre>
 *
 * <pre> -seed &lt;num&gt;
 *  Seed for the random number generator when -B is used.
 *  (default = 1)</pre>
 *
 <!-- options-end -->
 *
 * @author  Yasser EL-Manzalawy
 * @author  FracPete (fracpete at waikato dot ac dot nz)
 * @author  Eibe Frank
 * @version $Revision$
 * @see     weka.core.converters.LibSVMLoader
 * @see     weka.core.converters.LibSVMSaver
 */
public class LibSVM extends RandomizableClassifier implements TechnicalInformationHandler {

    /**
     * serial UID.
     */
    protected static final long serialVersionUID = 14172;

    /**
     * LibSVM Model.
     */
    protected svm_model m_Model;

    /**
     * for normalizing the data.
     */
    protected Filter m_Filter = null;

    /**
     * for converting mult-valued nominal attributes to binary
     */
    protected Filter m_NominalToBinary;

    /**
     * The filter used to get rid of missing values.
     */
    protected ReplaceMissingValues m_ReplaceMissingValues;

    /**
     * normalize input data.
     */
    protected boolean m_Normalize = false;

    /**
     * coefficients used by normalization filter for doing its linear transformation
     **/
    protected double m_x1 = 1.0;
    protected double m_x0 = 0.0;

    /**
     * If true, the replace missing values filter is not applied.
     */
    private boolean m_noReplaceMissingValues;

    /**
     * SVM type C-SVC (classification).
     */
    public static final int SVMTYPE_C_SVC = 0;
    /**
     * SVM type nu-SVC (classification).
     */
    public static final int SVMTYPE_NU_SVC = 1;
    /**
     * SVM type one-class SVM (classification).
     */
    public static final int SVMTYPE_ONE_CLASS_SVM = 2;
    /**
     * SVM type epsilon-SVR (regression).
     */
    public static final int SVMTYPE_EPSILON_SVR = 3;
    /**
     * SVM type nu-SVR (regression).
     */
    public static final int SVMTYPE_NU_SVR = 4;
    /**
     * SVM types.
     */
    public static final Tag[] TAGS_SVMTYPE = { new Tag(SVMTYPE_C_SVC, "C-SVC (classification)"),
            new Tag(SVMTYPE_NU_SVC, "nu-SVC (classification)"),
            new Tag(SVMTYPE_ONE_CLASS_SVM, "one-class SVM (classification)"),
            new Tag(SVMTYPE_EPSILON_SVR, "epsilon-SVR (regression)"),
            new Tag(SVMTYPE_NU_SVR, "nu-SVR (regression)") };

    /**
     * the SVM type.
     */
    protected int m_SVMType = SVMTYPE_C_SVC;

    /**
     * kernel type linear: u'*v.
     */
    public static final int KERNELTYPE_LINEAR = 0;
    /**
     * kernel type polynomial: (gamma*u'*v + coef0)^degree.
     */
    public static final int KERNELTYPE_POLYNOMIAL = 1;
    /**
     * kernel type radial basis function: exp(-gamma*|u-v|^2).
     */
    public static final int KERNELTYPE_RBF = 2;
    /**
     * kernel type sigmoid: tanh(gamma*u'*v + coef0).
     */
    public static final int KERNELTYPE_SIGMOID = 3;
    /**
     * the different kernel types.
     */
    public static final Tag[] TAGS_KERNELTYPE = { new Tag(KERNELTYPE_LINEAR, "linear: u'*v"),
            new Tag(KERNELTYPE_POLYNOMIAL, "polynomial: (gamma*u'*v + coef0)^degree"),
            new Tag(KERNELTYPE_RBF, "radial basis function: exp(-gamma*|u-v|^2)"),
            new Tag(KERNELTYPE_SIGMOID, "sigmoid: tanh(gamma*u'*v + coef0)") };

    /**
     * the kernel type.
     */
    protected int m_KernelType = KERNELTYPE_RBF;

    /**
     * for poly - in older versions of libsvm declared as a double.
     * At least since 2.82 it is an int.
     */
    protected int m_Degree = 3;

    /**
     * for poly/rbf/sigmoid.
     */
    protected double m_Gamma = 0;

    /**
     * for poly/rbf/sigmoid (the actual gamma).
     */
    protected double m_GammaActual = 0;

    /**
     * for poly/sigmoid.
     */
    protected double m_Coef0 = 0;

    /**
     * in MB.
     */
    protected double m_CacheSize = 40;

    /**
     * stopping criteria.
     */
    protected double m_eps = 1e-3;

    /**
     * cost, for C_SVC, EPSILON_SVR and NU_SVR.
     */
    protected double m_Cost = 1;

    /**
     * for C_SVC.
     */
    protected int[] m_WeightLabel = new int[0];

    /**
     * for C_SVC.
     */
    protected double[] m_Weight = new double[0];

    /**
     * for NU_SVC, ONE_CLASS, and NU_SVR.
     */
    protected double m_nu = 0.5;

    /**
     * loss, for EPSILON_SVR.
     */
    protected double m_Loss = 0.1;

    /**
     * use the shrinking heuristics.
     */
    protected boolean m_Shrinking = true;

    /**
     * whether to generate probability estimates instead of +1/-1 in case of
     * classification problems.
     */
    protected boolean m_ProbabilityEstimates = false;

    /**
     * the file to save the libsvm-internal model to.
     */
    protected File m_ModelFile = new File(System.getProperty("user.dir"));

    /**
     * Returns a string describing classifier.
     *
     * @return a description suitable for displaying in the
     * explorer/experimenter gui
     */
    public String globalInfo() {
        return "A wrapper class for the libsvm library. This wrapper supports the classifiers implemented in the libsvm "
                + "library, including one-class SVMs.\n"
                + "Note: To be consistent with other SVMs in WEKA, the target attribute is now normalized before "
                + "SVM regression is performed, if normalization is turned on.\n" + "\n"
                + getTechnicalInformation().toString();
    }

    /**
     * Returns an instance of a TechnicalInformation object, containing
     * detailed information about the technical background of this class,
     * e.g., paper reference or book this class is based on.
     *
     * @return the technical information about this class
     */
    public TechnicalInformation getTechnicalInformation() {
        TechnicalInformation result;
        TechnicalInformation additional;

        result = new TechnicalInformation(Type.MISC);
        result.setValue(TechnicalInformation.Field.AUTHOR, "Yasser EL-Manzalawy");
        result.setValue(TechnicalInformation.Field.YEAR, "2005");
        result.setValue(TechnicalInformation.Field.TITLE, "WLSVM");
        result.setValue(TechnicalInformation.Field.NOTE, "LibSVM was originally developed as 'WLSVM'");
        result.setValue(TechnicalInformation.Field.URL, "http://www.cs.iastate.edu/~yasser/wlsvm/");
        result.setValue(TechnicalInformation.Field.NOTE,
                "You don't need to include the WLSVM package in the CLASSPATH");

        additional = result.add(Type.MISC);
        additional.setValue(TechnicalInformation.Field.AUTHOR, "Chih-Chung Chang and Chih-Jen Lin");
        additional.setValue(TechnicalInformation.Field.TITLE, "LIBSVM - A Library for Support Vector Machines");
        additional.setValue(TechnicalInformation.Field.YEAR, "2001");
        additional.setValue(TechnicalInformation.Field.URL, "http://www.csie.ntu.edu.tw/~cjlin/libsvm/");
        additional.setValue(TechnicalInformation.Field.NOTE,
                "The Weka classifier works with version 2.82 of LIBSVM");

        return result;
    }

    /**
     * Returns an enumeration describing the available options.
     *
     * @return an enumeration of all the available options.
     */
    public Enumeration listOptions() {
        Vector result;

        result = new Vector();

        result.addElement(new Option(
                "\tSet type of SVM (default: 0)\n" + "\t\t 0 = C-SVC\n" + "\t\t 1 = nu-SVC\n"
                        + "\t\t 2 = one-class SVM\n" + "\t\t 3 = epsilon-SVR\n" + "\t\t 4 = nu-SVR",
                "S", 1, "-S <int>"));

        result.addElement(new Option("\tSet type of kernel function (default: 2)\n" + "\t\t 0 = linear: u'*v\n"
                + "\t\t 1 = polynomial: (gamma*u'*v + coef0)^degree\n"
                + "\t\t 2 = radial basis function: exp(-gamma*|u-v|^2)\n"
                + "\t\t 3 = sigmoid: tanh(gamma*u'*v + coef0)", "K", 1, "-K <int>"));

        result.addElement(new Option("\tSet degree in kernel function (default: 3)", "D", 1, "-D <int>"));

        result.addElement(new Option("\tSet gamma in kernel function (default: 1/k)", "G", 1, "-G <double>"));

        result.addElement(new Option("\tSet coef0 in kernel function (default: 0)", "R", 1, "-R <double>"));

        result.addElement(
                new Option("\tSet the parameter C of C-SVC, epsilon-SVR, and nu-SVR\n" + "\t (default: 1)", "C", 1,
                        "-C <double>"));

        result.addElement(
                new Option("\tSet the parameter nu of nu-SVC, one-class SVM, and nu-SVR\n" + "\t (default: 0.5)",
                        "N", 1, "-N <double>"));

        result.addElement(new Option("\tTurns on normalization of input data (default: off)", "Z", 0, "-Z"));

        result.addElement(new Option(
                "\tTurn off nominal to binary conversion." + "\n\tWARNING: use only if your data is all numeric!",
                "J", 0, "-J"));

        result.addElement(new Option("\tTurn off missing value replacement."
                + "\n\tWARNING: use only if your data has no missing " + "values.", "V", 0, "-V"));

        result.addElement(new Option("\tSet the epsilon in loss function of epsilon-SVR (default: 0.1)", "P", 1,
                "-P <double>"));

        result.addElement(new Option("\tSet cache memory size in MB (default: 40)", "M", 1, "-M <double>"));

        result.addElement(
                new Option("\tSet tolerance of termination criterion (default: 0.001)", "E", 1, "-E <double>"));

        result.addElement(new Option("\tTurns the shrinking heuristics off (default: on)", "H", 0, "-H"));

        result.addElement(new Option("\tSet the parameters C of class i to weight[i]*C, for C-SVC.\n"
                + "\tE.g., for a 3-class problem, you could use \"1 1 1\" for equally\n" + "\tweighted classes.\n"
                + "\t(default: 1 for all classes)", "W", 1, "-W <double>"));

        result.addElement(new Option("\tGenerate probability estimates for classification", "B", 0, "-B"));

        result.addElement(new Option("\tSpecifies the filename to save the libsvm-internal model to.\n"
                + "\tGets ignored if a directory is provided.", "model", 1, "-model <file>"));

        result.addElement(new Option("\tSeed for the random number generator when -B is used.\n\t(default = 1)",
                "seed", 1, "-seed <num>"));

        Enumeration en = super.listOptions();
        while (en.hasMoreElements()) {
            Option op = (Option) en.nextElement();
            if (!op.name().equals("S")) {
                result.addElement(op); // Need to skip -S flag from RandomizableClassifier
            }
        }

        return result.elements();
    }

    /**
     * Sets the classifier options <p/>
     * <p/>
     * <!-- options-start -->
     * Valid options are: <p/>
     * <p/>
     * <pre> -S &lt;int&gt;
     *  Set type of SVM (default: 0)
     *    0 = C-SVC
     *    1 = nu-SVC
     *    2 = one-class SVM
     *    3 = epsilon-SVR
     *    4 = nu-SVR</pre>
     * <p/>
     * <pre> -K &lt;int&gt;
     *  Set type of kernel function (default: 2)
     *    0 = linear: u'*v
     *    1 = polynomial: (gamma*u'*v + coef0)^degree
     *    2 = radial basis function: exp(-gamma*|u-v|^2)
     *    3 = sigmoid: tanh(gamma*u'*v + coef0)</pre>
     * <p/>
     * <pre> -D &lt;int&gt;
     *  Set degree in kernel function (default: 3)</pre>
     * <p/>
     * <pre> -G &lt;double&gt;
     *  Set gamma in kernel function (default: 1/k)</pre>
     * <p/>
     * <pre> -R &lt;double&gt;
     *  Set coef0 in kernel function (default: 0)</pre>
     * <p/>
     * <pre> -C &lt;double&gt;
     *  Set the parameter C of C-SVC, epsilon-SVR, and nu-SVR
     *   (default: 1)</pre>
     * <p/>
     * <pre> -N &lt;double&gt;
     *  Set the parameter nu of nu-SVC, one-class SVM, and nu-SVR
     *   (default: 0.5)</pre>
     * <p/>
     * <pre> -Z
     *  Turns on normalization of input data (default: off)</pre>
     * <p/>
     * <pre> -J
     *  Turn off nominal to binary conversion.
     *  WARNING: use only if your data is all numeric!</pre>
     * <p/>
     * <pre> -V
     *  Turn off missing value replacement.
     *  WARNING: use only if your data has no missing values.</pre>
     * <p/>
     * <pre> -P &lt;double&gt;
     *  Set the epsilon in loss function of epsilon-SVR (default: 0.1)</pre>
     * <p/>
     * <pre> -M &lt;double&gt;
     *  Set cache memory size in MB (default: 40)</pre>
     * <p/>
     * <pre> -E &lt;double&gt;
     *  Set tolerance of termination criterion (default: 0.001)</pre>
     * <p/>
     * <pre> -H
     *  Turns the shrinking heuristics off (default: on)</pre>
     * <p/>
     * <pre> -W &lt;double&gt;
     *  Set the parameters C of class i to weight[i]*C, for C-SVC.
     *  E.g., for a 3-class problem, you could use "1 1 1" for equally
     *  weighted classes.
     *  (default: 1 for all classes)</pre>
     * <p/>
     * <pre> -B
     *  Trains a SVC model instead of a SVR one (default: SVR)</pre>
     * <p/>
     * <pre> -model &lt;file&gt;
     *  Specifies the filename to save the libsvm-internal model to.
     *  Gets ignored if a directory is provided.</pre>
     * <p/>
     * <pre> -D
     *  If set, classifier is run in debug mode and
     *  may output additional info to the console</pre>
     * <p/>
     * <pre> -seed &lt;num&gt;
     *  Seed for the random number generator when -B is used.
     *  (default = 1)</pre>
     * <p/>
     * <!-- options-end -->
     *
     * @param options the options to parse
     * @throws Exception if parsing fails
     */
    public void setOptions(String[] options) throws Exception {
        String tmpStr;

        tmpStr = Utils.getOption('S', options);
        if (tmpStr.length() != 0)
            setSVMType(new SelectedTag(Integer.parseInt(tmpStr), TAGS_SVMTYPE));
        else
            setSVMType(new SelectedTag(SVMTYPE_C_SVC, TAGS_SVMTYPE));

        tmpStr = Utils.getOption('K', options);
        if (tmpStr.length() != 0)
            setKernelType(new SelectedTag(Integer.parseInt(tmpStr), TAGS_KERNELTYPE));
        else
            setKernelType(new SelectedTag(KERNELTYPE_RBF, TAGS_KERNELTYPE));

        tmpStr = Utils.getOption('D', options);
        if (tmpStr.length() != 0)
            setDegree(Integer.parseInt(tmpStr));
        else
            setDegree(3);

        tmpStr = Utils.getOption('G', options);
        if (tmpStr.length() != 0)
            setGamma(Double.parseDouble(tmpStr));
        else
            setGamma(0);

        tmpStr = Utils.getOption('R', options);
        if (tmpStr.length() != 0)
            setCoef0(Double.parseDouble(tmpStr));
        else
            setCoef0(0);

        tmpStr = Utils.getOption('N', options);
        if (tmpStr.length() != 0)
            setNu(Double.parseDouble(tmpStr));
        else
            setNu(0.5);

        tmpStr = Utils.getOption('M', options);
        if (tmpStr.length() != 0)
            setCacheSize(Double.parseDouble(tmpStr));
        else
            setCacheSize(40);

        tmpStr = Utils.getOption('C', options);
        if (tmpStr.length() != 0)
            setCost(Double.parseDouble(tmpStr));
        else
            setCost(1);

        tmpStr = Utils.getOption('E', options);
        if (tmpStr.length() != 0)
            setEps(Double.parseDouble(tmpStr));
        else
            setEps(1e-3);

        setNormalize(Utils.getFlag('Z', options));

        setDoNotReplaceMissingValues(Utils.getFlag("V", options));

        tmpStr = Utils.getOption('P', options);
        if (tmpStr.length() != 0)
            setLoss(Double.parseDouble(tmpStr));
        else
            setLoss(0.1);

        setShrinking(!Utils.getFlag('H', options));

        setWeights(Utils.getOption('W', options));

        setProbabilityEstimates(Utils.getFlag('B', options));

        tmpStr = Utils.getOption("model", options);
        if (tmpStr.length() == 0)
            m_ModelFile = new File(System.getProperty("user.dir"));
        else
            m_ModelFile = new File(tmpStr);

        String seedString = Utils.getOption("seed", options);
        if (seedString.length() > 0) {
            setSeed(Integer.parseInt(seedString.trim()));
        }

        if (Utils.getOption('S', options).length() != 0) {
            throw new IllegalArgumentException(
                    "Cannot use -S option twice in LibSVM. Use -seed to specify the seed "
                            + "for the random number generator.");
        }

        super.setOptions(options);

        Utils.checkForRemainingOptions(options);
    }

    /**
     * Returns the current options.
     *
     * @return the current setup
     */
    public String[] getOptions() {
        Vector result;

        result = new Vector();

        result.add("-S");
        result.add("" + m_SVMType);

        result.add("-K");
        result.add("" + m_KernelType);

        result.add("-D");
        result.add("" + getDegree());

        result.add("-G");
        result.add("" + getGamma());

        result.add("-R");
        result.add("" + getCoef0());

        result.add("-N");
        result.add("" + getNu());

        result.add("-M");
        result.add("" + getCacheSize());

        result.add("-C");
        result.add("" + getCost());

        result.add("-E");
        result.add("" + getEps());

        result.add("-P");
        result.add("" + getLoss());

        if (!getShrinking())
            result.add("-H");

        if (getNormalize())
            result.add("-Z");

        if (getDoNotReplaceMissingValues())
            result.add("-V");

        if (getWeights().length() != 0) {
            result.add("-W");
            result.add("" + getWeights());
        }

        if (getProbabilityEstimates())
            result.add("-B");

        result.add("-model");
        result.add(m_ModelFile.getAbsolutePath());

        result.add("-seed");
        result.add("" + getSeed());

        Vector<String> classifierOptions = new Vector<String>();
        Collections.addAll(classifierOptions, super.getOptions());
        Option.deleteOptionString(classifierOptions, "-S");
        result.addAll(classifierOptions);

        return (String[]) result.toArray(new String[result.size()]);
    }

    /**
     * Sets type of SVM (default SVMTYPE_C_SVC).
     *
     * @param value the type of the SVM
     */
    public void setSVMType(SelectedTag value) {
        if (value.getTags() == TAGS_SVMTYPE)
            m_SVMType = value.getSelectedTag().getID();
    }

    /**
     * Gets type of SVM.
     *
     * @return the type of the SVM
     */
    public SelectedTag getSVMType() {
        return new SelectedTag(m_SVMType, TAGS_SVMTYPE);
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String SVMTypeTipText() {
        return "The type of SVM to use.";
    }

    /**
     * Sets type of kernel function (default KERNELTYPE_RBF).
     *
     * @param value the kernel type
     */
    public void setKernelType(SelectedTag value) {
        if (value.getTags() == TAGS_KERNELTYPE)
            m_KernelType = value.getSelectedTag().getID();
    }

    /**
     * Gets type of kernel function.
     *
     * @return the kernel type
     */
    public SelectedTag getKernelType() {
        return new SelectedTag(m_KernelType, TAGS_KERNELTYPE);
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String kernelTypeTipText() {
        return "The type of kernel to use";
    }

    /**
     * Sets the degree of the kernel.
     *
     * @param value the degree of the kernel
     */
    public void setDegree(int value) {
        m_Degree = value;
    }

    /**
     * Gets the degree of the kernel.
     *
     * @return the degree of the kernel
     */
    public int getDegree() {
        return m_Degree;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String degreeTipText() {
        return "The degree of the kernel.";
    }

    /**
     * Sets gamma (default = 1/no of attributes).
     *
     * @param value the gamma value
     */
    public void setGamma(double value) {
        m_Gamma = value;
    }

    /**
     * Gets gamma.
     *
     * @return the current gamma
     */
    public double getGamma() {
        return m_Gamma;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String gammaTipText() {
        return "The gamma to use, if 0 then 1/max_index is used.";
    }

    /**
     * Sets coef (default 0).
     *
     * @param value the coef
     */
    public void setCoef0(double value) {
        m_Coef0 = value;
    }

    /**
     * Gets coef.
     *
     * @return the coef
     */
    public double getCoef0() {
        return m_Coef0;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String coef0TipText() {
        return "The coefficient to use.";
    }

    /**
     * Sets nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5).
     *
     * @param value the new nu value
     */
    public void setNu(double value) {
        m_nu = value;
    }

    /**
     * Gets nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5).
     *
     * @return the current nu value
     */
    public double getNu() {
        return m_nu;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String nuTipText() {
        return "The value of nu for nu-SVC, one-class SVM and nu-SVR.";
    }

    /**
     * Sets cache memory size in MB (default 40).
     *
     * @param value the memory size in MB
     */
    public void setCacheSize(double value) {
        m_CacheSize = value;
    }

    /**
     * Gets cache memory size in MB.
     *
     * @return the memory size in MB
     */
    public double getCacheSize() {
        return m_CacheSize;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String cacheSizeTipText() {
        return "The cache size in MB.";
    }

    /**
     * Sets the parameter C of C-SVC, epsilon-SVR, and nu-SVR (default 1).
     *
     * @param value the cost value
     */
    public void setCost(double value) {
        m_Cost = value;
    }

    /**
     * Sets the parameter C of C-SVC, epsilon-SVR, and nu-SVR.
     *
     * @return the cost value
     */
    public double getCost() {
        return m_Cost;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String costTipText() {
        return "The cost parameter C for C-SVC, epsilon-SVR and nu-SVR.";
    }

    /**
     * Sets tolerance of termination criterion (default 0.001).
     *
     * @param value the tolerance
     */
    public void setEps(double value) {
        m_eps = value;
    }

    /**
     * Gets tolerance of termination criterion.
     *
     * @return the current tolerance
     */
    public double getEps() {
        return m_eps;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String epsTipText() {
        return "The tolerance of the termination criterion.";
    }

    /**
     * Sets the epsilon in loss function of epsilon-SVR (default 0.1).
     *
     * @param value the loss epsilon
     */
    public void setLoss(double value) {
        m_Loss = value;
    }

    /**
     * Gets the epsilon in loss function of epsilon-SVR.
     *
     * @return the loss epsilon
     */
    public double getLoss() {
        return m_Loss;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String lossTipText() {
        return "The epsilon for the loss function in epsilon-SVR.";
    }

    /**
     * whether to use the shrinking heuristics.
     *
     * @param value true uses shrinking
     */
    public void setShrinking(boolean value) {
        m_Shrinking = value;
    }

    /**
     * whether to use the shrinking heuristics.
     *
     * @return true, if shrinking is used
     */
    public boolean getShrinking() {
        return m_Shrinking;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String shrinkingTipText() {
        return "Whether to use the shrinking heuristic.";
    }

    /**
     * whether to normalize input data.
     *
     * @param value whether to normalize the data
     */
    public void setNormalize(boolean value) {
        m_Normalize = value;
    }

    /**
     * whether to normalize input data.
     *
     * @return true, if the data is normalized
     */
    public boolean getNormalize() {
        return m_Normalize;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String normalizeTipText() {
        return "Whether to normalize the data.";
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String doNotReplaceMissingValuesTipText() {
        return "Whether to turn off automatic replacement of missing "
                + "values. WARNING: set to true only if the data does not " + "contain missing values.";
    }

    /**
     * Whether to turn off automatic replacement of missing values.
     * Set to true only if the data does not contain missing values.
     *
     * @param b true if automatic missing values replacement is
     *          to be disabled.
     */
    public void setDoNotReplaceMissingValues(boolean b) {
        m_noReplaceMissingValues = b;
    }

    /**
     * Gets whether automatic replacement of missing values is
     * disabled.
     *
     * @return true if automatic replacement of missing values
     * is disabled.
     */
    public boolean getDoNotReplaceMissingValues() {
        return m_noReplaceMissingValues;
    }

    /**
     * Sets the parameters C of class i to weight[i]*C, for C-SVC (default 1).
     * Blank separated list of doubles.
     *
     * @param weightsStr the weights (doubles, separated by blanks)
     */
    public void setWeights(String weightsStr) {
        StringTokenizer tok;
        int i;

        tok = new StringTokenizer(weightsStr, " ");
        m_Weight = new double[tok.countTokens()];
        m_WeightLabel = new int[tok.countTokens()];

        if (m_Weight.length == 0)
            System.out.println("Zero Weights processed. Default weights will be used");

        for (i = 0; i < m_Weight.length; i++) {
            m_Weight[i] = Double.parseDouble(tok.nextToken());
            m_WeightLabel[i] = i;
        }
    }

    /**
     * Gets the parameters C of class i to weight[i]*C, for C-SVC (default 1).
     * Blank separated doubles.
     *
     * @return the weights (doubles separated by blanks)
     */
    public String getWeights() {

        StringBuffer result = new StringBuffer("");

        for (int i = 0; i < m_Weight.length; i++) {
            if (i > 0)
                result.append(" ");
            result.append(m_Weight[i]);
        }

        return result.toString();
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String weightsTipText() {
        return "The weights to use for the classes (blank-separated list, eg, \"1 1 1\" for a 3-class problem), if empty 1 is used by default.";
    }

    /**
     * Sets whether probability estimates are generated instead of -1/+1 for
     * classification problems.
     *
     * @param value whether to predict probabilities
     */
    public void setProbabilityEstimates(boolean value) {
        m_ProbabilityEstimates = value;
    }

    /**
     * Returns whether to generate probability estimates instead of -1/+1 for
     * classification problems.
     *
     * @return true, if probability estimates should be returned
     */
    public boolean getProbabilityEstimates() {
        return m_ProbabilityEstimates;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String probabilityEstimatesTipText() {
        return "Whether to generate probability estimates instead of -1/+1 for classification problems.";
    }

    /**
     * Sets the file to save the libsvm-internal model to. No model is saved if
     * pointing to a directory.
     *
     * @param value the filename/directory
     */
    public void setModelFile(File value) {
        if (value == null)
            m_ModelFile = new File(System.getProperty("user.dir"));
        else
            m_ModelFile = value;
    }

    /**
     * Returns the file to save the libsvm-internal model to. No model is saved
     * if pointing to a directory.
     *
     * @return the file object
     */
    public File getModelFile() {
        return m_ModelFile;
    }

    /**
     * Returns the tip text for this property.
     *
     * @return tip text for this property suitable for
     * displaying in the explorer/experimenter gui
     */
    public String modelFileTipText() {
        return "The file to save the libsvm-internal model to; no model is saved if pointing to a directory.";
    }

    /**
     * transfers the local variables into a svm_parameter object.
     *
     * @return the configured svm_parameter object
     */
    protected svm_parameter getParameters() {

        svm_parameter p = new svm_parameter();

        p.svm_type = m_SVMType;
        p.kernel_type = m_KernelType;
        p.degree = m_Degree;
        p.gamma = m_GammaActual;
        p.coef0 = m_Coef0;
        p.nu = m_nu;
        p.cache_size = m_CacheSize;
        p.C = m_Cost;
        p.eps = m_eps;
        p.p = m_Loss;
        p.shrinking = m_Shrinking ? 1 : 0;
        p.nr_weight = m_Weight.length;
        p.probability = m_ProbabilityEstimates ? 1 : 0;

        p.weight = new double[m_Weight.length];
        p.weight_label = new int[m_Weight.length];
        for (int i = 0; i < m_Weight.length; i++) {
            p.weight[i] = m_Weight[i];
            p.weight_label[i] = m_WeightLabel[i];
        }
        return p;
    }

    /**
     * returns the svm_problem.
     *
     * @param vx the x values
     * @param vy the y values
     * @return the svm_problem object
     */
    protected svm_problem getProblem(svm_node[][] vx, double[] vy) {

        svm_problem p = new svm_problem();
        p.l = vy.length;
        p.y = vy;
        p.x = vx;
        return p;
    }

    /**
     * returns an instance into a sparse libsvm array.
     * 
     * @param instance   the instance to work on
     * @return      the libsvm array
     * @throws Exception   if setup of array fails
     */
    protected svm_node[] instanceToArray(Instance instance) throws Exception {

        int count = 0;
        for (int i = 0; i < instance.numValues(); i++) {
            if (instance.index(i) == instance.classIndex())
                continue;
            if (instance.valueSparse(i) != 0)
                count++;
        }

        svm_node[] r = new svm_node[count];
        int index = 0;
        for (int i = 0; i < instance.numValues(); i++) {

            int idx = instance.index(i);
            if (idx == instance.classIndex())
                continue;
            if (instance.valueSparse(i) == 0)
                continue;

            svm_node node = new svm_node();
            node.index = idx + 1;
            node.value = instance.valueSparse(i);
            r[index] = node;
            index++;
        }

        return r;
    }

    /**
     * Computes the distribution for a given instance. 
     * In case of 1-class classification, 1 is returned at index 0 if libsvm 
     * returns 1 and NaN (= missing) if libsvm returns -1.
     *
     * @param instance       the instance for which distribution is computed
     * @return          the distribution
     * @throws Exception       if the distribution can't be computed successfully
     */
    public double[] distributionForInstance(Instance instance) throws Exception {

        int[] labels = new int[instance.numClasses()];
        double[] prob_estimates = null;

        if (m_ProbabilityEstimates) {
            svm.svm_get_labels(m_Model, labels);

            prob_estimates = new double[instance.numClasses()];
        }

        if (!getDoNotReplaceMissingValues()) {
            m_ReplaceMissingValues.input(instance);
            m_ReplaceMissingValues.batchFinished();
            instance = m_ReplaceMissingValues.output();
        }

        if (m_Filter != null) {
            m_Filter.input(instance);
            m_Filter.batchFinished();
            instance = m_Filter.output();
        }

        m_NominalToBinary.input(instance);
        m_NominalToBinary.batchFinished();
        instance = m_NominalToBinary.output();

        svm_node[] x = instanceToArray(instance);
        double v;
        double[] result = new double[instance.numClasses()];
        if (m_ProbabilityEstimates && ((m_SVMType == SVMTYPE_C_SVC) || (m_SVMType == SVMTYPE_NU_SVC))) {
            v = svm.svm_predict_probability(m_Model, x, prob_estimates);

            // Return order of probabilities to canonical weka attribute order
            for (int k = 0; k < prob_estimates.length; k++) {
                result[labels[k]] = prob_estimates[k];
            }
        } else {
            v = svm.svm_predict(m_Model, x);

            if (instance.classAttribute().isNominal()) {
                if (m_SVMType == SVMTYPE_ONE_CLASS_SVM) {
                    if (v > 0)
                        result[0] = 1;
                    else
                        // outlier (interface for Classifier specifies that unclassified instances
                        // should return a distribution of all zeros)
                        result[0] = 0;
                } else {
                    result[(int) v] = 1;
                }
            } else {
                result[0] = v * m_x1 + m_x0;
            }
        }

        return result;
    }

    /**
     * Returns default capabilities of the classifier.
     *
     * @return      the capabilities of this classifier
     */
    public Capabilities getCapabilities() {
        Capabilities result = super.getCapabilities();
        result.disableAll();

        // attributes
        result.enable(Capability.NOMINAL_ATTRIBUTES);
        result.enable(Capability.NUMERIC_ATTRIBUTES);
        result.enable(Capability.DATE_ATTRIBUTES);
        result.enable(Capability.MISSING_VALUES);

        // class
        result.enableDependency(Capability.UNARY_CLASS);
        result.enableDependency(Capability.NOMINAL_CLASS);
        result.enableDependency(Capability.NUMERIC_CLASS);
        result.enableDependency(Capability.DATE_CLASS);

        switch (m_SVMType) {
        case SVMTYPE_C_SVC:
        case SVMTYPE_NU_SVC:
            result.enable(Capability.NOMINAL_CLASS);
            break;

        case SVMTYPE_ONE_CLASS_SVM:
            result.enable(Capability.UNARY_CLASS);
            break;

        case SVMTYPE_EPSILON_SVR:
        case SVMTYPE_NU_SVR:
            result.enable(Capability.NUMERIC_CLASS);
            result.enable(Capability.DATE_CLASS);
            break;

        default:
            throw new IllegalArgumentException("SVMType " + m_SVMType + " is not supported!");
        }
        result.enable(Capability.MISSING_CLASS_VALUES);

        return result;
    }

    /**
     * builds the classifier.
     * 
     * @param insts       the training instances
     * @throws Exception  if libsvm encountered a problem
     */
    public void buildClassifier(Instances insts) throws Exception {
        m_Filter = null;

        // remove instances with missing class
        insts = new Instances(insts);
        insts.deleteWithMissingClass();

        if (!getDoNotReplaceMissingValues()) {
            m_ReplaceMissingValues = new ReplaceMissingValues();
            m_ReplaceMissingValues.setInputFormat(insts);
            insts = Filter.useFilter(insts, m_ReplaceMissingValues);
        }

        // can classifier handle the data?
        // we check this here so that if the user turns off
        // replace missing values filtering, it will fail
        // if the data actually does have missing values
        getCapabilities().testWithFail(insts);

        double y0 = Double.NaN;
        double y1 = y0;
        int index = -1;
        if (!insts.classAttribute().isNominal()) {
            y0 = insts.instance(0).classValue();
            index = 1;
            while (index < insts.numInstances() && insts.instance(index).classValue() == y0) {
                index++;
            }
            if (index == insts.numInstances()) {
                // degenerate case, all class values are equal
                // we don't want to deal with this, too much hassle
                throw new Exception("All class values are the same. At least two class values should be different");
            }
            y1 = insts.instance(index).classValue();
        }

        if (getNormalize()) {
            m_Filter = new Normalize();
            ((Normalize) m_Filter).setIgnoreClass(true); // Normalize class as well
            m_Filter.setInputFormat(insts);
            insts = Filter.useFilter(insts, m_Filter);
        }

        if (!insts.classAttribute().isNominal()) {
            if (m_Filter != null) {
                double z0 = insts.instance(0).classValue();
                double z1 = insts.instance(index).classValue();
                m_x1 = (y0 - y1) / (z0 - z1); // no division by zero, since y0 != y1 guaranteed => z0 != z1 ???
                m_x0 = (y0 - m_x1 * z0); // = y1 - m_x1 * z1
            } else {
                m_x1 = 1.0;
                m_x0 = 0.0;
            }
        } else {
            m_x0 = Double.NaN;
            m_x1 = m_x0;
        }

        // nominal to binary
        m_NominalToBinary = new NominalToBinary();
        m_NominalToBinary.setInputFormat(insts);
        insts = Filter.useFilter(insts, m_NominalToBinary);

        double[] vy = new double[insts.numInstances()];
        svm_node[][] vx = new svm_node[insts.numInstances()][];
        int max_index = 0;
        for (int d = 0; d < insts.numInstances(); d++) {
            Instance inst = insts.instance(d);
            vx[d] = instanceToArray(inst);
            if (vx[d].length > 0) {
                max_index = Math.max(max_index, vx[d][vx[d].length - 1].index);
            }
            vy[d] = inst.classValue();
        }

        // calculate actual gamma
        if (getGamma() == 0)
            m_GammaActual = 1.0 / max_index;
        else
            m_GammaActual = m_Gamma;

        svm_problem p = getProblem(vx, vy);
        svm_parameter pars = getParameters();

        // check parameters
        String error_msg = svm.svm_check_parameter(p, pars);

        if (error_msg != null)
            throw new Exception("Error: " + error_msg);

        // make probability estimates deterministic from run to run
        svm.rand.setSeed(m_Seed);

        // Change printing function if no debugging output is required
        if (!getDebug()) {
            svm.svm_set_print_string_function(new svm_print_interface() {
                @Override
                public void print(String s) {
                    // Do nothing
                }
            });
        }

        // train model
        m_Model = svm.svm_train(p, pars);

        // save internal model?
        if (!m_ModelFile.isDirectory()) {
            svm.svm_save_model(m_ModelFile.getAbsolutePath(), m_Model);
        }
    }

    /**
     * returns a string representation.
     * 
     * @return            a string representation
     */
    public String toString() {
        return "LibSVM wrapper, original code by Yasser EL-Manzalawy (= WLSVM)";
    }

    /**
     * Returns the revision string.
     * 
     * @return      the revision
     */
    public String getRevision() {
        return RevisionUtils.extract("$Revision$");
    }

    /**
     * Main method for testing this class.
     * 
     * @param args the options
     */
    public static void main(String[] args) {
        runClassifier(new LibSVM(), args);
    }
}