edu.duke.cs.banjo.utility
Class InfluenceScorer

java.lang.Object
  extended byedu.duke.cs.banjo.utility.InfluenceScorer

public class InfluenceScorer
extends java.lang.Object

Computes the influence score for all the edges in a network, based on the work of Jing Yu and Alexander Hartemink, as published in Yu, et al., Bioinformatics (2004).

Details:

Change History:
Created on May 10, 2005

9/2/2005 (v1.0.2) hjs Change mapping of configuration indexes, between "counting" and "voting" code (defect correction) 11/10/2005 (v2.0) hjs Use computed maxValueCount instead of max. allowed value.

Author:
Jurgen Sladeczek (hjs)
For the latest info, please visit www.cs.duke.edu.

Field Summary
protected  double alpha
           
protected  double[] alpha_ij
           
protected  double[] alpha_ijk
           
protected  double checkBestNetworkScore
           
protected  double[] cum_ij
           
protected  double[][] cum_ijk
           
protected  int maxMarkovLag
           
(package private)  int maxParentConfigs
           
(package private)  int maxParentCount
           
protected  int maxValueCount
           
protected  int minMarkovLag
           
protected  int[] N_ij
           
protected  int[][] N_ijk
           
protected  int observationCount
           
protected  ObservationsAsMatrix observations
           
(package private)  Settings processData
           
protected  double scoreDiff
           
protected  double[] Theta_ij
           
protected  double[][] Theta_ijk
           
protected  double unreachableBDeScore
           
protected  int varCount
           
 
Constructor Summary
InfluenceScorer(BayesNetStructureI _bayesNetStructure, Settings _processData)
           
 
Method Summary
 java.lang.StringBuffer computeInfluenceScoreForNode(EdgesI _edges, int _currentNodeID)
           
 java.lang.StringBuffer computeInfluenceScores(BayesNetStructureI _bayesNetStructure)
           
private  boolean validateRequiredData()
          Validates the settings values required for the influence scorer.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

varCount

protected final int varCount

minMarkovLag

protected final int minMarkovLag

maxMarkovLag

protected final int maxMarkovLag

observationCount

protected final int observationCount

maxParentCount

final int maxParentCount

maxParentConfigs

final int maxParentConfigs

observations

protected ObservationsAsMatrix observations

alpha

protected final double alpha

maxValueCount

protected final int maxValueCount

N_ij

protected int[] N_ij

N_ijk

protected int[][] N_ijk

Theta_ij

protected double[] Theta_ij

Theta_ijk

protected double[][] Theta_ijk

alpha_ij

protected double[] alpha_ij

alpha_ijk

protected double[] alpha_ijk

cum_ij

protected double[] cum_ij

cum_ijk

protected double[][] cum_ijk

processData

Settings processData

scoreDiff

protected final double scoreDiff
See Also:
Constant Field Values

unreachableBDeScore

protected final double unreachableBDeScore
See Also:
Constant Field Values

checkBestNetworkScore

protected double checkBestNetworkScore
Constructor Detail

InfluenceScorer

public InfluenceScorer(BayesNetStructureI _bayesNetStructure,
                       Settings _processData)
                throws java.lang.Exception
Method Detail

computeInfluenceScores

public java.lang.StringBuffer computeInfluenceScores(BayesNetStructureI _bayesNetStructure)
                                              throws java.lang.Exception
Throws:
java.lang.Exception

computeInfluenceScoreForNode

public java.lang.StringBuffer computeInfluenceScoreForNode(EdgesI _edges,
                                                           int _currentNodeID)
                                                    throws java.lang.Exception
Throws:
java.lang.Exception

validateRequiredData

private boolean validateRequiredData()
                              throws java.lang.Exception
Validates the settings values required for the influence scorer.

Returns:
Returns the boolean flag that indicates whether a crucial setting could not be validated.
Throws:
java.lang.Exception