hillclimber.java

数据挖掘聚类算法：bayes源代码,使用JAVA语言实现

/*
 * 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.
 */

/*
 * HillClimber.java
 * Copyright (C) 2004 University of Waikato, Hamilton, New Zealand
 * 
 */
 
package weka.classifiers.bayes.net.search.local;

import weka.classifiers.bayes.BayesNet;
import weka.classifiers.bayes.net.ParentSet;
import weka.core.Instances;
import weka.core.Option;
import weka.core.RevisionHandler;
import weka.core.RevisionUtils;
import weka.core.Utils;

import java.io.Serializable;
import java.util.Enumeration;
import java.util.Vector;

/** 
 <!-- globalinfo-start -->
 * This Bayes Network learning algorithm uses a hill climbing algorithm adding, deleting and reversing arcs. The search is not restricted by an order on the variables (unlike K2). The difference with B and B2 is that this hill climber also considers arrows part of the naive Bayes structure for deletion.
 * <p/>
 <!-- globalinfo-end -->
 *
 <!-- options-start -->
 * Valid options are: <p/>
 * 
 * <pre> -P &lt;nr of parents&gt;
 *  Maximum number of parents</pre>
 * 
 * <pre> -R
 *  Use arc reversal operation.
 *  (default false)</pre>
 * 
 * <pre> -N
 *  Initial structure is empty (instead of Naive Bayes)</pre>
 * 
 * <pre> -mbc
 *  Applies a Markov Blanket correction to the network structure, 
 *  after a network structure is learned. This ensures that all 
 *  nodes in the network are part of the Markov blanket of the 
 *  classifier node.</pre>
 * 
 * <pre> -S [BAYES|MDL|ENTROPY|AIC|CROSS_CLASSIC|CROSS_BAYES]
 *  Score type (BAYES, BDeu, MDL, ENTROPY and AIC)</pre>
 * 
 <!-- options-end -->
 * 
 * @author Remco Bouckaert ([e-mail])
 * @version $Revision: 1.9 $
 */
public class HillClimber 
    extends LocalScoreSearchAlgorithm {
  
    /** for serialization */
    static final long serialVersionUID = 4322783593818122403L;

	/** the Operation class contains info on operations performed
	 * on the current Bayesian network.
	 */
    class Operation 
    	implements Serializable, RevisionHandler {
      
      	/** for serialization */
        static final long serialVersionUID = -4880888790432547895L;
      
    	// constants indicating the type of an operation
    	final static int OPERATION_ADD = 0;
    	final static int OPERATION_DEL = 1;
    	final static int OPERATION_REVERSE = 2;
    	
    	/** 
    	 * c'tor
    	 */
        public Operation() {
        }
        
		/** c'tor + initializers
		 * 
		 * @param nTail
		 * @param nHead
		 * @param nOperation
		 */ 
	    public Operation(int nTail, int nHead, int nOperation) {
			m_nHead = nHead;
			m_nTail = nTail;
			m_nOperation = nOperation;
		}
		/** compare this operation with another
		 * @param other operation to compare with
		 * @return true if operation is the same
		 */
		public boolean equals(Operation other) {
			if (other == null) {
				return false;
			}
			return ((	m_nOperation == other.m_nOperation) &&
			(m_nHead == other.m_nHead) &&
			(m_nTail == other.m_nTail));
		} // equals
		
		/** number of the tail node **/
        public int m_nTail;
        
		/** number of the head node **/
        public int m_nHead;
        
		/** type of operation (ADD, DEL, REVERSE) **/
        public int m_nOperation;
        
        /** change of score due to this operation **/
        public double m_fDeltaScore = -1E100;
        
        /**
         * Returns the revision string.
         * 
         * @return		the revision
         */
        public String getRevision() {
          return RevisionUtils.extract("$Revision: 1.9 $");
        }
    } // class Operation

	/** cache for remembering the change in score for steps in the search space
	 */
	class Cache implements RevisionHandler {
	  
		/** change in score due to adding an arc **/
		double [] [] m_fDeltaScoreAdd;
		/** change in score due to deleting an arc **/
		double [] [] m_fDeltaScoreDel;
		/** c'tor
		 * @param nNrOfNodes number of nodes in network, used to determine memory size to reserve
		 */
		Cache(int nNrOfNodes) {
			m_fDeltaScoreAdd = new double [nNrOfNodes][nNrOfNodes];
			m_fDeltaScoreDel = new double [nNrOfNodes][nNrOfNodes];
		}

		/** set cache entry
		 * @param oOperation operation to perform
		 * @param fValue value to put in cache
		 */
		public void put(Operation oOperation, double fValue) {
			if (oOperation.m_nOperation == Operation.OPERATION_ADD) {
				m_fDeltaScoreAdd[oOperation.m_nTail][oOperation.m_nHead] = fValue;
			} else {
				m_fDeltaScoreDel[oOperation.m_nTail][oOperation.m_nHead] = fValue;
			}
		} // put

		/** get cache entry
		 * @param oOperation operation to perform
		 * @return cache value
		 */
		public double get(Operation oOperation) {
			switch(oOperation.m_nOperation) {
				case Operation.OPERATION_ADD:
					return m_fDeltaScoreAdd[oOperation.m_nTail][oOperation.m_nHead];
				case Operation.OPERATION_DEL:
					return m_fDeltaScoreDel[oOperation.m_nTail][oOperation.m_nHead];
				case Operation.OPERATION_REVERSE:
				return m_fDeltaScoreDel[oOperation.m_nTail][oOperation.m_nHead] + 
						m_fDeltaScoreAdd[oOperation.m_nHead][oOperation.m_nTail];
			}
			// should never get here
			return 0;
		} // get

		/**
		 * Returns the revision string.
		 * 
		 * @return		the revision
		 */
		public String getRevision() {
		  return RevisionUtils.extract("$Revision: 1.9 $");
		}
	} // class Cache

	/** cache for storing score differences **/
	Cache m_Cache = null;
	
    /** use the arc reversal operator **/
    boolean m_bUseArcReversal = false;
    	

    /**
     * search determines the network structure/graph of the network
     * with the Taby algorithm.
     * 
     * @param bayesNet the network to use
     * @param instances the data to use
     * @throws Exception if something goes wrong
     */
    protected void search(BayesNet bayesNet, Instances instances) throws Exception {
        initCache(bayesNet, instances);

        // go do the search        
		Operation oOperation = getOptimalOperation(bayesNet, instances);
		while ((oOperation != null) && (oOperation.m_fDeltaScore > 0)) {
			performOperation(bayesNet, instances, oOperation);
			oOperation = getOptimalOperation(bayesNet, instances);
        }
        
		// free up memory
		m_Cache = null;
    } // search


	/** 
	 * initCache initializes the cache
	 * 
	 * @param bayesNet Bayes network to be learned
	 * @param instances data set to learn from
	 * @throws Exception if something goes wrong
	 */
    void initCache(BayesNet bayesNet, Instances instances)  throws Exception {
    	
        // determine base scores
		double[] fBaseScores = new double[instances.numAttributes()];
        int nNrOfAtts = instances.numAttributes();

		m_Cache = new Cache (nNrOfAtts);
		
		for (int iAttribute = 0; iAttribute < nNrOfAtts; iAttribute++) {
			updateCache(iAttribute, nNrOfAtts, bayesNet.getParentSet(iAttribute));
		}


        for (int iAttribute = 0; iAttribute < nNrOfAtts; iAttribute++) {
            fBaseScores[iAttribute] = calcNodeScore(iAttribute);
        }

        for (int iAttributeHead = 0; iAttributeHead < nNrOfAtts; iAttributeHead++) {
                for (int iAttributeTail = 0; iAttributeTail < nNrOfAtts; iAttributeTail++) {
                	if (iAttributeHead != iAttributeTail) {
	                    Operation oOperation = new Operation(iAttributeTail, iAttributeHead, Operation.OPERATION_ADD);
	                    m_Cache.put(oOperation, calcScoreWithExtraParent(iAttributeHead, iAttributeTail) - fBaseScores[iAttributeHead]);
					}
            }
        }

    } // initCache

	/** check whether the operation is not in the forbidden.
	 * For base hill climber, there are no restrictions on operations,
	 * so we always return true.
	 * @param oOperation operation to be checked
	 * @return true if operation is not in the tabu list
	 */
	boolean isNotTabu(Operation oOperation) {
		return true;
	} // isNotTabu

	/** 
	 * getOptimalOperation finds the optimal operation that can be performed
	 * on the Bayes network that is not in the tabu list.
	 * 
	 * @param bayesNet Bayes network to apply operation on
	 * @param instances data set to learn from
	 * @return optimal operation found
	 * @throws Exception if something goes wrong
	 */
    Operation getOptimalOperation(BayesNet bayesNet, Instances instances) throws Exception {
        Operation oBestOperation = new Operation();

		// Add???
		oBestOperation = findBestArcToAdd(bayesNet, instances, oBestOperation);
		// Delete???
		oBestOperation = findBestArcToDelete(bayesNet, instances, oBestOperation);
		// Reverse???
		if (getUseArcReversal()) {
			oBestOperation = findBestArcToReverse(bayesNet, instances, oBestOperation);
		}

		// did we find something?
		if (oBestOperation.m_fDeltaScore == -1E100) {
			return null;
		}

        return oBestOperation;
    } // getOptimalOperation

	/** 
	 * performOperation applies an operation 
	 * on the Bayes network and update the cache.
	 * 
	 * @param bayesNet Bayes network to apply operation on
	 * @param instances data set to learn from
	 * @param oOperation operation to perform
	 * @throws Exception if something goes wrong
	 */
	void performOperation(BayesNet bayesNet, Instances instances, Operation oOperation) throws Exception {
		// perform operation
		switch (oOperation.m_nOperation) {
			case Operation.OPERATION_ADD:
				applyArcAddition(bayesNet, oOperation.m_nHead, oOperation.m_nTail, instances);
				if (bayesNet.getDebug()) {
					System.out.print("Add " + oOperation.m_nHead + " -> " + oOperation.m_nTail);
				}
				break;
			case Operation.OPERATION_DEL:
				applyArcDeletion(bayesNet, oOperation.m_nHead, oOperation.m_nTail, instances);
				if (bayesNet.getDebug()) {
					System.out.print("Del " + oOperation.m_nHead + " -> " + oOperation.m_nTail);
				}
				break;
			case Operation.OPERATION_REVERSE:
				applyArcDeletion(bayesNet, oOperation.m_nHead, oOperation.m_nTail, instances);
				applyArcAddition(bayesNet, oOperation.m_nTail, oOperation.m_nHead, instances);
				if (bayesNet.getDebug()) {
					System.out.print("Rev " + oOperation.m_nHead+ " -> " + oOperation.m_nTail);