bvdecompose.java

一个数据挖掘软件ALPHAMINERR的整个过程的JAVA版源代码

   * @param newClassifier the Classifier to use.
   */
  public void setClassifier(Classifier newClassifier) {

    m_Classifier = newClassifier;
  }

  /**
   * Gets the name of the classifier being analysed
   *
   * @return the classifier being analysed.
   */
  public Classifier getClassifier() {

    return m_Classifier;
  }

  /**
   * Sets debugging mode
   *
   * @param debug true if debug output should be printed
   */
  public void setDebug(boolean debug) {

    m_Debug = debug;
  }

  /**
   * Gets whether debugging is turned on
   *
   * @return true if debugging output is on
   */
  public boolean getDebug() {

    return m_Debug;
  }

  /**
   * Sets the random number seed
   */
  public void setSeed(int seed) {

    m_Seed = seed;
  }

  /**
   * Gets the random number seed
   *
   * @return the random number seed
   */
  public int getSeed() {

    return m_Seed;
  }

  /**
   * Sets the maximum number of boost iterations
   */
  public void setTrainIterations(int trainIterations) {

    m_TrainIterations = trainIterations;
  }

  /**
   * Gets the maximum number of boost iterations
   *
   * @return the maximum number of boost iterations
   */
  public int getTrainIterations() {

    return m_TrainIterations;
  }

  /**
   * Sets the maximum number of boost iterations
   */
  public void setDataFileName(String dataFileName) {

    m_DataFileName = dataFileName;
  }

  /**
   * Get the name of the data file used for the decomposition
   *
   * @return the name of the data file
   */
  public String getDataFileName() {

    return m_DataFileName;
  }

  /**
   * Get the index (starting from 1) of the attribute used as the class.
   *
   * @return the index of the class attribute
   */
  public int getClassIndex() {

    return m_ClassIndex + 1;
  }

  /**
   * Sets index of attribute to discretize on
   *
   * @param index the index (starting from 1) of the class attribute
   */
  public void setClassIndex(int classIndex) {

    m_ClassIndex = classIndex - 1;
  }

  /**
   * Get the calculated bias squared
   *
   * @return the bias squared
   */
  public double getBias() {

    return m_Bias;
  } 

  /**
   * Get the calculated variance
   *
   * @return the variance
   */
  public double getVariance() {

    return m_Variance;
  }

  /**
   * Get the calculated sigma squared
   *
   * @return the sigma squared
   */
  public double getSigma() {

    return m_Sigma;
  }

  /**
   * Get the calculated error rate
   *
   * @return the error rate
   */
  public double getError() {

    return m_Error;
  }

  /**
   * Carry out the bias-variance decomposition
   *
   * @exception Exception if the decomposition couldn't be carried out
   */
  public void decompose() throws Exception {

    Reader dataReader = new BufferedReader(new FileReader(m_DataFileName));
    Instances data = new Instances(dataReader);

    if (m_ClassIndex < 0) {
      data.setClassIndex(data.numAttributes() - 1);
    } else {
      data.setClassIndex(m_ClassIndex);
    }
    if (data.classAttribute().type() != Attribute.NOMINAL) {
      throw new Exception("Class attribute must be nominal");
    }
    int numClasses = data.numClasses();

    data.deleteWithMissingClass();
    if (data.checkForStringAttributes()) {
      throw new Exception("Can't handle string attributes!");
    }

    if (data.numInstances() < 2 * m_TrainPoolSize) {
      throw new Exception("The dataset must contain at least "
			  + (2 * m_TrainPoolSize) + " instances");
    }
    Random random = new Random(m_Seed);
    data.randomize(random);
    Instances trainPool = new Instances(data, 0, m_TrainPoolSize);
    Instances test = new Instances(data, m_TrainPoolSize, 
				   data.numInstances() - m_TrainPoolSize);
    int numTest = test.numInstances();
    double [][] instanceProbs = new double [numTest][numClasses];

    m_Error = 0;
    for (int i = 0; i < m_TrainIterations; i++) {
      if (m_Debug) {
	System.err.println("Iteration " + (i + 1));
      }
      trainPool.randomize(random);
      Instances train = new Instances(trainPool, 0, m_TrainPoolSize / 2);

      m_Classifier.buildClassifier(train);

      //// Evaluate the classifier on test, updating BVD stats
      for (int j = 0; j < numTest; j++) {
	int pred = (int)m_Classifier.classifyInstance(test.instance(j));
	if (pred != test.instance(j).classValue()) {
	  m_Error++;
	}
	instanceProbs[j][pred]++;
      }
    }
    m_Error /= (m_TrainIterations * numTest);

    // Average the BV over each instance in test.
    m_Bias = 0;
    m_Variance = 0;
    m_Sigma = 0;
    for (int i = 0; i < numTest; i++) {
      Instance current = test.instance(i);
      double [] predProbs = instanceProbs[i];
      double pActual, pPred;
      double bsum = 0, vsum = 0, ssum = 0;
      for (int j = 0; j < numClasses; j++) {
	pActual = (current.classValue() == j) ? 1 : 0; // Or via 1NN from test data?
	pPred = predProbs[j] / m_TrainIterations;
	bsum += (pActual - pPred) * (pActual - pPred) 
	- pPred * (1 - pPred) / (m_TrainIterations - 1);
	vsum += pPred * pPred;
	ssum += pActual * pActual;
      }
      m_Bias += bsum;
      m_Variance += (1 - vsum);
      m_Sigma += (1 - ssum);
    }
    m_Bias /= (2 * numTest);
    m_Variance /= (2 * numTest);
    m_Sigma /= (2 * numTest);

    if (m_Debug) {
      System.err.println("Decomposition finished");
    }
  }


  /**
   * Returns description of the bias-variance decomposition results.
   *
   * @return the bias-variance decomposition results as a string
   */
  public String toString() {

    String result = "\nBias-Variance Decomposition\n";

    if (getClassifier() == null) {
      return "Invalid setup";
    }

    result += "\nClassifier   : " + getClassifier().getClass().getName();
    if (getClassifier() instanceof OptionHandler) {
      result += Utils.joinOptions(((OptionHandler)m_Classifier).getOptions());
    }
    result += "\nData File    : " + getDataFileName();
    result += "\nClass Index  : ";
    if (getClassIndex() == 0) {
      result += "last";
    } else {
      result += getClassIndex();
    }
    result += "\nTraining Pool: " + getTrainPoolSize();
    result += "\nIterations   : " + getTrainIterations();
    result += "\nSeed         : " + getSeed();
    result += "\nError        : " + Utils.doubleToString(getError(), 6, 4);
    result += "\nSigma^2      : " + Utils.doubleToString(getSigma(), 6, 4);
    result += "\nBias^2       : " + Utils.doubleToString(getBias(), 6, 4);
    result += "\nVariance     : " + Utils.doubleToString(getVariance(), 6, 4);

    return result + "\n";
  }
  

  /**
   * Test method for this class
   *
   * @param args the command line arguments
   */
  public static void main(String [] args) {

    try {
      BVDecompose bvd = new BVDecompose();

      try {
	bvd.setOptions(args);
	Utils.checkForRemainingOptions(args);
      } catch (Exception ex) {
	String result = ex.getMessage() + "\nBVDecompose Options:\n\n";
	Enumeration em = bvd.listOptions();
	while (em.hasMoreElements()) {
	  Option option = (Option) em.nextElement();
	  result += option.synopsis() + "\n" + option.description() + "\n";
	}
	throw new Exception(result);
      }

      bvd.decompose();
      System.out.println(bvd.toString());
    } catch (Exception ex) {
      System.err.println(ex.getMessage());
    }
  }
}