source: branches/MetisMQI/src/main/java/weka/classifiers/mi/TLD.java

/*
 *    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 2 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, write to the Free Software
 *    Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 * TLD.java
 * Copyright (C) 2005 University of Waikato, Hamilton, New Zealand
 *
 */

package weka.classifiers.mi;

import weka.classifiers.RandomizableClassifier;
import weka.core.Capabilities;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.MultiInstanceCapabilitiesHandler;
import weka.core.Optimization;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.core.Capabilities.Capability;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;

import java.util.Enumeration;
import java.util.Random;
import java.util.Vector;

/** 
 <!-- globalinfo-start -->
 * Two-Level Distribution approach, changes the starting value of the searching algorithm, supplement the cut-off modification and check missing values.<br/>
 * <br/>
 * For more information see:<br/>
 * <br/>
 * Xin Xu (2003). Statistical learning in multiple instance problem. Hamilton, NZ.
 * <p/>
 <!-- globalinfo-end -->
 *
 <!-- technical-bibtex-start -->
 * BibTeX:
 * <pre>
 * &#64;mastersthesis{Xu2003,
 *    address = {Hamilton, NZ},
 *    author = {Xin Xu},
 *    note = {0657.594},
 *    school = {University of Waikato},
 *    title = {Statistical learning in multiple instance problem},
 *    year = {2003}
 * }
 * </pre>
 * <p/>
 <!-- technical-bibtex-end -->
 *
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -C
 *  Set whether or not use empirical
 *  log-odds cut-off instead of 0</pre>
 * 
 * <pre> -R &lt;numOfRuns&gt;
 *  Set the number of multiple runs 
 *  needed for searching the MLE.</pre>
 * 
 * <pre> -S &lt;num&gt;
 *  Random number seed.
 *  (default 1)</pre>
 * 
 * <pre> -D
 *  If set, classifier is run in debug mode and
 *  may output additional info to the console</pre>
 * 
 <!-- options-end -->
 *
 * @author Eibe Frank (eibe@cs.waikato.ac.nz)
 * @author Xin Xu (xx5@cs.waikato.ac.nz)
 * @version $Revision: 5481 $ 
 */
public class TLD 
  extends RandomizableClassifier 
  implements OptionHandler, MultiInstanceCapabilitiesHandler,
             TechnicalInformationHandler {

  /** for serialization */
  static final long serialVersionUID = 6657315525171152210L;
  
  /** The mean for each attribute of each positive exemplar */
  protected double[][] m_MeanP = null;

  /** The variance for each attribute of each positive exemplar */
  protected double[][] m_VarianceP = null;

  /** The mean for each attribute of each negative exemplar */
  protected double[][] m_MeanN = null;

  /** The variance for each attribute of each negative exemplar */
  protected double[][] m_VarianceN = null;

  /** The effective sum of weights of each positive exemplar in each dimension*/
  protected double[][] m_SumP = null;

  /** The effective sum of weights of each negative exemplar in each dimension*/
  protected double[][] m_SumN = null;

  /** The parameters to be estimated for each positive exemplar*/
  protected double[] m_ParamsP = null;

  /** The parameters to be estimated for each negative exemplar*/
  protected double[] m_ParamsN = null;

  /** The dimension of each exemplar, i.e. (numAttributes-2) */
  protected int m_Dimension = 0;

  /** The class label of each exemplar */
  protected double[] m_Class = null;

  /** The number of class labels in the data */
  protected int m_NumClasses = 2;

  /** The very small number representing zero */
  static public double ZERO = 1.0e-6;   

  /** The number of runs to perform */
  protected int m_Run = 1;

  protected double m_Cutoff;

  protected boolean m_UseEmpiricalCutOff = false;   

  /**
   * Returns a string describing this filter
   *
   * @return a description of the filter suitable for
   * displaying in the explorer/experimenter gui
   */
  public String globalInfo() {
    return 
        "Two-Level Distribution approach, changes the starting value of "
      + "the searching algorithm, supplement the cut-off modification and "
      + "check missing values.\n\n"
      + "For more information see:\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;
    
    result = new TechnicalInformation(Type.MASTERSTHESIS);
    result.setValue(Field.AUTHOR, "Xin Xu");
    result.setValue(Field.YEAR, "2003");
    result.setValue(Field.TITLE, "Statistical learning in multiple instance problem");
    result.setValue(Field.SCHOOL, "University of Waikato");
    result.setValue(Field.ADDRESS, "Hamilton, NZ");
    result.setValue(Field.NOTE, "0657.594");
    
    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.RELATIONAL_ATTRIBUTES);
    result.enable(Capability.MISSING_VALUES);

    // class
    result.enable(Capability.BINARY_CLASS);
    result.enable(Capability.MISSING_CLASS_VALUES);
    
    // other
    result.enable(Capability.ONLY_MULTIINSTANCE);
    
    return result;
  }

  /**
   * Returns the capabilities of this multi-instance classifier for the
   * relational data.
   *
   * @return            the capabilities of this object
   * @see               Capabilities
   */
  public Capabilities getMultiInstanceCapabilities() {
    Capabilities result = super.getCapabilities();
    result.disableAll();
    
    // attributes
    result.enable(Capability.NUMERIC_ATTRIBUTES);
    result.enable(Capability.MISSING_VALUES);

    // class
    result.disableAllClasses();
    result.enable(Capability.NO_CLASS);
    
    return result;
  }

  /**
   *
   * @param exs the training exemplars
   * @throws Exception if the model cannot be built properly
   */    
  public void buildClassifier(Instances exs)throws Exception{
    // can classifier handle the data?
    getCapabilities().testWithFail(exs);

    // remove instances with missing class
    exs = new Instances(exs);
    exs.deleteWithMissingClass();
    
    int numegs = exs.numInstances();
    m_Dimension = exs.attribute(1).relation(). numAttributes();
    Instances pos = new Instances(exs, 0), neg = new Instances(exs, 0);

    for(int u=0; u<numegs; u++){
      Instance example = exs.instance(u);
      if(example.classValue() == 1)
        pos.add(example);
      else
        neg.add(example);
    }

    int pnum = pos.numInstances(), nnum = neg.numInstances();   

    m_MeanP = new double[pnum][m_Dimension];
    m_VarianceP = new double[pnum][m_Dimension];
    m_SumP = new double[pnum][m_Dimension];
    m_MeanN = new double[nnum][m_Dimension];
    m_VarianceN = new double[nnum][m_Dimension];
    m_SumN = new double[nnum][m_Dimension];
    m_ParamsP = new double[4*m_Dimension];
    m_ParamsN = new double[4*m_Dimension];

    // Estimation of the parameters: as the start value for search
    double[] pSumVal=new double[m_Dimension], // for m 
      nSumVal=new double[m_Dimension]; 
    double[] maxVarsP=new double[m_Dimension], // for a
      maxVarsN=new double[m_Dimension]; 
    // Mean of sample variances: for b, b=a/E(\sigma^2)+2
    double[] varMeanP = new double[m_Dimension],
      varMeanN = new double[m_Dimension]; 
    // Variances of sample means: for w, w=E[var(\mu)]/E[\sigma^2]
    double[] meanVarP = new double[m_Dimension],
      meanVarN = new double[m_Dimension];
    // number of exemplars without all values missing
    double[] numExsP = new double[m_Dimension],
      numExsN = new double[m_Dimension];

    // Extract metadata fro both positive and negative bags
    for(int v=0; v < pnum; v++){
      /*Exemplar px = pos.exemplar(v);
        m_MeanP[v] = px.meanOrMode();
        m_VarianceP[v] = px.variance();
        Instances pxi =  px.getInstances();
        */

      Instances pxi =  pos.instance(v).relationalValue(1);
      for (int k=0; k<pxi.numAttributes(); k++) { 
        m_MeanP[v][k] = pxi.meanOrMode(k);
        m_VarianceP[v][k] = pxi.variance(k);
      }

      for (int w=0,t=0; w < m_Dimension; w++,t++){              
        //if((t==m_ClassIndex) || (t==m_IdIndex))
        //  t++;                

        if(!Double.isNaN(m_MeanP[v][w])){
          for(int u=0;u<pxi.numInstances();u++){
            Instance ins = pxi.instance(u);                     
            if(!ins.isMissing(t))
              m_SumP[v][w] += ins.weight();                        
          }   
          numExsP[w]++;  
          pSumVal[w] += m_MeanP[v][w];
          meanVarP[w] += m_MeanP[v][w]*m_MeanP[v][w];    
          if(maxVarsP[w] < m_VarianceP[v][w])
            maxVarsP[w] = m_VarianceP[v][w];
          varMeanP[w] += m_VarianceP[v][w];
          m_VarianceP[v][w] *= (m_SumP[v][w]-1.0);
          if(m_VarianceP[v][w] < 0.0)
            m_VarianceP[v][w] = 0.0;
        }
      }
    }

    for(int v=0; v < nnum; v++){
      /*Exemplar nx = neg.exemplar(v);
        m_MeanN[v] = nx.meanOrMode();
        m_VarianceN[v] = nx.variance();
        Instances nxi =  nx.getInstances();
        */
      Instances nxi =  neg.instance(v).relationalValue(1);
      for (int k=0; k<nxi.numAttributes(); k++) {
        m_MeanN[v][k] = nxi.meanOrMode(k);
        m_VarianceN[v][k] = nxi.variance(k);
      }

      for (int w=0,t=0; w < m_Dimension; w++,t++){              
        //if((t==m_ClassIndex) || (t==m_IdIndex))
        //  t++;                

        if(!Double.isNaN(m_MeanN[v][w])){
          for(int u=0;u<nxi.numInstances();u++)
            if(!nxi.instance(u).isMissing(t))
              m_SumN[v][w] += nxi.instance(u).weight();
          numExsN[w]++;         
          nSumVal[w] += m_MeanN[v][w];
          meanVarN[w] += m_MeanN[v][w]*m_MeanN[v][w]; 
          if(maxVarsN[w] < m_VarianceN[v][w])
            maxVarsN[w] = m_VarianceN[v][w];
          varMeanN[w] += m_VarianceN[v][w];
          m_VarianceN[v][w] *= (m_SumN[v][w]-1.0);
          if(m_VarianceN[v][w] < 0.0)
            m_VarianceN[v][w] = 0.0;
        }
      }
    }

    for(int w=0; w<m_Dimension; w++){
      pSumVal[w] /= numExsP[w];
      nSumVal[w] /= numExsN[w];
      if(numExsP[w]>1)
        meanVarP[w] = meanVarP[w]/(numExsP[w]-1.0) 
          - pSumVal[w]*numExsP[w]/(numExsP[w]-1.0);
      if(numExsN[w]>1)
        meanVarN[w] = meanVarN[w]/(numExsN[w]-1.0) 
          - nSumVal[w]*numExsN[w]/(numExsN[w]-1.0);
      varMeanP[w] /= numExsP[w];
      varMeanN[w] /= numExsN[w];
    }

    //Bounds and parameter values for each run
    double[][] bounds = new double[2][4];
    double[] pThisParam = new double[4], 
      nThisParam = new double[4];

    // Initial values for parameters
    double a, b, w, m;

    // Optimize for one dimension
    for (int x=0; x < m_Dimension; x++){
      if (getDebug())
        System.err.println("\n\n!!!!!!!!!!!!!!!!!!!!!!???Dimension #"+x);

      // Positive examplars: first run
      a = (maxVarsP[x]>ZERO) ? maxVarsP[x]:1.0; 
      if (varMeanP[x]<=ZERO)   varMeanP[x] = ZERO;  // modified by LinDong (09/2005)
      b = a/varMeanP[x]+2.0; // a/(b-2) = E(\sigma^2)
      w = meanVarP[x]/varMeanP[x]; // E[var(\mu)] = w*E[\sigma^2]           
      if(w<=ZERO)  w=1.0;

      m = pSumVal[x];     
      pThisParam[0] = a;    // a
      pThisParam[1] = b;  // b
      pThisParam[2] = w;  // w
      pThisParam[3] = m;  // m

      // Negative examplars: first run
      a = (maxVarsN[x]>ZERO) ? maxVarsN[x]:1.0; 
      if (varMeanN[x]<=ZERO)   varMeanN[x] = ZERO; // modified by LinDong (09/2005)
      b = a/varMeanN[x]+2.0; // a/(b-2) = E(\sigma^2)
      w = meanVarN[x]/varMeanN[x]; // E[var(\mu)] = w*E[\sigma^2]           
      if(w<=ZERO) w=1.0;

      m = nSumVal[x];     
      nThisParam[0] = a;    // a
      nThisParam[1] = b;  // b
      nThisParam[2] = w;  // w
      nThisParam[3] = m;  // m

      // Bound constraints
      bounds[0][0] = ZERO; // a > 0
      bounds[0][1] = 2.0+ZERO;  // b > 2 
      bounds[0][2] = ZERO; // w > 0
      bounds[0][3] = Double.NaN;

      for(int t=0; t<4; t++){
        bounds[1][t] = Double.NaN;
        m_ParamsP[4*x+t] = pThisParam[t];       
        m_ParamsN[4*x+t] = nThisParam[t];
      }
      double pminVal=Double.MAX_VALUE, nminVal=Double.MAX_VALUE;
      Random whichEx = new Random(m_Seed); 
      TLD_Optm pOp=null, nOp=null;      
      boolean isRunValid = true;
      double[] sumP=new double[pnum], meanP=new double[pnum],
        varP=new double[pnum];
      double[] sumN=new double[nnum], meanN=new double[nnum],
        varN=new double[nnum];

      // One dimension
      for(int p=0; p<pnum; p++){
        sumP[p] = m_SumP[p][x];
        meanP[p] = m_MeanP[p][x];
        varP[p] = m_VarianceP[p][x];
      }
      for(int q=0; q<nnum; q++){
        sumN[q] = m_SumN[q][x];
        meanN[q] = m_MeanN[q][x];
        varN[q] = m_VarianceN[q][x];
      }

      for(int y=0; y<m_Run;){
        if (getDebug())
          System.err.println("\n\n!!!!!!!!!!!!!!!!!!!!!!???Run #"+y);
        double thisMin;

        if (getDebug())
          System.err.println("\nPositive exemplars");
        pOp = new TLD_Optm();
        pOp.setNum(sumP);
        pOp.setSSquare(varP);
        pOp.setXBar(meanP);

        pThisParam = pOp.findArgmin(pThisParam, bounds);
        while(pThisParam==null){
          pThisParam = pOp.getVarbValues();                 
          if (getDebug())
            System.err.println("!!! 200 iterations finished, not enough!");
          pThisParam = pOp.findArgmin(pThisParam, bounds);
        }       

        thisMin = pOp.getMinFunction();
        if(!Double.isNaN(thisMin) && (thisMin<pminVal)){
          pminVal = thisMin;
          for(int z=0; z<4; z++)
            m_ParamsP[4*x+z] = pThisParam[z];
        }

        if(Double.isNaN(thisMin)){
          pThisParam = new double[4];
          isRunValid =false;
        }

        if (getDebug())
          System.err.println("\nNegative exemplars");
        nOp = new TLD_Optm();
        nOp.setNum(sumN);
        nOp.setSSquare(varN);
        nOp.setXBar(meanN);

        nThisParam = nOp.findArgmin(nThisParam, bounds);
        while(nThisParam==null){
          nThisParam = nOp.getVarbValues();
          if (getDebug())
            System.err.println("!!! 200 iterations finished, not enough!");
          nThisParam = nOp.findArgmin(nThisParam, bounds);
        }       
        thisMin = nOp.getMinFunction();
        if(!Double.isNaN(thisMin) && (thisMin<nminVal)){
          nminVal = thisMin;
          for(int z=0; z<4; z++)
            m_ParamsN[4*x+z] = nThisParam[z];     
        }

        if(Double.isNaN(thisMin)){
          nThisParam = new double[4];
          isRunValid =false;
        }

        if(!isRunValid){ y--; isRunValid=true; }                

        if(++y<m_Run){
          // Change the initial parameters and restart              
          int pone = whichEx.nextInt(pnum), // Randomly pick one pos. exmpl.
              none = whichEx.nextInt(nnum);

          // Positive exemplars: next run 
          while((m_SumP[pone][x]<=1.0)||Double.isNaN(m_MeanP[pone][x]))
            pone = whichEx.nextInt(pnum);

          a = m_VarianceP[pone][x]/(m_SumP[pone][x]-1.0);               
          if(a<=ZERO) a=m_ParamsN[4*x]; // Change to negative params
          m = m_MeanP[pone][x];
          double sq = (m-m_ParamsP[4*x+3])*(m-m_ParamsP[4*x+3]);

          b = a*m_ParamsP[4*x+2]/sq+2.0; // b=a/Var+2, assuming Var=Sq/w'
          if((b<=ZERO) || Double.isNaN(b) || Double.isInfinite(b))
            b=m_ParamsN[4*x+1];

          w = sq*(m_ParamsP[4*x+1]-2.0)/m_ParamsP[4*x];//w=Sq/Var, assuming Var=a'/(b'-2)
          if((w<=ZERO) || Double.isNaN(w) || Double.isInfinite(w))
            w=m_ParamsN[4*x+2];

          pThisParam[0] = a;    // a
          pThisParam[1] = b;  // b
          pThisParam[2] = w;  // w
          pThisParam[3] = m;  // m          

          // Negative exemplars: next run 
          while((m_SumN[none][x]<=1.0)||Double.isNaN(m_MeanN[none][x]))
            none = whichEx.nextInt(nnum);           

          a = m_VarianceN[none][x]/(m_SumN[none][x]-1.0);       
          if(a<=ZERO) a=m_ParamsP[4*x];       
          m = m_MeanN[none][x];
          sq = (m-m_ParamsN[4*x+3])*(m-m_ParamsN[4*x+3]);

          b = a*m_ParamsN[4*x+2]/sq+2.0; // b=a/Var+2, assuming Var=Sq/w'
          if((b<=ZERO) || Double.isNaN(b) || Double.isInfinite(b))
            b=m_ParamsP[4*x+1];

          w = sq*(m_ParamsN[4*x+1]-2.0)/m_ParamsN[4*x];//w=Sq/Var, assuming Var=a'/(b'-2)
          if((w<=ZERO) || Double.isNaN(w) || Double.isInfinite(w))
            w=m_ParamsP[4*x+2];

          nThisParam[0] = a;    // a
          nThisParam[1] = b;  // b
          nThisParam[2] = w;  // w
          nThisParam[3] = m;  // m                      
        }
      }                     
    }

    for (int x=0, y=0; x<m_Dimension; x++, y++){
      //if((x==exs.classIndex()) || (x==exs.idIndex()))
      //y++;
      a=m_ParamsP[4*x]; b=m_ParamsP[4*x+1]; 
      w=m_ParamsP[4*x+2]; m=m_ParamsP[4*x+3];
      if (getDebug())
        System.err.println("\n\n???Positive: ( "+exs.attribute(1).relation().attribute(y)+
          "): a="+a+", b="+b+", w="+w+", m="+m);

      a=m_ParamsN[4*x]; b=m_ParamsN[4*x+1]; 
      w=m_ParamsN[4*x+2]; m=m_ParamsN[4*x+3];
      if (getDebug())
        System.err.println("???Negative: ("+exs.attribute(1).relation().attribute(y)+
          "): a="+a+", b="+b+", w="+w+", m="+m);
    }

    if(m_UseEmpiricalCutOff){   
      // Find the empirical cut-off
      double[] pLogOdds=new double[pnum], nLogOdds=new double[nnum];  
      for(int p=0; p<pnum; p++)
        pLogOdds[p] = 
          likelihoodRatio(m_SumP[p], m_MeanP[p], m_VarianceP[p]);

      for(int q=0; q<nnum; q++)
        nLogOdds[q] = 
          likelihoodRatio(m_SumN[q], m_MeanN[q], m_VarianceN[q]);

      // Update m_Cutoff
      findCutOff(pLogOdds, nLogOdds);
    }
    else
      m_Cutoff = -Math.log((double)pnum/(double)nnum);

    if (getDebug())
      System.err.println("???Cut-off="+m_Cutoff);
  }        

  /**
   *
   * @param ex the given test exemplar
   * @return the classification 
   * @throws Exception if the exemplar could not be classified
   * successfully
   */
  public double classifyInstance(Instance ex)throws Exception{
    //Exemplar ex = new Exemplar(e);
    Instances exi = ex.relationalValue(1);
    double[] n = new double[m_Dimension];
    double [] xBar = new double[m_Dimension];
    double [] sSq = new double[m_Dimension];
    for (int i=0; i<exi.numAttributes() ; i++){
      xBar[i] = exi.meanOrMode(i);
      sSq[i] = exi.variance(i);
    }

    for (int w=0, t=0; w < m_Dimension; w++, t++){
      //if((t==m_ClassIndex) || (t==m_IdIndex))
      //t++;    
      for(int u=0;u<exi.numInstances();u++)
        if(!exi.instance(u).isMissing(t))
          n[w] += exi.instance(u).weight();

      sSq[w] = sSq[w]*(n[w]-1.0);
      if(sSq[w] <= 0.0)
        sSq[w] = 0.0;
    }

    double logOdds = likelihoodRatio(n, xBar, sSq);
    return (logOdds > m_Cutoff) ? 1 : 0 ;
  }

  private double likelihoodRatio(double[] n, double[] xBar, double[] sSq){      
    double LLP = 0.0, LLN = 0.0;

    for (int x=0; x<m_Dimension; x++){
      if(Double.isNaN(xBar[x])) continue; // All missing values

      int halfN = ((int)n[x])/2;        
      //Log-likelihood for positive 
      double a=m_ParamsP[4*x], b=m_ParamsP[4*x+1], 
             w=m_ParamsP[4*x+2], m=m_ParamsP[4*x+3];
      LLP += 0.5*b*Math.log(a) + 0.5*(b+n[x]-1.0)*Math.log(1.0+n[x]*w)
        - 0.5*(b+n[x])*Math.log((1.0+n[x]*w)*(a+sSq[x])+
            n[x]*(xBar[x]-m)*(xBar[x]-m))
        - 0.5*n[x]*Math.log(Math.PI);
      for(int y=1; y<=halfN; y++)
        LLP += Math.log(b/2.0+n[x]/2.0-(double)y);

      if(n[x]/2.0 > halfN) // n is odd
        LLP += TLD_Optm.diffLnGamma(b/2.0);

      //Log-likelihood for negative 
      a=m_ParamsN[4*x];
      b=m_ParamsN[4*x+1]; 
      w=m_ParamsN[4*x+2];
      m=m_ParamsN[4*x+3];
      LLN += 0.5*b*Math.log(a) + 0.5*(b+n[x]-1.0)*Math.log(1.0+n[x]*w)
        - 0.5*(b+n[x])*Math.log((1.0+n[x]*w)*(a+sSq[x])+
            n[x]*(xBar[x]-m)*(xBar[x]-m))
        - 0.5*n[x]*Math.log(Math.PI);
      for(int y=1; y<=halfN; y++)
        LLN += Math.log(b/2.0+n[x]/2.0-(double)y);      

      if(n[x]/2.0 > halfN) // n is odd
        LLN += TLD_Optm.diffLnGamma(b/2.0);   
    }

    return LLP - LLN;
  }

  private void findCutOff(double[] pos, double[] neg){
    int[] pOrder = Utils.sort(pos),
      nOrder = Utils.sort(neg);
    /*
       System.err.println("\n\n???Positive: ");
       for(int t=0; t<pOrder.length; t++)
       System.err.print(t+":"+Utils.doubleToString(pos[pOrder[t]],0,2)+" ");
       System.err.println("\n\n???Negative: ");
       for(int t=0; t<nOrder.length; t++)
       System.err.print(t+":"+Utils.doubleToString(neg[nOrder[t]],0,2)+" ");
       */
    int pNum = pos.length, nNum = neg.length, count, p=0, n=0;  
    double fstAccu=0.0, sndAccu=(double)pNum, split; 
    double maxAccu = 0, minDistTo0 = Double.MAX_VALUE;

    // Skip continuous negatives        
    for(;(n<nNum)&&(pos[pOrder[0]]>=neg[nOrder[n]]); n++, fstAccu++);

    if(n>=nNum){ // totally seperate
      m_Cutoff = (neg[nOrder[nNum-1]]+pos[pOrder[0]])/2.0;      
      //m_Cutoff = neg[nOrder[nNum-1]];
      return;  
    }   

    count=n;
    while((p<pNum)&&(n<nNum)){
      // Compare the next in the two lists
      if(pos[pOrder[p]]>=neg[nOrder[n]]){ // Neg has less log-odds
        fstAccu += 1.0;    
        split=neg[nOrder[n]];
        n++;     
      }
      else{
        sndAccu -= 1.0;
        split=pos[pOrder[p]];
        p++;
      }           
      count++;
      if((fstAccu+sndAccu > maxAccu) 
          || ((fstAccu+sndAccu == maxAccu) && (Math.abs(split)<minDistTo0))){
        maxAccu = fstAccu+sndAccu;
        m_Cutoff = split;
        minDistTo0 = Math.abs(split);
      }     
    }           
  }

  /**
   * Returns an enumeration describing the available options
   *
   * @return an enumeration of all the available options
   */
  public Enumeration listOptions() {
    Vector result = new Vector();
    
    result.addElement(new Option(
          "\tSet whether or not use empirical\n"
          + "\tlog-odds cut-off instead of 0",
          "C", 0, "-C"));
    
    result.addElement(new Option(
          "\tSet the number of multiple runs \n"
          + "\tneeded for searching the MLE.",
          "R", 1, "-R <numOfRuns>"));
    
    Enumeration enu = super.listOptions();
    while (enu.hasMoreElements()) {
      result.addElement(enu.nextElement());
    }

    return result.elements();
  }

  /**
   * Parses a given list of options. <p/>
   * 
   <!-- options-start -->
   * Valid options are: <p/>
   * 
   * <pre> -C
   *  Set whether or not use empirical
   *  log-odds cut-off instead of 0</pre>
   * 
   * <pre> -R &lt;numOfRuns&gt;
   *  Set the number of multiple runs 
   *  needed for searching the MLE.</pre>
   * 
   * <pre> -S &lt;num&gt;
   *  Random number seed.
   *  (default 1)</pre>
   * 
   * <pre> -D
   *  If set, classifier is run in debug mode and
   *  may output additional info to the console</pre>
   * 
   <!-- options-end -->
   *
   * @param options the list of options as an array of strings
   * @throws Exception if an option is not supported
   */
  public void setOptions(String[] options) throws Exception{
    setDebug(Utils.getFlag('D', options));

    setUsingCutOff(Utils.getFlag('C', options));

    String runString = Utils.getOption('R', options);
    if (runString.length() != 0) 
      setNumRuns(Integer.parseInt(runString));
    else 
      setNumRuns(1);

    super.setOptions(options);
  }

  /**
   * Gets the current settings of the Classifier.
   *
   * @return an array of strings suitable for passing to setOptions
   */
  public String[] getOptions() {
    Vector        result;
    String[]      options;
    int           i;
    
    result  = new Vector();
    options = super.getOptions();
    for (i = 0; i < options.length; i++)
      result.add(options[i]);

    if (getDebug())
      result.add("-D");
    
    if (getUsingCutOff())
      result.add("-C");

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

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

  /**
   * Returns the tip text for this property
   *
   * @return tip text for this property suitable for
   * displaying in the explorer/experimenter gui
   */
  public String numRunsTipText() {
    return "The number of runs to perform.";
  }

  /**
   * Sets the number of runs to perform.
   *
   * @param numRuns   the number of runs to perform
   */
  public void setNumRuns(int numRuns) {
    m_Run = numRuns;
  }

  /**
   * Returns the number of runs to perform.
   *
   * @return          the number of runs to perform
   */
  public int getNumRuns() {
    return m_Run;
  }

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

  /**
   * Sets whether to use an empirical cutoff.
   *
   * @param cutOff      whether to use an empirical cutoff
   */
  public void setUsingCutOff (boolean cutOff) {
    m_UseEmpiricalCutOff = cutOff;
  }

  /**
   * Returns whether an empirical cutoff is used
   *
   * @return            true if an empirical cutoff is used
   */
  public boolean getUsingCutOff() {
    return m_UseEmpiricalCutOff;
  }
  
  /**
   * Returns the revision string.
   * 
   * @return            the revision
   */
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 5481 $");
  }

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

class TLD_Optm extends Optimization {

  private double[] num;
  private double[] sSq;
  private double[] xBar;

  public void setNum(double[] n) {num = n;}
  public void setSSquare(double[] s){sSq = s;}
  public void setXBar(double[] x){xBar = x;}

  /**
   * Compute Ln[Gamma(b+0.5)] - Ln[Gamma(b)]
   *
   * @param b the value in the above formula
   * @return the result
   */    
  public static double diffLnGamma(double b){
    double[] coef= {76.18009172947146, -86.50532032941677,
      24.01409824083091, -1.231739572450155, 
      0.1208650973866179e-2, -0.5395239384953e-5};
    double rt = -0.5;
    rt += (b+1.0)*Math.log(b+6.0) - (b+0.5)*Math.log(b+5.5);
    double series1=1.000000000190015, series2=1.000000000190015;
    for(int i=0; i<6; i++){
      series1 += coef[i]/(b+1.5+(double)i);
      series2 += coef[i]/(b+1.0+(double)i);
    }

    rt += Math.log(series1*b)-Math.log(series2*(b+0.5));
    return rt;
  }

  /**
   * Compute dLn[Gamma(x+0.5)]/dx - dLn[Gamma(x)]/dx
   *
   * @param x the value in the above formula
   * @return the result
   */    
  protected double diffFstDervLnGamma(double x){
    double rt=0, series=1.0;// Just make it >0
    for(int i=0;series>=m_Zero*1e-3;i++){
      series = 0.5/((x+(double)i)*(x+(double)i+0.5));
      rt += series;
    }
    return rt;
  }

  /**
   * Compute {Ln[Gamma(x+0.5)]}'' - {Ln[Gamma(x)]}''
   *
   * @param x the value in the above formula
   * @return the result
   */    
  protected double diffSndDervLnGamma(double x){
    double rt=0, series=1.0;// Just make it >0
    for(int i=0;series>=m_Zero*1e-3;i++){
      series = (x+(double)i+0.25)/
        ((x+(double)i)*(x+(double)i)*(x+(double)i+0.5)*(x+(double)i+0.5));
      rt -= series;
    }
    return rt;
  }

  /**
   * Implement this procedure to evaluate objective
   * function to be minimized
   */
  protected double objectiveFunction(double[] x){
    int numExs = num.length;
    double NLL = 0; // Negative Log-Likelihood

    double a=x[0], b=x[1], w=x[2], m=x[3];
    for(int j=0; j < numExs; j++){

      if(Double.isNaN(xBar[j])) continue; // All missing values

      NLL += 0.5*(b+num[j])*
        Math.log((1.0+num[j]*w)*(a+sSq[j]) + 
            num[j]*(xBar[j]-m)*(xBar[j]-m));        

      if(Double.isNaN(NLL) && m_Debug){
        System.err.println("???????????1: "+a+" "+b+" "+w+" "+m
            +"|x-: "+xBar[j] + 
            "|n: "+num[j] + "|S^2: "+sSq[j]);
        System.exit(1);
      }

      // Doesn't affect optimization
      //NLL += 0.5*num[j]*Math.log(Math.PI);            

      NLL -= 0.5*(b+num[j]-1.0)*Math.log(1.0+num[j]*w);


      if(Double.isNaN(NLL) && m_Debug){
        System.err.println("???????????2: "+a+" "+b+" "+w+" "+m
            +"|x-: "+xBar[j] + 
            "|n: "+num[j] + "|S^2: "+sSq[j]);
        System.exit(1);
      }

      int halfNum = ((int)num[j])/2;
      for(int z=1; z<=halfNum; z++)
        NLL -= Math.log(0.5*b+0.5*num[j]-(double)z);

      if(0.5*num[j] > halfNum) // num[j] is odd
        NLL -= diffLnGamma(0.5*b);

      if(Double.isNaN(NLL) && m_Debug){
        System.err.println("???????????3: "+a+" "+b+" "+w+" "+m
            +"|x-: "+xBar[j] + 
            "|n: "+num[j] + "|S^2: "+sSq[j]);
        System.exit(1);
      }                         

      NLL -= 0.5*Math.log(a)*b;
      if(Double.isNaN(NLL) && m_Debug){
        System.err.println("???????????4:"+a+" "+b+" "+w+" "+m);
        System.exit(1);
      }     
    }
    if(m_Debug)
      System.err.println("?????????????5: "+NLL);
    if(Double.isNaN(NLL))          
      System.exit(1);

    return NLL;
  }

  /**
   * Subclass should implement this procedure to evaluate gradient
   * of the objective function
   */
  protected double[] evaluateGradient(double[] x){
    double[] g = new double[x.length];
    int numExs = num.length;

    double a=x[0],b=x[1],w=x[2],m=x[3];

    double da=0.0, db=0.0, dw=0.0, dm=0.0; 
    for(int j=0; j < numExs; j++){

      if(Double.isNaN(xBar[j])) continue; // All missing values

      double denorm = (1.0+num[j]*w)*(a+sSq[j]) + 
        num[j]*(xBar[j]-m)*(xBar[j]-m);

      da += 0.5*(b+num[j])*(1.0+num[j]*w)/denorm-0.5*b/a;

      db += 0.5*Math.log(denorm) 
        - 0.5*Math.log(1.0+num[j]*w)
        - 0.5*Math.log(a);

      int halfNum = ((int)num[j])/2;
      for(int z=1; z<=halfNum; z++)
        db -= 1.0/(b+num[j]-2.0*(double)z);             
      if(num[j]/2.0 > halfNum) // num[j] is odd
        db -= 0.5*diffFstDervLnGamma(0.5*b);            

      dw += 0.5*(b+num[j])*(a+sSq[j])*num[j]/denorm -
        0.5*(b+num[j]-1.0)*num[j]/(1.0+num[j]*w);

      dm += num[j]*(b+num[j])*(m-xBar[j])/denorm;
    }

    g[0] = da;
    g[1] = db;
    g[2] = dw;
    g[3] = dm;
    return g;
  }

  /**
   * Subclass should implement this procedure to evaluate second-order
   * gradient of the objective function
   */
  protected double[] evaluateHessian(double[] x, int index){
    double[] h = new double[x.length];

    // # of exemplars, # of dimensions
    // which dimension and which variable for 'index'
    int numExs = num.length;
    double a,b,w,m;
    // Take the 2nd-order derivative
    switch(index){
      case 0:  // a        
        a=x[0];b=x[1];w=x[2];m=x[3];

        for(int j=0; j < numExs; j++){
          if(Double.isNaN(xBar[j])) continue; //All missing values
          double denorm = (1.0+num[j]*w)*(a+sSq[j]) + 
            num[j]*(xBar[j]-m)*(xBar[j]-m);

          h[0] += 0.5*b/(a*a) 
            - 0.5*(b+num[j])*(1.0+num[j]*w)*(1.0+num[j]*w)
            /(denorm*denorm);

          h[1] += 0.5*(1.0+num[j]*w)/denorm - 0.5/a;

          h[2] += 0.5*num[j]*num[j]*(b+num[j])*
            (xBar[j]-m)*(xBar[j]-m)/(denorm*denorm);

          h[3] -= num[j]*(b+num[j])*(m-xBar[j])
            *(1.0+num[j]*w)/(denorm*denorm);
        }
        break;

      case 1: // b      
        a=x[0];b=x[1];w=x[2];m=x[3];

        for(int j=0; j < numExs; j++){
          if(Double.isNaN(xBar[j])) continue; //All missing values
          double denorm = (1.0+num[j]*w)*(a+sSq[j]) + 
            num[j]*(xBar[j]-m)*(xBar[j]-m);

          h[0] += 0.5*(1.0+num[j]*w)/denorm - 0.5/a;

          int halfNum = ((int)num[j])/2;
          for(int z=1; z<=halfNum; z++)
            h[1] += 
              1.0/((b+num[j]-2.0*(double)z)*(b+num[j]-2.0*(double)z));
          if(num[j]/2.0 > halfNum) // num[j] is odd
            h[1] -= 0.25*diffSndDervLnGamma(0.5*b); 

          h[2] += 0.5*(a+sSq[j])*num[j]/denorm -
            0.5*num[j]/(1.0+num[j]*w);

          h[3] += num[j]*(m-xBar[j])/denorm;
        }
        break;

      case 2: // w   
        a=x[0];b=x[1];w=x[2];m=x[3];

        for(int j=0; j < numExs; j++){
          if(Double.isNaN(xBar[j])) continue; //All missing values
          double denorm = (1.0+num[j]*w)*(a+sSq[j]) + 
            num[j]*(xBar[j]-m)*(xBar[j]-m);

          h[0] += 0.5*num[j]*num[j]*(b+num[j])*
            (xBar[j]-m)*(xBar[j]-m)/(denorm*denorm);

          h[1] += 0.5*(a+sSq[j])*num[j]/denorm -
            0.5*num[j]/(1.0+num[j]*w);

          h[2] += 0.5*(b+num[j]-1.0)*num[j]*num[j]/
            ((1.0+num[j]*w)*(1.0+num[j]*w)) -
            0.5*(b+num[j])*(a+sSq[j])*(a+sSq[j])*
            num[j]*num[j]/(denorm*denorm);

          h[3] -= num[j]*num[j]*(b+num[j])*
            (m-xBar[j])*(a+sSq[j])/(denorm*denorm);
        }
        break;

      case 3: // m
        a=x[0];b=x[1];w=x[2];m=x[3];

        for(int j=0; j < numExs; j++){
          if(Double.isNaN(xBar[j])) continue; //All missing values
          double denorm = (1.0+num[j]*w)*(a+sSq[j]) + 
            num[j]*(xBar[j]-m)*(xBar[j]-m);

          h[0] -= num[j]*(b+num[j])*(m-xBar[j])
            *(1.0+num[j]*w)/(denorm*denorm);

          h[1] += num[j]*(m-xBar[j])/denorm;

          h[2] -= num[j]*num[j]*(b+num[j])*
            (m-xBar[j])*(a+sSq[j])/(denorm*denorm);

          h[3] += num[j]*(b+num[j])*
            ((1.0+num[j]*w)*(a+sSq[j])-
             num[j]*(m-xBar[j])*(m-xBar[j]))
            /(denorm*denorm);
        }
    }

    return h;
  }
  
  /**
   * Returns the revision string.
   * 
   * @return            the revision
   */
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 5481 $");
  }
}