mdd.java

代码是一个分类器的实现,其中使用了部分weka的源代码。可以将项目导入eclipse运行

    protected double[] evaluateGradient(double[] x){
      double[] grad = new double[x.length];
      for(int i=0; i<m_Classes.length; i++){ // ith bag
        int nI = m_Data[i][0].length; // numInstances in ith bag 

        double denom=0.0;
        double[] numrt = new double[x.length];

        for(int j=0; j<nI; j++){
          double exp=0.0;
          for(int k=0; k<m_Data[i].length; k++)
            exp += (m_Data[i][k][j]-x[k*2])*(m_Data[i][k][j]-x[k*2])/
              (x[k*2+1]*x[k*2+1]);			
          exp = Math.exp(-exp);
          if(m_Classes[i]==1)
            denom += exp;
          else
            denom += (1.0-exp);		   

          // Instance-wise update
          for(int p=0; p<m_Data[i].length; p++){  // pth variable
            numrt[2*p] += exp*2.0*(x[2*p]-m_Data[i][p][j])/
              (x[2*p+1]*x[2*p+1]);
            numrt[2*p+1] += 
              exp*(x[2*p]-m_Data[i][p][j])*(x[2*p]-m_Data[i][p][j])/
              (x[2*p+1]*x[2*p+1]*x[2*p+1]);
          }			
        }

        if(denom <= m_Zero){
          denom = m_Zero;
        }

        // Bag-wise update 
        for(int q=0; q<m_Data[i].length; q++){
          if(m_Classes[i]==1){
            grad[2*q] += numrt[2*q]/denom;
            grad[2*q+1] -= numrt[2*q+1]/denom;
          }else{
            grad[2*q] -= numrt[2*q]/denom;
            grad[2*q+1] += numrt[2*q+1]/denom;
          }
        }
      }

      return grad;
    }
  }

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

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

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

  /**
   * Builds the classifier
   *
   * @param train the training data to be used for generating the
   * boosted classifier.
   * @throws Exception if the classifier could not be built successfully
   */
  public void buildClassifier(Instances train) throws Exception {
    // can classifier handle the data?
    getCapabilities().testWithFail(train);

    // remove instances with missing class
    train = new Instances(train);
    train.deleteWithMissingClass();
    
    m_ClassIndex = train.classIndex();
    m_NumClasses = train.numClasses();

    int nR = train.attribute(1).relation().numAttributes();
    int nC = train.numInstances();
    int [] bagSize=new int [nC];
    Instances datasets= new Instances(train.attribute(1).relation(),0);

    m_Data  = new double [nC][nR][];              // Data values
    m_Classes  = new int [nC];                    // Class values
    m_Attributes = datasets.stringFreeStructure();		
    double sY1=0, sY0=0;                          // Number of classes

    if (m_Debug) {
      System.out.println("Extracting data...");
    }
    FastVector maxSzIdx=new FastVector();
    int maxSz=0;

    for(int h=0; h<nC; h++){
      Instance current = train.instance(h);
      m_Classes[h] = (int)current.classValue();  // Class value starts from 0
      Instances currInsts = current.relationalValue(1);
      int nI = currInsts.numInstances();
      bagSize[h]=nI;

      for (int i=0; i<nI;i++){
        Instance inst=currInsts.instance(i);
        datasets.add(inst);
      }

      if(m_Classes[h]==1){
        if(nI>maxSz){
          maxSz=nI;
          maxSzIdx=new FastVector(1);
          maxSzIdx.addElement(new Integer(h));
        }
        else if(nI == maxSz)
          maxSzIdx.addElement(new Integer(h));
      }
    }

    /* filter the training data */
    if (m_filterType == FILTER_STANDARDIZE)  
      m_Filter = new Standardize();
    else if (m_filterType == FILTER_NORMALIZE)
      m_Filter = new Normalize();
    else 
      m_Filter = null; 

    if (m_Filter!=null) {
      m_Filter.setInputFormat(datasets);
      datasets = Filter.useFilter(datasets, m_Filter); 	
    }

    m_Missing.setInputFormat(datasets);
    datasets = Filter.useFilter(datasets, m_Missing);

    int instIndex=0;
    int start=0;	
    for(int h=0; h<nC; h++)  {	
      for (int i = 0; i < datasets.numAttributes(); i++) {
        // initialize m_data[][][]
        m_Data[h][i] = new double[bagSize[h]];
        instIndex=start;
        for (int k=0; k<bagSize[h]; k++){
          m_Data[h][i][k]=datasets.instance(instIndex).value(i);
          instIndex ++;
        }
      }
      start=instIndex;

      // Class count	
      if (m_Classes[h] == 1)
        sY1++;		
      else
        sY0++;
    }

    if (m_Debug) {
      System.out.println("\nIteration History..." );
    }

    double[] x = new double[nR*2], tmp = new double[x.length];
    double[][] b = new double[2][x.length]; 

    OptEng opt;
    double nll, bestnll = Double.MAX_VALUE;
    for (int t=0; t<x.length; t++){
      b[0][t] = Double.NaN;
      b[1][t] = Double.NaN; 
    }

    // Largest positive exemplar
    for(int s=0; s<maxSzIdx.size(); s++){
      int exIdx = ((Integer)maxSzIdx.elementAt(s)).intValue();
      for(int p=0; p<m_Data[exIdx][0].length; p++){
        for (int q=0; q < nR;q++){
          x[2*q] = m_Data[exIdx][q][p];  // pick one instance
          x[2*q+1] = 1.0;
        }		

        opt = new OptEng();	
        tmp = opt.findArgmin(x, b);
        while(tmp==null){
          tmp = opt.getVarbValues();
          if (m_Debug)
            System.out.println("200 iterations finished, not enough!");
          tmp = opt.findArgmin(tmp, b);
        }
        nll = opt.getMinFunction();

        if(nll < bestnll){
          bestnll = nll;
          m_Par = tmp;
          if (m_Debug)
            System.out.println("!!!!!!!!!!!!!!!!Smaller NLL found: "+nll);
        }
        if (m_Debug)
          System.out.println(exIdx+":  -------------<Converged>--------------");
      }
    }
    }		

  /**
   * Computes the distribution for a given exemplar
   *
   * @param exmp the exemplar for which distribution is computed
   * @return the distribution
   * @throws Exception if the distribution can't be computed successfully
   */
  public double[] distributionForInstance(Instance exmp) 
    throws Exception {

    // Extract the data
    Instances ins = exmp.relationalValue(1);
    if(m_Filter!=null)
      ins = Filter.useFilter(ins, m_Filter);

    ins = Filter.useFilter(ins, m_Missing);

    int nI = ins.numInstances(), nA = ins.numAttributes();
    double[][] dat = new double [nI][nA];
    for(int j=0; j<nI; j++){
      for(int k=0; k<nA; k++){ 
        dat[j][k] = ins.instance(j).value(k);
      }
    }

    // Compute the probability of the bag
    double [] distribution = new double[2];
    distribution[1]=0.0;  // Prob. for class 1

    for(int i=0; i<nI; i++){
      double exp = 0.0;
      for(int r=0; r<nA; r++)
        exp += (m_Par[r*2]-dat[i][r])*(m_Par[r*2]-dat[i][r])/
          ((m_Par[r*2+1])*(m_Par[r*2+1]));
      exp = Math.exp(-exp);

      // Prob. updated for one instance
      distribution[1] += exp/(double)nI;
      distribution[0] += (1.0-exp)/(double)nI;
    }

    return distribution;
  }

  /**
   * Gets a string describing the classifier.
   *
   * @return a string describing the classifer built.
   */
  public String toString() {

    String result = "Modified Logistic Regression";
    if (m_Par == null) {
      return result + ": No model built yet.";
    }

    result += "\nCoefficients...\n"
      + "Variable      Coeff.\n";
    for (int j = 0, idx=0; j < m_Par.length/2; j++, idx++) {

      result += m_Attributes.attribute(idx).name();
      result += " "+Utils.doubleToString(m_Par[j*2], 12, 4); 
      result += " "+Utils.doubleToString(m_Par[j*2+1], 12, 4)+"\n";
    }

    return result;
  }

  /**
   * Main method for testing this class.
   *
   * @param argv should contain the command line arguments to the
   * scheme (see Evaluation)
   */
  public static void main(String[] argv) {
    runClassifier(new MDD(), argv);
  }
}