bayesnet.java

MacroWeka扩展了著名数据挖掘工具weka

                if (iAttribute == m_Instances.classIndex()) {
                    fCount += ((DiscreteEstimatorBayes) m_Distributions[iAttribute][(int) iCPT]).getCount(iClass);
                } else {
                    fCount
                        += ((DiscreteEstimatorBayes) m_Distributions[iAttribute][(int) iCPT]).getCount(
                            instance.value(iAttribute));
                }
            }

            fCounts[iClass] += fCount;
        }
        return fCounts;
    } // countsForInstance

    /**
     * Returns an enumeration describing the available options
     * 
     * @return an enumeration of all the available options
     */
    public Enumeration listOptions() {
        Vector newVector = new Vector(4);

        newVector.addElement(new Option("\tDo not use ADTree data structure\n", "D", 0, "-D"));
        newVector.addElement(new Option("\tBIF file to compare with\n", "B", 1, "-B <BIF file>"));
        newVector.addElement(new Option("\tSearch algorithm\n", "Q", 1, "-Q weka.classifiers.bayes.net.search.SearchAlgorithm"));
        newVector.addElement(new Option("\tEstimator algorithm\n", "E", 1, "-E weka.classifiers.bayes.net.estimate.SimpleEstimator"));

        return newVector.elements();
    } // listOptions

    /**
     * Parses a given list of options. Valid options are:<p>
     * 
     * @param options the list of options as an array of strings
     * @exception Exception if an option is not supported
     */
    public void setOptions(String[] options) throws Exception {
        m_bUseADTree = !(Utils.getFlag('D', options));

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

        String searchAlgorithmName = Utils.getOption('Q', options);
        if (searchAlgorithmName.length() != 0) {
          setSearchAlgorithm(
              (SearchAlgorithm) Utils.forName(
                  SearchAlgorithm.class,
                  searchAlgorithmName,
                  partitionOptions(options)));
        }
        else {
          setSearchAlgorithm(new K2());
        }


        String estimatorName = Utils.getOption('E', options);
        if (estimatorName.length() != 0) {
          setEstimator(
              (BayesNetEstimator) Utils.forName(
                  BayesNetEstimator.class,
                  estimatorName,
                  Utils.partitionOptions(options)));
        }
        else {
          setEstimator(new SimpleEstimator());
        }
        
        Utils.checkForRemainingOptions(options);
    } // setOptions

    /**
     * Returns the secondary set of options (if any) contained in
     * the supplied options array. The secondary set is defined to
     * be any options after the first "--" but before the "-E". These 
     * options are removed from the original options array.
     *
     * @param options the input array of options
     * @return the array of secondary options
     */
    public static String [] partitionOptions(String [] options) {

      for (int i = 0; i < options.length; i++) {
        if (options[i].equals("--")) {
        	// ensure it follows by a -E option
        	int j = i;
			while ((j < options.length) && !(options[j].equals("-E"))) {
			  j++;
			}
			if (j >= options.length) {
				return new String[0];
			}
  	options[i++] = "";
  	String [] result = new String [options.length - i];
	j = i;
  	while ((j < options.length) && !(options[j].equals("-E"))) {
  	  result[j - i] = options[j];
  	  options[j] = "";
	  j++;
  	}
	while(j < options.length) {
  	  result[j - i] = "";
	  j++;
  	}		 
  	return result;
        }
      }
      return new String [0];
    }

    
    /**
     * Gets the current settings of the classifier.
     * 
     * @return an array of strings suitable for passing to setOptions
     */
    public String[] getOptions() {
		String[] searchOptions = m_SearchAlgorithm.getOptions();
		String[] estimatorOptions = m_BayesNetEstimator.getOptions();
        String[] options = new String[11 + searchOptions.length + estimatorOptions.length];
        int current = 0;

        if (!m_bUseADTree) {
            options[current++] = "-D";
        }

        if (m_otherBayesNet != null) {
            options[current++] = "-B";
            options[current++] = ((BIFReader) m_otherBayesNet).getFileName();
        }

        options[current++] = "-Q";
        options[current++] = "" + getSearchAlgorithm().getClass().getName();
		options[current++] = "--";
		for (int iOption = 0; iOption < searchOptions.length; iOption++) {
			options[current++] = searchOptions[iOption];
		}

        options[current++] = "-E";
        options[current++] = "" + getEstimator().getClass().getName();
		options[current++] = "--";
		for (int iOption = 0; iOption < estimatorOptions.length; iOption++) {
			options[current++] = estimatorOptions[iOption];
		}

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

        return options;
    } // getOptions

    /**
    	* Set the SearchAlgorithm used in searching for network structures. 
    	* @param newSearchAlgorithm the SearchAlgorithm to use.
    	*/
    public void setSearchAlgorithm(SearchAlgorithm newSearchAlgorithm) {
        m_SearchAlgorithm = newSearchAlgorithm;
    }

    /**
    	* Get the SearchAlgorithm used as the search algorithm
    	* @return the SearchAlgorithm used as the search algorithm
    	*/
    public SearchAlgorithm getSearchAlgorithm() {
        return m_SearchAlgorithm;
    }

    /**
        * Set the Estimator Algorithm used in calculating the CPTs 
        * @param newEstimator the Estimator to use.
        */
    public void setEstimator(BayesNetEstimator newBayesNetEstimator) {
        m_BayesNetEstimator = newBayesNetEstimator;
    }

    /**
        * Get the BayesNetEstimator used for calculating the CPTs
        * @return the BayesNetEstimator used.
        */
    public BayesNetEstimator getEstimator() {
        return m_BayesNetEstimator;
    }

    /**
     * Set whether ADTree structure is used or not
     * @param bUseADTree
     */
    public void setUseADTree(boolean bUseADTree) {
        m_bUseADTree = bUseADTree;
    }

    /**
     * Method declaration
     * @return whether ADTree structure is used or not
     */
    public boolean getUseADTree() {
        return m_bUseADTree;
    }

    /**
     * Set name of network in BIF file to compare with
     * @param sBIFFile
     */
    public void setBIFFile(String sBIFFile) {
        try {
            m_otherBayesNet = new BIFReader().processFile(sBIFFile);
        } catch (Throwable t) {
            m_otherBayesNet = null;
        }
    }

    /**
     * Get name of network in BIF file to compare with
     * @return BIF file name
     */
    public String getBIFFile() {
        if (m_otherBayesNet != null) {
        	return m_otherBayesNet.getFileName();
        }
        return "";
    }


    /**
     * Returns a description of the classifier.
     * 
     * @return a description of the classifier as a string.
     */
    public String toString() {
        StringBuffer text = new StringBuffer();

        text.append("Bayes Network Classifier");
        text.append("\n" + (m_bUseADTree ? "Using " : "not using ") + "ADTree");

        if (m_Instances == null) {
            text.append(": No model built yet.");
        } else {

            // flatten BayesNet down to text
            text.append("\n#attributes=");
            text.append(m_Instances.numAttributes());
            text.append(" #classindex=");
            text.append(m_Instances.classIndex());
            text.append("\nNetwork structure (nodes followed by parents)\n");

            for (int iAttribute = 0; iAttribute < m_Instances.numAttributes(); iAttribute++) {
                text.append(
                    m_Instances.attribute(iAttribute).name()
                        + "("
                        + m_Instances.attribute(iAttribute).numValues()
                        + "): ");

                for (int iParent = 0; iParent < m_ParentSets[iAttribute].getNrOfParents(); iParent++) {
                    text.append(m_Instances.attribute(m_ParentSets[iAttribute].getParent(iParent)).name() + " ");
                }

                text.append("\n");

                // Description of distributions tends to be too much detail, so it is commented out here
                // for (int iParent = 0; iParent < m_ParentSets[iAttribute].GetCardinalityOfParents(); iParent++) {
                // text.append('(' + m_Distributions[iAttribute][iParent].toString() + ')');
                // }
                // text.append("\n");
            }

			text.append("LogScore Bayes: " + measureBayesScore() + "\n");
			text.append("LogScore BDeu: " + measureBDeuScore() + "\n");
            text.append("LogScore MDL: " + measureMDLScore() + "\n");
            text.append("LogScore ENTROPY: " + measureEntropyScore() + "\n");
            text.append("LogScore AIC: " + measureAICScore() + "\n");

            if (m_otherBayesNet != null) {
                text.append(
                    "Missing: "
                        + m_otherBayesNet.missingArcs(this)
                        + " Extra: "
                        + m_otherBayesNet.extraArcs(this)
                        + " Reversed: "
                        + m_otherBayesNet.reversedArcs(this)
                        + "\n");
                text.append("Divergence: " + m_otherBayesNet.divergence(this) + "\n");
            }
        }

        return text.toString();
    } // toString


  /**
   *  Returns the type of graph this classifier
   *  represents.
   *  @return Drawable.TREE
   */   
  public int graphType() {
	  return Drawable.BayesNet;
  }

  /**
	 Returns a BayesNet graph in XMLBIF ver
	 0.3 format.
	 @return - String representing this
			   BayesNet in XMLBIF ver  0.3
  */
  public String graph() throws Exception {
	  return toXMLBIF03();
  }
       
  /**
   * Returns a description of the classifier in XML BIF 0.3 format.
   * See http://www-2.cs.cmu.edu/~fgcozman/Research/InterchangeFormat/
   * for details on XML BIF.
   * @return an XML BIF 0.3 description of the classifier as a string.
   */
  public String toXMLBIF03() {
    if (m_Instances == null) {
      return("<!--No model built yet-->");
    }
    
    StringBuffer text = new StringBuffer();
    
    text.append("<?xml version=\"1.0\"?>\n");
    text.append("<!-- DTD for the XMLBIF 0.3 format -->\n");
    text.append("<!DOCTYPE BIF [\n");
    text.append("	<!ELEMENT BIF ( NETWORK )*>\n");
    text.append("	      <!ATTLIST BIF VERSION CDATA #REQUIRED>\n");
    text.append("	<!ELEMENT NETWORK ( NAME, ( PROPERTY | VARIABLE | DEFINITION )* )>\n");
    text.append("	<!ELEMENT NAME (#PCDATA)>\n");
    text.append("	<!ELEMENT VARIABLE ( NAME, ( OUTCOME |  PROPERTY )* ) >\n");
    text.append("	      <!ATTLIST VARIABLE TYPE (nature|decision|utility) \"nature\">\n");
    text.append("	<!ELEMENT OUTCOME (#PCDATA)>\n");
    text.append("	<!ELEMENT DEFINITION ( FOR | GIVEN | TABLE | PROPERTY )* >\n");
    text.append("	<!ELEMENT FOR (#PCDATA)>\n");
    text.append("	<!ELEMENT GIVEN (#PCDATA)>\n");
    text.append("	<!ELEMENT TABLE (#PCDATA)>\n");