Package edu.cmu.tetrad.search.score

Class BdeScore

java.lang.Object

edu.cmu.tetrad.search.score.BdeScore

All Implemented Interfaces:

DiscreteScore, Score

public class BdeScore
extends Object
implements DiscreteScore

Calculates the BDe score (Bayes Dirichlet Equivalent) score for analyzing discrete multinomial data. A good discussion of BD* scores can be found here:

Heckerman, D., Geiger, D. & Chickering, D.M. Learning Bayesian networks: The combination of knowledge and statistical data. Mach Learn 20, 197–243 (1995).

As for all scores in Tetrad, higher scores mean more dependence, and negative scores indicate independence.

Version:

$Id: $Id

Author:

josephramsey

See Also:

• BdeuScore

Constructor Summary

Constructors

Constructor	Description
BdeScore(DataSet dataSet)	Constructs a BDe score for the given dataset.

Method Summary

Modifier and Type	Method	Description
DataSet	getDataSet()	Returns the DataSet associated with this method.
int	getMaxDegree()	Gets the maximum degree of the BDe Score.
int	getSampleSize()	Returns the sample size of the data set.
List<Node>	getVariables()	Returns the variables present in the DataSet associated with this method.
boolean	isEffectEdge(double bump)	Determines if an edge has an effect.
double	localScore(int i, int[] parents)	Returns the score for the given parent given its parents, where these are specified as column indices into the dataset.
double	localScoreDiff(int x, int y, int[] z)	Returns the score difference of the graph.
void	setSamplePrior(double samplePrior)	Sets the sample prior for the BDe score.
void	setStructurePrior(double structurePrior)	Sets the structure prior for the BDe score.
String	toString()	Returns a string representation of the object.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.cmu.tetrad.search.score.Score

append, determines, getVariable, localScore, localScore, localScoreDiff

Constructor Details

BdeScore

public BdeScore(DataSet dataSet)

Constructs a BDe score for the given dataset.

Parameters:

dataSet - A discrete dataset.

Method Details

localScore

public double localScore(int i,
 int[] parents)

Returns the score for the given parent given its parents, where these are specified as column indices into the dataset.

Specified by:

localScore in interface Score

Parameters:

i - The index of the variable.

parents - The indices of the parents of the variables.

Returns:

the score, or NaN if the score can't be calculated.

localScoreDiff

public double localScoreDiff(int x,
 int y,
 int[] z)

Returns the score difference of the graph.

Returns the difference between localScore(y | z, x) and localScore(y | z)

Specified by:

localScoreDiff in interface Score

Parameters:

x - A node.

y - TAhe node.

z - A set of nodes.

Returns:

The score difference.

getDataSet

public DataSet getDataSet()

Returns the DataSet associated with this method.

Specified by:

getDataSet in interface DiscreteScore

Returns:

The DataSet object.

setStructurePrior

public void setStructurePrior(double structurePrior)

Sets the structure prior for the BDe score.

Specified by:

setStructurePrior in interface DiscreteScore

Parameters:

structurePrior - The structure prior value.

setSamplePrior

public void setSamplePrior(double samplePrior)

Sets the sample prior for the BDe score.

Specified by:

setSamplePrior in interface DiscreteScore

Parameters:

samplePrior - The sample prior value.

getVariables

public List<Node> getVariables()

Returns the variables present in the DataSet associated with this method.

Specified by:

getVariables in interface Score

Returns:

A list of Node objects representing the variables.

getSampleSize

public int getSampleSize()

Returns the sample size of the data set.

Specified by:

getSampleSize in interface Score

Returns:

The sample size.

isEffectEdge

public boolean isEffectEdge(double bump)

Determines if an edge has an effect.

Specified by:

isEffectEdge in interface Score

Parameters:

bump - The bump value.

Returns:

true if the bump value is greater than -20, false otherwise.

getMaxDegree

public int getMaxDegree()

Gets the maximum degree of the BDe Score.

Specified by:

getMaxDegree in interface Score

Returns:

The maximum degree.

toString

public String toString()

Returns a string representation of the object.

Specified by:

toString in interface Score

Overrides:

toString in class Object

Returns:

A string representation of the object.