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• BayesNetGenerator.java

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weka.classifiers.bayes.net.BayesNetGenerator Maven / Gradle / Ivy

/*
 *   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 .
 */

/*
 * BayesNet.java
 * Copyright (C) 2003-2012 University of Waikato, Hamilton, New Zealand
 * 
 */

package weka.classifiers.bayes.net;

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

import weka.classifiers.bayes.net.estimate.DiscreteEstimatorBayes;
import weka.core.Attribute;
import weka.core.DenseInstance;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.Utils;
import weka.estimators.Estimator;

/**
 *  Bayes Network learning using various search
 * algorithms and quality measures.

 * Base class for a Bayes Network classifier. Provides datastructures (network
 * structure, conditional probability distributions, etc.) and facilities common
 * to Bayes Network learning algorithms like K2 and B.

 * 

 * For more information see:

 * 

 * http://www.cs.waikato.ac.nz/~remco/weka.pdf
 * 

 * 
 * 
 *  Valid options are:
 * 

 * 
 * 
 * -B
 *  Generate network (instead of instances)
 * 
 * 
 * 
 * -N <integer>
 *  Nr of nodes
 * 
 * 
 * 
 * -A <integer>
 *  Nr of arcs
 * 
 * 
 * 
 * -M <integer>
 *  Nr of instances
 * 
 * 
 * 
 * -C <integer>
 *  Cardinality of the variables
 * 
 * 
 * 
 * -S <integer>
 *  Seed for random number generator
 * 
 * 
 * 
 * -F <file>
 *  The BIF file to obtain the structure from.
 * 
 * 
 * 
 * 
 * @author Remco Bouckaert ([email protected])
 * @version $Revision: 10153 $
 */
public class BayesNetGenerator extends EditableBayesNet {
  /** the seed value */
  int m_nSeed = 1;

  /** the random number generator */
  Random random;

  /** for serialization */
  static final long serialVersionUID = -7462571170596157720L;

  /**
   * Constructor for BayesNetGenerator.
   */
  public BayesNetGenerator() {
    super();
  } // c'tor

  /**
   * Generate random connected Bayesian network with discrete nodes having all
   * the same cardinality.
   * 
   * @throws Exception if something goes wrong
   */
  public void generateRandomNetwork() throws Exception {
    if (m_otherBayesNet == null) {
      // generate from scratch
      Init(m_nNrOfNodes, m_nCardinality);
      generateRandomNetworkStructure(m_nNrOfNodes, m_nNrOfArcs);
      generateRandomDistributions(m_nNrOfNodes, m_nCardinality);
    } else {
      // read from file, just copy parent sets and distributions
      m_nNrOfNodes = m_otherBayesNet.getNrOfNodes();
      m_ParentSets = m_otherBayesNet.getParentSets();
      m_Distributions = m_otherBayesNet.getDistributions();

      random = new Random(m_nSeed);
      // initialize m_Instances
      ArrayList attInfo = new ArrayList(m_nNrOfNodes);
      // generate value strings

      for (int iNode = 0; iNode < m_nNrOfNodes; iNode++) {
        int nValues = m_otherBayesNet.getCardinality(iNode);
        ArrayList nomStrings = new ArrayList(nValues + 1);
        for (int iValue = 0; iValue < nValues; iValue++) {
          nomStrings.add(m_otherBayesNet.getNodeValue(iNode, iValue));
        }
        Attribute att = new Attribute(m_otherBayesNet.getNodeName(iNode),
          nomStrings);
        attInfo.add(att);
      }

      m_Instances = new Instances(m_otherBayesNet.getName(), attInfo, 100);
      m_Instances.setClassIndex(m_nNrOfNodes - 1);
    }
  } // GenerateRandomNetwork

  /**
   * Init defines a minimal Bayes net with no arcs
   * 
   * @param nNodes number of nodes in the Bayes net
   * @param nValues number of values each of the nodes can take
   * @throws Exception if something goes wrong
   */
  public void Init(int nNodes, int nValues) throws Exception {
    random = new Random(m_nSeed);
    // initialize structure
    ArrayList attInfo = new ArrayList(nNodes);
    // generate value strings
    ArrayList nomStrings = new ArrayList(nValues + 1);
    for (int iValue = 0; iValue < nValues; iValue++) {
      nomStrings.add("Value" + (iValue + 1));
    }

    for (int iNode = 0; iNode < nNodes; iNode++) {
      Attribute att = new Attribute("Node" + (iNode + 1), nomStrings);
      attInfo.add(att);
    }
    m_Instances = new Instances("RandomNet", attInfo, 100);
    m_Instances.setClassIndex(nNodes - 1);
    setUseADTree(false);
    // m_bInitAsNaiveBayes = false;
    // m_bMarkovBlanketClassifier = false;
    initStructure();

    // initialize conditional distribution tables
    m_Distributions = new Estimator[nNodes][1];
    for (int iNode = 0; iNode < nNodes; iNode++) {
      m_Distributions[iNode][0] = new DiscreteEstimatorBayes(nValues,
        getEstimator().getAlpha());
    }
    m_nEvidence = new ArrayList(nNodes);
    for (int i = 0; i < nNodes; i++) {
      m_nEvidence.add(-1);
    }
    m_fMarginP = new ArrayList(nNodes);
    for (int i = 0; i < nNodes; i++) {
      double[] P = new double[getCardinality(i)];
      m_fMarginP.add(P);
    }

    m_nPositionX = new ArrayList(nNodes);
    m_nPositionY = new ArrayList(nNodes);
    for (int iNode = 0; iNode < nNodes; iNode++) {
      m_nPositionX.add(iNode % 10 * 50);
      m_nPositionY.add((iNode / 10) * 50);
    }
  } // DefineNodes

  /**
   * GenerateRandomNetworkStructure generate random connected Bayesian network
   * 
   * @param nNodes number of nodes in the Bayes net to generate
   * @param nArcs number of arcs to generate. Must be between nNodes - 1 and
   *          nNodes * (nNodes-1) / 2
   * @throws Exception if number of arcs is incorrect
   */
  public void generateRandomNetworkStructure(int nNodes, int nArcs)
    throws Exception {
    if (nArcs < nNodes - 1) {
      throw new Exception("Number of arcs should be at least (nNodes - 1) = "
        + (nNodes - 1) + " instead of " + nArcs);
    }
    if (nArcs > nNodes * (nNodes - 1) / 2) {
      throw new Exception(
        "Number of arcs should be at most nNodes * (nNodes - 1) / 2 = "
          + (nNodes * (nNodes - 1) / 2) + " instead of " + nArcs);
    }
    if (nArcs == 0) {
      return;
    } // deal with patalogical case for nNodes = 1

    // first generate tree connecting all nodes
    generateTree(nNodes);
    // The tree contains nNodes - 1 arcs, so there are
    // nArcs - (nNodes-1) to add at random.
    // All arcs point from lower to higher ordered nodes
    // so that acyclicity is ensured.
    for (int iArc = nNodes - 1; iArc < nArcs; iArc++) {
      boolean bDone = false;
      while (!bDone) {
        int nNode1 = random.nextInt(nNodes);
        int nNode2 = random.nextInt(nNodes);
        if (nNode1 == nNode2) {
          nNode2 = (nNode1 + 1) % nNodes;
        }
        if (nNode2 < nNode1) {
          int h = nNode1;
          nNode1 = nNode2;
          nNode2 = h;
        }
        if (!m_ParentSets[nNode2].contains(nNode1)) {
          m_ParentSets[nNode2].addParent(nNode1, m_Instances);
          bDone = true;
        }
      }
    }

  } // GenerateRandomNetworkStructure

  /**
   * GenerateTree creates a tree-like network structure (actually a forest) by
   * starting with a randomly selected pair of nodes, add an arc between. Then
   * keep on selecting one of the connected nodes and one of the unconnected
   * ones and add an arrow between them, till all nodes are connected.
   * 
   * @param nNodes number of nodes in the Bayes net to generate
   */
  void generateTree(int nNodes) {
    boolean[] bConnected = new boolean[nNodes];
    // start adding an arc at random
    int nNode1 = random.nextInt(nNodes);
    int nNode2 = random.nextInt(nNodes);
    if (nNode1 == nNode2) {
      nNode2 = (nNode1 + 1) % nNodes;
    }
    if (nNode2 < nNode1) {
      int h = nNode1;
      nNode1 = nNode2;
      nNode2 = h;
    }
    m_ParentSets[nNode2].addParent(nNode1, m_Instances);
    bConnected[nNode1] = true;
    bConnected[nNode2] = true;
    // Repeatedly, select one of the connected nodes, and one of
    // the unconnected nodes and add an arc.
    // All arcs point from lower to higher ordered nodes
    // so that acyclicity is ensured.
    for (int iArc = 2; iArc < nNodes; iArc++) {
      int nNode = random.nextInt(nNodes);
      nNode1 = 0; // one of the connected nodes
      while (nNode >= 0) {
        nNode1 = (nNode1 + 1) % nNodes;
        while (!bConnected[nNode1]) {
          nNode1 = (nNode1 + 1) % nNodes;
        }
        nNode--;
      }
      nNode = random.nextInt(nNodes);
      nNode2 = 0; // one of the unconnected nodes
      while (nNode >= 0) {
        nNode2 = (nNode2 + 1) % nNodes;
        while (bConnected[nNode2]) {
          nNode2 = (nNode2 + 1) % nNodes;
        }
        nNode--;
      }
      if (nNode2 < nNode1) {
        int h = nNode1;
        nNode1 = nNode2;
        nNode2 = h;
      }
      m_ParentSets[nNode2].addParent(nNode1, m_Instances);
      bConnected[nNode1] = true;
      bConnected[nNode2] = true;
    }
  } // GenerateTree

  /**
   * GenerateRandomDistributions generates discrete conditional distribution
   * tables for all nodes of a Bayes network once a network structure has been
   * determined.
   * 
   * @param nNodes number of nodes in the Bayes net
   * @param nValues number of values each of the nodes can take
   */
  void generateRandomDistributions(int nNodes, int nValues) {
    // Reserve space for CPTs
    int nMaxParentCardinality = 1;
    for (int iAttribute = 0; iAttribute < nNodes; iAttribute++) {
      if (m_ParentSets[iAttribute].getCardinalityOfParents() > nMaxParentCardinality) {
        nMaxParentCardinality = m_ParentSets[iAttribute]
          .getCardinalityOfParents();
      }
    }

    // Reserve plenty of memory
    m_Distributions = new Estimator[m_Instances.numAttributes()][nMaxParentCardinality];

    // estimate CPTs
    for (int iAttribute = 0; iAttribute < nNodes; iAttribute++) {
      int[] nPs = new int[nValues + 1];
      nPs[0] = 0;
      nPs[nValues] = 1000;
      for (int iParent = 0; iParent < m_ParentSets[iAttribute]
        .getCardinalityOfParents(); iParent++) {
        // fill array with random nr's
        for (int iValue = 1; iValue < nValues; iValue++) {
          nPs[iValue] = random.nextInt(1000);
        }
        // sort
        for (int iValue = 1; iValue < nValues; iValue++) {
          for (int iValue2 = iValue + 1; iValue2 < nValues; iValue2++) {
            if (nPs[iValue2] < nPs[iValue]) {
              int h = nPs[iValue2];
              nPs[iValue2] = nPs[iValue];
              nPs[iValue] = h;
            }
          }
        }
        // assign to probability tables
        DiscreteEstimatorBayes d = new DiscreteEstimatorBayes(nValues,
          getEstimator().getAlpha());
        for (int iValue = 0; iValue < nValues; iValue++) {
          d.addValue(iValue, nPs[iValue + 1] - nPs[iValue]);
        }
        m_Distributions[iAttribute][iParent] = d;
      }
    }
  } // GenerateRandomDistributions

  /**
   * GenerateInstances generates random instances sampling from the distribution
   * represented by the Bayes network structure. It assumes a Bayes network
   * structure has been initialized
   * 
   * @throws Exception if something goes wrong
   */
  public void generateInstances() throws Exception {
    int[] order = getOrder();
    for (int iInstance = 0; iInstance < m_nNrOfInstances; iInstance++) {
      int nNrOfAtts = m_Instances.numAttributes();
      Instance instance = new DenseInstance(nNrOfAtts);
      instance.setDataset(m_Instances);
      for (int iAtt2 = 0; iAtt2 < nNrOfAtts; iAtt2++) {
        int iAtt = order[iAtt2];

        double iCPT = 0;

        for (int iParent = 0; iParent < m_ParentSets[iAtt].getNrOfParents(); iParent++) {
          int nParent = m_ParentSets[iAtt].getParent(iParent);
          iCPT = iCPT * m_Instances.attribute(nParent).numValues()
            + instance.value(nParent);
        }

        double fRandom = random.nextInt(1000) / 1000.0f;
        int iValue = 0;
        while (fRandom > m_Distributions[iAtt][(int) iCPT]
          .getProbability(iValue)) {
          fRandom = fRandom
            - m_Distributions[iAtt][(int) iCPT].getProbability(iValue);
          iValue++;
        }
        instance.setValue(iAtt, iValue);
      }
      m_Instances.add(instance);
    }
  } // GenerateInstances

  /**
   * @throws Exception if there's a cycle in the graph
   */
  int[] getOrder() throws Exception {
    int nNrOfAtts = m_Instances.numAttributes();
    int[] order = new int[nNrOfAtts];
    boolean[] bDone = new boolean[nNrOfAtts];
    for (int iAtt = 0; iAtt < nNrOfAtts; iAtt++) {
      int iAtt2 = 0;
      boolean allParentsDone = false;
      while (!allParentsDone && iAtt2 < nNrOfAtts) {
        if (!bDone[iAtt2]) {
          allParentsDone = true;
          int iParent = 0;
          while (allParentsDone
            && iParent < m_ParentSets[iAtt2].getNrOfParents()) {
            allParentsDone = bDone[m_ParentSets[iAtt2].getParent(iParent++)];
          }
          if (allParentsDone && iParent == m_ParentSets[iAtt2].getNrOfParents()) {
            order[iAtt] = iAtt2;
            bDone[iAtt2] = true;
          } else {
            iAtt2++;
          }
        } else {
          iAtt2++;
        }
      }
      if (!allParentsDone && iAtt2 == nNrOfAtts) {
        throw new Exception("There appears to be a cycle in the graph");
      }
    }
    return order;
  } // getOrder

  /**
   * Returns either the net (if BIF format) or the generated instances
   * 
   * @return either the net or the generated instances
   */
  @Override
  public String toString() {
    if (m_bGenerateNet) {
      return toXMLBIF03();
    }
    return m_Instances.toString();
  } // toString

  boolean m_bGenerateNet = false;
  int m_nNrOfNodes = 10;
  int m_nNrOfArcs = 10;
  int m_nNrOfInstances = 10;
  int m_nCardinality = 2;
  String m_sBIFFile = "";

  void setNrOfNodes(int nNrOfNodes) {
    m_nNrOfNodes = nNrOfNodes;
  }

  void setNrOfArcs(int nNrOfArcs) {
    m_nNrOfArcs = nNrOfArcs;
  }

  void setNrOfInstances(int nNrOfInstances) {
    m_nNrOfInstances = nNrOfInstances;
  }

  void setCardinality(int nCardinality) {
    m_nCardinality = nCardinality;
  }

  void setSeed(int nSeed) {
    m_nSeed = nSeed;
  }

  /**
   * Returns an enumeration describing the available options
   * 
   * @return an enumeration of all the available options
   */
  @Override
  public Enumeration listOptions() {
    Vector newVector = new Vector(6);

    newVector.addElement(new Option(
      "\tGenerate network (instead of instances)\n", "B", 0, "-B"));
    newVector.addElement(new Option("\tNr of nodes\n", "N", 1, "-N "));
    newVector.addElement(new Option("\tNr of arcs\n", "A", 1, "-A "));
    newVector.addElement(new Option("\tNr of instances\n", "M", 1,
      "-M "));
    newVector.addElement(new Option("\tCardinality of the variables\n", "C", 1,
      "-C "));
    newVector.addElement(new Option("\tSeed for random number generator\n",
      "S", 1, "-S "));
    newVector.addElement(new Option(
      "\tThe BIF file to obtain the structure from.\n", "F", 1, "-F "));

    return newVector.elements();
  } // listOptions

  /**
   * Parses a given list of options.
   * 

   * 
   *  Valid options are:
   * 

   * 
   * 
   * -B
   *  Generate network (instead of instances)
   * 
   * 
   * 
   * -N <integer>
   *  Nr of nodes
   * 
   * 
   * 
   * -A <integer>
   *  Nr of arcs
   * 
   * 
   * 
   * -M <integer>
   *  Nr of instances
   * 
   * 
   * 
   * -C <integer>
   *  Cardinality of the variables
   * 
   * 
   * 
   * -S <integer>
   *  Seed for random number generator
   * 
   * 
   * 
   * -F <file>
   *  The BIF file to obtain the structure from.
   * 
   * 
   * 
   * 
   * @param options the list of options as an array of strings
   * @exception Exception if an option is not supported
   */
  @Override
  public void setOptions(String[] options) throws Exception {
    m_bGenerateNet = Utils.getFlag('B', options);

    String sNrOfNodes = Utils.getOption('N', options);
    if (sNrOfNodes.length() != 0) {
      setNrOfNodes(Integer.parseInt(sNrOfNodes));
    } else {
      setNrOfNodes(10);
    }

    String sNrOfArcs = Utils.getOption('A', options);
    if (sNrOfArcs.length() != 0) {
      setNrOfArcs(Integer.parseInt(sNrOfArcs));
    } else {
      setNrOfArcs(10);
    }

    String sNrOfInstances = Utils.getOption('M', options);
    if (sNrOfInstances.length() != 0) {
      setNrOfInstances(Integer.parseInt(sNrOfInstances));
    } else {
      setNrOfInstances(10);
    }

    String sCardinality = Utils.getOption('C', options);
    if (sCardinality.length() != 0) {
      setCardinality(Integer.parseInt(sCardinality));
    } else {
      setCardinality(2);
    }

    String sSeed = Utils.getOption('S', options);
    if (sSeed.length() != 0) {
      setSeed(Integer.parseInt(sSeed));
    } else {
      setSeed(1);
    }

    String sBIFFile = Utils.getOption('F', options);
    if ((sBIFFile != null) && (sBIFFile != "")) {
      setBIFFile(sBIFFile);
    }
  } // setOptions

  /**
   * Gets the current settings of the classifier.
   * 
   * @return an array of strings suitable for passing to setOptions
   */
  @Override
  public String[] getOptions() {
    String[] options = new String[13];
    int current = 0;
    if (m_bGenerateNet) {
      options[current++] = "-B";
    }

    options[current++] = "-N";
    options[current++] = "" + m_nNrOfNodes;

    options[current++] = "-A";
    options[current++] = "" + m_nNrOfArcs;

    options[current++] = "-M";
    options[current++] = "" + m_nNrOfInstances;

    options[current++] = "-C";
    options[current++] = "" + m_nCardinality;

    options[current++] = "-S";
    options[current++] = "" + m_nSeed;

    if (m_sBIFFile.length() != 0) {
      options[current++] = "-F";
      options[current++] = "" + m_sBIFFile;
    }

    // Fill up rest with empty strings, not nulls!
    while (current < options.length) {
      options[current++] = "";
    }

    return options;
  } // getOptions

  /**
   * prints all the options to stdout
   */
  protected static void printOptions(OptionHandler o) {
    Enumeration enm = o.listOptions();

    System.out.println("Options for " + o.getClass().getName() + ":\n");

    while (enm.hasMoreElements()) {
      Option option = enm.nextElement();
      System.out.println(option.synopsis());
      System.out.println(option.description());
    }
  }

  /**
   * Returns the revision string.
   * 
   * @return the revision
   */
  @Override
  public String getRevision() {
    return RevisionUtils.extract("$Revision: 10153 $");
  }

  /**
   * Main method
   * 
   * @param args the commandline parameters
   */
  static public void main(String[] args) {
    BayesNetGenerator b = new BayesNetGenerator();
    try {
      if ((args.length == 0) || (Utils.getFlag('h', args))) {
        printOptions(b);
        return;
      }
      b.setOptions(args);

      b.generateRandomNetwork();
      if (!b.m_bGenerateNet) { // skip if not required
        b.generateInstances();
      }
      System.out.println(b.toString());
    } catch (Exception e) {
      e.printStackTrace();
      printOptions(b);
    }
  } // main

} // class BayesNetGenerator