A B C D E F G H I J L M N O P Q R S T U V W

A

AttributeSpecs - class jbnc.dataset.AttributeSpecs.

Describes a single attribute/feature in a data set.

AttributeSpecs() - Constructor for class jbnc.dataset.AttributeSpecs

By default created attribute with type IGNORE.

AttributeSpecs(String, AttributeType) - Constructor for class jbnc.dataset.AttributeSpecs

Can create attribute with type CONTINUOUS or IGNORE.

AttributeSpecs(String, String[]) - Constructor for class jbnc.dataset.AttributeSpecs

Creates a DISCRETE attribute.

AttributeSpecs(String, int) - Constructor for class jbnc.dataset.AttributeSpecs

Creates a disctete attribute with n states (DISCRETE_N).

AttributeSpecs.AttributeException - exception jbnc.dataset.AttributeSpecs.AttributeException.

Exception specific to the AttributeSpecs class.

AttributeSpecs.AttributeException() - Constructor for class jbnc.dataset.AttributeSpecs.AttributeException

Constructor for the AttributeException object.

AttributeSpecs.AttributeException(String) - Constructor for class jbnc.dataset.AttributeSpecs.AttributeException

Constructor for the AttributeException object.

AttributeType - class jbnc.dataset.AttributeType.

Types of values represented by an attribute.

Augmenter - class jbnc.operators.Augmenter.

Abstract BNC Augmenter operator.

Augmenter() - Constructor for class jbnc.operators.Augmenter

Augmenter.Result - class jbnc.operators.Augmenter.Result.

Augmenter.Result() - Constructor for class jbnc.operators.Augmenter.Result

addCase(int[]) - Method in class jbnc.util.FrequencyTable

Adds a feature to the Case attribute of the FrequencyTable object

addEdge(Vertex, Vertex) - Method in class jbnc.graphs.Graph

addEdge(Edge) - Method in class jbnc.graphs.Graph

addVertex(Vertex) - Method in class jbnc.graphs.Graph

algorithmName - Variable in class jbnc.Classifier

alphaK - Variable in class jbnc.measures.QualityMeasure

Value of the prior.

attribNodes - Variable in class jbnc.util.BNCTester

B

BNCInference - class jbnc.graphs.BNCInference.

Efficient calculation of the joint probability distribution and and conditional probability of the class variable given values of all attributes.

BNCInference(BayesNet) - Constructor for class jbnc.graphs.BNCInference

BNCTester - class jbnc.util.BNCTester.

Description of the Class

BNCTester() - Constructor for class jbnc.util.BNCTester

BNCTester.Result - class jbnc.util.BNCTester.Result.

BNCTester.Result(int, int) - Constructor for class jbnc.util.BNCTester.Result

Constructor for the Result object

BNTools - class jbnc.util.BNTools.

Utilities for Bayesian networks.

BNTools() - Constructor for class jbnc.util.BNTools

BayesianInducer - class jbnc.inducers.BayesianInducer.

Abstract class for Bayesian network inducers.

BayesianInducer() - Constructor for class jbnc.inducers.BayesianInducer

BayesianInducer.NetLayout - class jbnc.inducers.BayesianInducer.NetLayout.

Network layout.

BayesianInducer.NetLayout() - Constructor for class jbnc.inducers.BayesianInducer.NetLayout

bayesNet - Variable in class jbnc.operators.Augmenter.Result

beta_ijk - Static variable in class jbnc.util.BNTools

A some small value larger than zero.

buildDiscretizer(Case[]) - Method in class jbnc.discretize.EntropyDiscretizer

Performs construction of the discretizer for a set of cases (class + continous attribute pairs).

C

CONTINUOUS - Static variable in class jbnc.dataset.AttributeType

Attribute with continuous values represented as double.

CVGenerator - class jbnc.util.CVGenerator.

Generates cross validation data sets.

CVGenerator() - Constructor for class jbnc.util.CVGenerator

Case - class jbnc.discretize.Case.

Represents attribute instance: a pair of an attribute value and a class to which this attribute value belongs.

Case(int, double) - Constructor for class jbnc.discretize.Case

Constructor.

ClassDepend - class jbnc.operators.ClassDepend.

Constructs a selective naive Bayes classifier.

ClassDepend() - Constructor for class jbnc.operators.ClassDepend

Classifier - class jbnc.Classifier.

Classifier tester.

Classifier() - Constructor for class jbnc.Classifier

CondMutualInfo - class jbnc.util.CondMutualInfo.

Estimate a joint probability distribution of three discreate variables

CondMutualInfo(FrequencyCalc) - Constructor for class jbnc.util.CondMutualInfo

Constructor for the CondMutualInfo object

CrossVal - class jbnc.CrossVal.

Cross validation classifier tester.

CrossVal() - Constructor for class jbnc.CrossVal

calcFreqXYZ() - Method in class jbnc.util.FrequencyCalc

Calculate values of freqXYZ

calcFreqXY_X() - Method in class jbnc.util.FrequencyCalc

Calculate values of freqX and freqXY.

caseList - Variable in class jbnc.util.CVGenerator

cases - Variable in class jbnc.dataset.Dataset

Vector of vectors representing cases.

className - Variable in class jbnc.Classifier

className - Variable in class jbnc.util.BNCTester

classNameDefault - Static variable in class jbnc.Classifier

classNameDefault - Static variable in class jbnc.util.BNCTester

classNode - Variable in class jbnc.util.BNCTester

clean() - Method in class jbnc.inducers.BayesianInducer

Clean member variables.

clear() - Method in class jbnc.dataset.Dataset

clear() - Method in class jbnc.graphs.Graph

Remove all vertices and edges.

clear() - Method in class jbnc.util.BNCTester

clone() - Method in class jbnc.dataset.Dataset

Performs a shallow copy of itself.

clone() - Method in class jbnc.dataset.DatasetInt

Performs a shallow copy of itself.

close() - Method in class jbnc.database.DBLog

Closes connection to a database.

cmi - Variable in class jbnc.operators.Augmenter

condClassProb - Variable in class jbnc.graphs.BNCInference

contains(Vertex) - Method in class jbnc.graphs.Graph

Returns true if vertex x is present in the graph.

convertCase(Vector, AttributeSpecs[]) - Method in class jbnc.dataset.DatasetReader

Convert case from a raw format.

convertCaseInt(Vector, AttributeSpecs[]) - Method in class jbnc.dataset.DatasetReaderInt

Convert case from a raw format.

countClasses(Vector, AttributeSpecs[]) - Static method in class jbnc.DatasetInfo

create(Graph, Collection, AttributeSpecs[]) - Static method in class jbnc.operators.ClassDepend

createFullGraph(double[][], LinkedList, AttributeSpecs[]) - Static method in class jbnc.operators.Augmenter

cvFolds - Variable in class jbnc.measures.QualityMeasureLCV

Number of cross-validation folds.

cvTimes - Variable in class jbnc.measures.QualityMeasureLCV

Number of times the cross validation is repeated (averaged).

D

DBLog - class jbnc.database.DBLog.

Enables loging of testing results to a database.

DBLog() - Constructor for class jbnc.database.DBLog

DEFAULT_APLHA_IJK - Static variable in class jbnc.inducers.BayesianInducer

DISCRETE - Static variable in class jbnc.dataset.AttributeType

Attribute with enumrated discrete values.

DISCRETE_N - Static variable in class jbnc.dataset.AttributeType

Attribute with N discrete values (0 to N-1).

Dataset - class jbnc.dataset.Dataset.

Represents a data set.

Dataset() - Constructor for class jbnc.dataset.Dataset

Set everything to null .

DatasetInfo - class jbnc.DatasetInfo.

Reads data sets in C4.5 format and prints information about the content.

DatasetInfo() - Constructor for class jbnc.DatasetInfo

DatasetInt - class jbnc.dataset.DatasetInt.

Represents a data set of discreate values.

DatasetInt() - Constructor for class jbnc.dataset.DatasetInt

Default constructor.

DatasetInt(int[][], AttributeSpecs[]) - Constructor for class jbnc.dataset.DatasetInt

Set names to null.

DatasetReader - class jbnc.dataset.DatasetReader.

Functions for reading data sets with test cases.

DatasetReader() - Constructor for class jbnc.dataset.DatasetReader

DatasetReaderInt - class jbnc.dataset.DatasetReaderInt.

Functions for reading data sets with test cases.

DatasetReaderInt() - Constructor for class jbnc.dataset.DatasetReaderInt

DiscardingBayesianInducer - class jbnc.inducers.DiscardingBayesianInducer.

Abstract Bayesian network clasifier inducer that is able to discard attribute nodes that are not dependent on the class node.

DiscardingBayesianInducer() - Constructor for class jbnc.inducers.DiscardingBayesianInducer

DisjointSets - class jbnc.graphs.DisjointSets.

Maintains a collection of disjoint sets.

dataFileName - Variable in class jbnc.util.BNCTester

databaseURL - Static variable in class jbnc.Classifier

dataset - Variable in class jbnc.measures.QualityMeasure

dataset - Variable in class jbnc.util.BNCTester

dataset - Variable in class jbnc.util.FrequencyCalc

debugMode - Variable in class jbnc.Classifier

debugMode - Variable in class jbnc.inducers.BayesianInducer

debugMode - Variable in class jbnc.operators.Operator

debugMode - Variable in class jbnc.util.BNCTester

discardAllOfType(AttributeType) - Method in class jbnc.dataset.Dataset

Discards all attributes that match the given type.

discardAllOfType(AttributeType) - Method in class jbnc.dataset.DatasetInt

Discards all attributes that match the given type.

discardIncompleteCases - Variable in class jbnc.dataset.Dataset

LOCAL

discardNonDependent - Variable in class jbnc.inducers.DiscardingBayesianInducer

Whether nodes that are not dependent on the class node should be dsiscarded from augmenting tree creation.

discardNonDependent - Variable in class jbnc.operators.SAN

Whether nodes that are not dependent on the class node should be dsiscarded from augmenting tree creation.

discretize(double) - Method in class jbnc.discretize.EntropyDiscretizer

Discretize single continous value.

dump() - Method in class jbnc.graphs.Graph

Description of the Method

E

Edge - class jbnc.graphs.Edge.

Description of the Class

EdgeWithWeight - class jbnc.graphs.EdgeWithWeight.

Description of the Class

EdgeWithWeight() - Constructor for class jbnc.graphs.EdgeWithWeight

EdgeWithWeight(Vertex, Vertex) - Constructor for class jbnc.graphs.EdgeWithWeight

EdgeWithWeight(Vertex, Vertex, double) - Constructor for class jbnc.graphs.EdgeWithWeight

EntropyDiscretizer - class jbnc.discretize.EntropyDiscretizer.

Implements entropy based discretisation algotithm by
U.M.

EntropyDiscretizer() - Constructor for class jbnc.discretize.EntropyDiscretizer

equals(Object) - Method in class jbnc.discretize.Case

Indicates whether some other object is "equal to" this one.

evaluate(BayesNet) - Method in class jbnc.measures.QualityMeasure

Calculate the quality measure for the given network and data set.

evaluate(BayesNet) - Method in class jbnc.measures.QualityMeasureHGC

Description of the Method

evaluate(BayesNet) - Method in class jbnc.measures.QualityMeasureLC

Description of the Method

evaluate(BayesNet) - Method in class jbnc.measures.QualityMeasureLCV

Description of the Method

evaluate(BayesNet) - Method in class jbnc.measures.QualityMeasureLCV_LOO

Description of the Method

evaluate(BayesNet) - Method in class jbnc.measures.QualityMeasureSB

Description of the Method

F

FANInducer - class jbnc.inducers.FANInducer.

Constructs Forest Augmented Naive Bayes classifier (FAN).

FANInducer() - Constructor for class jbnc.inducers.FANInducer

ForestAugmenter - class jbnc.operators.ForestAugmenter.

Constructs Forest Augmented Naive Bayes classifier (FAN).

ForestAugmenter() - Constructor for class jbnc.operators.ForestAugmenter

FrequencyCalc - class jbnc.util.FrequencyCalc.

Calculate variable frequencies given a dataset.

FrequencyCalc(DatasetInt) - Constructor for class jbnc.util.FrequencyCalc

Constructor for the FrequencyCalc object

FrequencyTable - class jbnc.util.FrequencyTable.

Description of the Class

FrequencyTable(BayesNet) - Constructor for class jbnc.util.FrequencyTable

Constructor for the FrequencyTable object

fc - Variable in class jbnc.measures.QualityMeasureLCV

fileNameStem - Variable in class jbnc.Classifier

findSet(Object) - Method in class jbnc.graphs.DisjointSets

Returns a pointer to the representative of the (unique) set containing x .

freqX - Variable in class jbnc.util.FrequencyCalc

Frequency of variable values X.

freqXY - Variable in class jbnc.util.FrequencyCalc

Joint frequency of variable values X and Y.

freqXYZ - Variable in class jbnc.util.FrequencyCalc

Joint frequency of variable values X, Y and Z.

frequencyNodes - Variable in class jbnc.util.FrequencyTable

G

Graph - class jbnc.graphs.Graph.

Description of the Class

Graph() - Constructor for class jbnc.graphs.Graph

gammaLn(double) - Static method in class jbnc.util.BNTools

Returns the value ln[ gamma(xx)] for xx > 0 Implementation based on W.H.

generateSets(int, Vector[], Vector[]) - Method in class jbnc.util.CVGenerator

get(boolean[], boolean, double) - Method in class jbnc.util.CondMutualInfo

Return conditional mutual information matrix I.

getASBMParamComponent(BayesNet, DatasetInt, boolean, double) - Static method in class jbnc.util.BNTools

Return network parameters component of the asymptotic standard Bayesian measure (ASBM).

getAccuracy() - Method in class jbnc.util.BNCTester.Result

getAlphaK() - Method in class jbnc.measures.QualityMeasure

Gets value of the prior.

getCVFolds() - Method in class jbnc.measures.QualityMeasureLCV

Gets the number of cross-validation folds.

getCVTimes() - Method in class jbnc.measures.QualityMeasureLCV

Gets the number of times the cross validation is repeated (averaged).

getChildrenOf(Vertex) - Method in class jbnc.graphs.Graph

Return all children nodes of the given parent node.

getChildrenOf(int) - Method in class jbnc.graphs.Graph

Return all children nodes of the parent node with given index.

getCondClassProb(int[]) - Method in class jbnc.graphs.BNCInference

Return values of the class node conditional probability given instantiation of attribute variables.

getDebugMode() - Method in class jbnc.inducers.BayesianInducer

Gets the debug mode flag.

getDebugMode() - Method in class jbnc.operators.Operator

Gets the DebugMode attribute of the Operator object

getDirectedEdges(Graph, Vertex) - Method in class jbnc.graphs.MinSpanTree

Returns edges of a minimum spanning tree of a graph.

getDiscardIncompleteCases() - Method in class jbnc.dataset.Dataset

getDiscardIncompleteCases() - Method in class jbnc.dataset.DatasetReader

getDiscardNonDependent() - Method in class jbnc.inducers.DiscardingBayesianInducer

Gets discardNonDependent flag.

getDiscardNonDependent() - Method in class jbnc.operators.SAN

getEdges() - Method in class jbnc.graphs.Graph

getError() - Method in class jbnc.util.BNCTester.Result

getInVertex() - Method in class jbnc.graphs.Edge

Gets the InVertex attribute of the Edge object

getIndex() - Method in class jbnc.graphs.Vertex

Gets the Index attribute of the Vertex object

getJointProb(int[]) - Method in class jbnc.graphs.BNCInference

Return the value of the joint probability for the instantiation of the variables given by parameter 'vars'.

getN(int, int, int) - Method in class jbnc.util.FrequencyTable

Gets the N attribute of the FrequencyTable object

getN(int, int) - Method in class jbnc.util.FrequencyTable

Gets the N attribute of the FrequencyTable object

getName() - Method in class jbnc.dataset.AttributeSpecs

Get attribute name.

getName() - Method in class jbnc.graphs.Vertex

Gets the Name attribute of the Vertex object

getName() - Method in class jbnc.measures.QualityMeasure

Gets name of the quality measure.

getName() - Method in class jbnc.measures.QualityMeasureHGC

Gets the Name attribute of the QualityMeasureHGC object

getName() - Method in class jbnc.measures.QualityMeasureLC

Gets the Name attribute of the QualityMeasureLC object

getName() - Method in class jbnc.measures.QualityMeasureLCV

Gets the Name attribute of the QualityMeasureLCV object

getName() - Method in class jbnc.measures.QualityMeasureLCV_LOO

Gets the Name attribute of the QualityMeasureLCV_LOO object

getName() - Method in class jbnc.measures.QualityMeasureSB

Gets the Name attribute of the QualityMeasureSB object

getNbCases() - Method in class jbnc.util.FrequencyTable

Gets the NbCases attribute of the FrequencyTable object

getNetwork() - Method in class jbnc.inducers.BayesianInducer

Gets Bayesian network representing the classifier.

getNetworkDimension(BayesNet) - Static method in class jbnc.util.BNTools

Returns dimension of a Bayesian network.

getNodes(Dataset, InferenceGraph) - Static method in class jbnc.util.BNTools

Get node names from a graph in an order they appear in the dataset.

getNumberOfVertices() - Method in class jbnc.graphs.Graph

Returns number of vertices in the graph.

getOutVertex() - Method in class jbnc.graphs.Edge

Gets the OutVertex attribute of the Edge object

getPartitionBoundaries() - Method in class jbnc.discretize.EntropyDiscretizer

Return array representing partition boundaries.

getPartitionNames() - Method in class jbnc.discretize.EntropyDiscretizer

Return symbolic names describing discretization partitions.

getProbX() - Method in class jbnc.util.CondMutualInfo

Return copy of mariginal probability of class variable, p(X).

getQualityMeasure() - Method in class jbnc.inducers.BayesianInducer

Gets the current quality measure.

getState(int) - Method in class jbnc.dataset.AttributeSpecs

Returns state name for a state with the given state index.

getState(String) - Method in class jbnc.dataset.AttributeSpecs

Returns state index for a state with the given state name.

getStates() - Method in class jbnc.dataset.AttributeSpecs

Return states of a discrete attribute.

getTheoreticalStdDev() - Method in class jbnc.util.BNCTester.Result

getTimeMillis() - Method in class jbnc.util.Timer

Returns time elapsed in milliseconds

getType() - Method in class jbnc.dataset.AttributeSpecs

Get attribute type.

getUsePriors() - Method in class jbnc.measures.QualityMeasure

Gets usePriors flag.

getVertex(int) - Method in class jbnc.graphs.Graph

Return vertex with given index.

getVertices() - Method in class jbnc.graphs.Graph

Return vertices as an array.

getWeight() - Method in class jbnc.graphs.EdgeWithWeight

graph - Variable in class jbnc.util.BNCTester

H

hashCode() - Method in class jbnc.discretize.Case

I

IGNORE - Static variable in class jbnc.dataset.AttributeType

Attribute to be ignored.

in - Variable in class jbnc.graphs.Edge

index - Variable in class jbnc.graphs.Vertex

infoData(String, AttributeSpecs[]) - Static method in class jbnc.DatasetInfo

infoNames(String) - Static method in class jbnc.DatasetInfo

init(Dataset) - Method in class jbnc.util.FrequencyCalc

insert(String, String, String, double, double) - Method in class jbnc.database.DBLog

Inserts a results into a two result tables.

invert() - Method in class jbnc.graphs.Edge

Description of the Method

invertEdges(Graph) - Static method in class jbnc.operators.ClassDepend

J

jbnc - package jbnc

jbnc.database - package jbnc.database

jbnc.dataset - package jbnc.dataset

jbnc.discretize - package jbnc.discretize

jbnc.graphs - package jbnc.graphs

jbnc.inducers - package jbnc.inducers

jbnc.measures - package jbnc.measures

jbnc.operators - package jbnc.operators

jbnc.util - package jbnc.util

L

layout - Variable in class jbnc.inducers.BayesianInducer

learnNetParam(BayesNet, boolean, double) - Method in class jbnc.util.FrequencyTable

Description of the Method

learnParameters(BayesNet, FrequencyCalc, boolean, double) - Static method in class jbnc.util.BNTools

Learns parameters for the current network structure.

learnParameters(BayesNet, DatasetInt, boolean, double) - Static method in class jbnc.util.BNTools

Learns parameters for the current network structure.

learnParameters_old(BayesNet, Dataset, boolean, double) - Static method in class jbnc.util.BNTools

Learns parameters for the current network structure.

listFilestem(String) - Static method in class jbnc.DatasetInfo

Description of the Method

loadDataset(String, String) - Method in class jbnc.Classifier

Wrapper for loading a dataset in C4.5 format.

loadDataset(String, String) - Method in class jbnc.CrossVal

Dataset loading wrapper.

loadDataset() - Method in class jbnc.util.BNCTester

loadNetwork() - Method in class jbnc.util.BNCTester

logC - Variable in class jbnc.measures.QualityMeasureLCV

M

MinSpanTree - class jbnc.graphs.MinSpanTree.

Minimum Spanning Tree algorithm.

MinSpanTree() - Constructor for class jbnc.graphs.MinSpanTree

main(String[]) - Static method in class jbnc.Classifier

Main function.

main(String[]) - Static method in class jbnc.CrossVal

Main function.

main(String[]) - Static method in class jbnc.DatasetInfo

Description of the Method

main(String[]) - Static method in class jbnc.ReVal

Description of the Method

main(String[]) - Static method in class jbnc.database.DBLog

The main program for the DBLog class

main(String[]) - Static method in class jbnc.graphs.DisjointSets

Test the class operation.

main(String[]) - Static method in class jbnc.graphs.Graph

Test class Graph.

main(String[]) - Static method in class jbnc.graphs.MinSpanTree

Test the class.

main(String[]) - Static method in class jbnc.inducers.FANInducer

Used for testing of the FAN algorithm.

main(String[]) - Static method in class jbnc.inducers.NaiveBayesInducer

Used for testing of the naive-Bayes algorithm.

main(String[]) - Static method in class jbnc.inducers.SFANInducer

Used for testing of the SFAN algorithm.

main(String[]) - Static method in class jbnc.inducers.STANInducer

Used for testing of the STAN algorithm.

main(String[]) - Static method in class jbnc.inducers.TANInducer

Used for testing of the TAN algorithm.

main(String[]) - Static method in class jbnc.util.BNCTester

main(String[]) - Static method in class jbnc.util.BNTools

Description of the Method

makeSet(Object) - Method in class jbnc.graphs.DisjointSets

Create a new set whose only member (and thus representative) is pointed by x .

measureName - Variable in class jbnc.Classifier

N

NaiveBayesInducer - class jbnc.inducers.NaiveBayesInducer.

Constructs discrete naive-Bayes classifier.

NaiveBayesInducer() - Constructor for class jbnc.inducers.NaiveBayesInducer

NamesReader - class jbnc.dataset.NamesReader.

Read C4.5's '.names' files describing the class and each of the attributes.

NamesReader() - Constructor for class jbnc.dataset.NamesReader

name - Variable in class jbnc.graphs.Vertex

names - Variable in class jbnc.dataset.Dataset

Description of each of the attributes in a case.

names - Variable in class jbnc.util.FrequencyCalc

Specs for variables in the dataset from which the frequecies were calculated.

namesFileName - Variable in class jbnc.Classifier

namesFileName - Variable in class jbnc.util.BNCTester

nbAlphas - Variable in class jbnc.Classifier

nbCases - Variable in class jbnc.util.FrequencyCalc

Number of cases in the dataset the dataset.

nbCases - Variable in class jbnc.util.FrequencyTable

nbClasses - Variable in class jbnc.graphs.BNCInference

nbFail - Variable in class jbnc.util.BNCTester.Result

nbFail - Variable in class jbnc.util.BNCTester

nbPass - Variable in class jbnc.util.BNCTester.Result

nbPass - Variable in class jbnc.util.BNCTester

nbVars - Variable in class jbnc.graphs.BNCInference

net - Variable in class jbnc.inducers.BayesianInducer

Bayesian network representing the classifier.

netFileName - Variable in class jbnc.Classifier

netFileName - Variable in class jbnc.util.BNCTester

O

Operator - class jbnc.operators.Operator.

Abstract BNC Augment operator.

Operator() - Constructor for class jbnc.operators.Operator

open(String, String, String) - Method in class jbnc.database.DBLog

Attempts to establish a connection to the given database URL.

open(String, AttributeSpecs[]) - Method in class jbnc.dataset.DatasetReader

Reads a data file with cases - comma delimited, no header.

open(String, String) - Method in class jbnc.dataset.DatasetReader

Reads a data file with cases - comma delimited, with header.

open(String, AttributeSpecs[]) - Method in class jbnc.dataset.DatasetReaderInt

Reads a data file with cases - comma delimited, no header.

open(String, String) - Method in class jbnc.dataset.DatasetReaderInt

Reads a data file with cases - comma delimited, with header.

open(String) - Static method in class jbnc.dataset.NamesReader

Reads '.names' file containing description of a class and variables.

openC45(String) - Method in class jbnc.dataset.Dataset

openC45(String, String) - Method in class jbnc.dataset.Dataset

openC45(String, String) - Method in class jbnc.dataset.DatasetInt

orientEdges(Edge[], Vertex) - Method in class jbnc.graphs.MinSpanTree

Make sure that graph represents a directed tree (each vertex has at most one parent

out - Variable in class jbnc.graphs.Edge

P

printClassificationReport() - Method in class jbnc.util.BNCTester

println(String) - Method in class jbnc.util.Timer

Prints the current elapsed time to the standard output.

probFuncs - Variable in class jbnc.graphs.BNCInference

Probability function values for each of the network nodes.

processCommandLine(String[]) - Method in class jbnc.Classifier

Process command line arguments.

processCommandLine(String[]) - Method in class jbnc.util.BNCTester

Process command line arguments.

Q

QualityMeasure - class jbnc.measures.QualityMeasure.

Implements an abstract quality measure used by search algorithms to rank Bayesian networks.

QualityMeasure() - Constructor for class jbnc.measures.QualityMeasure

Default constructor.

QualityMeasure(DatasetInt) - Constructor for class jbnc.measures.QualityMeasure

Create a quality measure based on a dataset.

QualityMeasureHGC - class jbnc.measures.QualityMeasureHGC.

Return value of the Heckerman-Geiger-Chickering measure for a Bayesian network structure (also called Baysian Dirihlet metric).

QualityMeasureHGC() - Constructor for class jbnc.measures.QualityMeasureHGC

Constructor for the QualityMeasureHGC object

QualityMeasureHGC(DatasetInt) - Constructor for class jbnc.measures.QualityMeasureHGC

Constructor for the QualityMeasureHGC object

QualityMeasureLC - class jbnc.measures.QualityMeasureLC.

Measure the quality of the bayesian network on the dataset using local criterion measure.

QualityMeasureLC() - Constructor for class jbnc.measures.QualityMeasureLC

Constructor for the QualityMeasureLC object

QualityMeasureLC(DatasetInt) - Constructor for class jbnc.measures.QualityMeasureLC

Constructor for the QualityMeasureLC object

QualityMeasureLCV - class jbnc.measures.QualityMeasureLCV.

LCV - Local Cross Validation.

QualityMeasureLCV() - Constructor for class jbnc.measures.QualityMeasureLCV

Constructor for the QualityMeasureLCV object

QualityMeasureLCV(int) - Constructor for class jbnc.measures.QualityMeasureLCV

Create quality measure for given a number of cross-validation folds.

QualityMeasureLCV(DatasetInt, int) - Constructor for class jbnc.measures.QualityMeasureLCV

Create quality measure for given a dataset and a number of cross-validation folds.

QualityMeasureLCV(int, int) - Constructor for class jbnc.measures.QualityMeasureLCV

Create quality measure for given a number of cross-validation folds and a number of cross-validation repetitions.

QualityMeasureLCV(DatasetInt, int, int) - Constructor for class jbnc.measures.QualityMeasureLCV

Create quality measure for given a dataset and a number of cross-validation folds and a number of cross-validation repetitions.

QualityMeasureLCV_LOO - class jbnc.measures.QualityMeasureLCV_LOO.

LCV_LOO - Local Cross Validation, Leave-One-Out.

QualityMeasureLCV_LOO() - Constructor for class jbnc.measures.QualityMeasureLCV_LOO

Constructor for the QualityMeasureLCV_LOO object

QualityMeasureLCV_LOO(DatasetInt) - Constructor for class jbnc.measures.QualityMeasureLCV_LOO

Constructor for the QualityMeasureLCV_LOO object

QualityMeasureSB - class jbnc.measures.QualityMeasureSB.

Measure the quality of the bayesian network on the dataset using asymptotic estimate of the standard bayes measure.

QualityMeasureSB() - Constructor for class jbnc.measures.QualityMeasureSB

Constructor for the QualityMeasureSB object

QualityMeasureSB(DatasetInt) - Constructor for class jbnc.measures.QualityMeasureSB

Constructor for the QualityMeasureSB object

quality - Variable in class jbnc.operators.Augmenter.Result

qualityMeasure - Variable in class jbnc.inducers.BayesianInducer

Some Bayesian network inducers may use a quality measure to select the most optimal networ architecture for a given training data set.

R

ReVal - class jbnc.ReVal.

Reads data sets in C4.5 format and converts representtion of discrete values to integers (0 to n-1).

ReVal() - Constructor for class jbnc.ReVal

radix - Variable in class jbnc.graphs.BNCInference

Used to calculate index within the probFunction.

random - Variable in class jbnc.util.CVGenerator

randomize() - Method in class jbnc.util.CVGenerator

Set the internal random number generator to a "random" seed based on current time.

removeAllCases() - Method in class jbnc.util.FrequencyTable

Description of the Method

removeCase(int[]) - Method in class jbnc.util.FrequencyTable

Description of the Method

removeEdge(Vertex, Vertex) - Method in class jbnc.graphs.Graph

Remove directed edge from the graph.

report() - Method in class jbnc.util.BNCTester

Print test results to the standard output.

reportShort() - Method in class jbnc.util.BNCTester.Result

Print test results to the standard output in the short form (single line).

reportShort() - Method in class jbnc.util.BNCTester

Print test results to the standard output in the short form (single line).

reset() - Method in class jbnc.inducers.BayesianInducer

Reset the inducer.

restart() - Method in class jbnc.util.Timer

Starts the timer.

run() - Method in class jbnc.Classifier

Create and test a classifier.

run(String[]) - Method in class jbnc.Classifier

run(String[]) - Method in class jbnc.CrossVal

run() - Method in class jbnc.CrossVal

run(Graph, Vertex) - Method in class jbnc.graphs.MinSpanTree

Return a minimum spanning tree for a graph.

run() - Method in class jbnc.util.BNCTester

S

SAN - class jbnc.operators.SAN.

Constructs Selective Augmented Naive Bayes operator (SAN).

SAN() - Constructor for class jbnc.operators.SAN

SFANInducer - class jbnc.inducers.SFANInducer.

Constructs Selective Forest Augmented Naive Bayes classifier (SFAN).

SFANInducer() - Constructor for class jbnc.inducers.SFANInducer

STANInducer - class jbnc.inducers.STANInducer.

Constructs Selective TAN classifier (STAN).

STANInducer() - Constructor for class jbnc.inducers.STANInducer

saveC45(String) - Method in class jbnc.dataset.Dataset

saveC45(String, String) - Method in class jbnc.dataset.Dataset

saveCasesC45(String) - Method in class jbnc.dataset.Dataset

saveCasesC45(String) - Method in class jbnc.dataset.DatasetInt

saveNamesC45(String) - Method in class jbnc.dataset.Dataset

setAlphaK(double) - Method in class jbnc.measures.QualityMeasure

Sets value of the prior.

setCases(Vector) - Method in class jbnc.util.CVGenerator

Sets the Cases attribute of the CVGenerator object

setCases(Vector) - Method in class jbnc.util.FrequencyTable

Sets the Cases attribute of the FrequencyTable object

setDataset(DatasetInt) - Method in class jbnc.measures.QualityMeasure

Sets dataset used for grading Bayesian networks.

setDataset(DatasetInt) - Method in class jbnc.measures.QualityMeasureLCV

setDebugMode(boolean) - Method in class jbnc.inducers.BayesianInducer

Sets the debug mode flag.

setDebugMode(boolean) - Method in class jbnc.operators.Operator

Sets the DebugMode attribute of the Operator object

setDebugMode(boolean) - Method in class jbnc.util.BNCTester

Sets the DebugMode attribute of the BNCTester object

setDiscardIncompleteCases(boolean) - Method in class jbnc.dataset.Dataset

setDiscardIncompleteCases(boolean) - Method in class jbnc.dataset.DatasetReader

setDiscardNonDependent(boolean) - Method in class jbnc.inducers.DiscardingBayesianInducer

Sets discardNonDependent flag.

setDiscardNonDependent(boolean) - Method in class jbnc.operators.SAN

setName(String) - Method in class jbnc.dataset.AttributeSpecs

Set attribute name.

setQualityMeasure(QualityMeasure) - Method in class jbnc.inducers.BayesianInducer

Sets new quality measure.

setSeed(long) - Method in class jbnc.util.CVGenerator

Sets the seed of random number generator used for creation of cross validation sets.

setStates(String[]) - Method in class jbnc.dataset.AttributeSpecs

Set states of a discrete attribute.

setType(AttributeType) - Method in class jbnc.dataset.AttributeSpecs

Set attribute type.

setType(AttributeType, int) - Method in class jbnc.dataset.AttributeSpecs

Set attribute type to DISCRETE_N and specify number of states n.

setUsageMsg(String) - Static method in class jbnc.Classifier

Print usage message for the command line interface.

setUsePriors(boolean) - Method in class jbnc.measures.QualityMeasure

Sets usePriors flag.

setWeight(double) - Method in class jbnc.graphs.EdgeWithWeight

sets - Variable in class jbnc.graphs.DisjointSets

List of disjoint sets.

stop() - Method in class jbnc.util.Timer

Stops the timer.

T

TANInducer - class jbnc.inducers.TANInducer.

Constructs Tree Augmented naive-Bayes classifier (TAN).

Friedman N, Geiger D, Goldszmidt M.

TANInducer() - Constructor for class jbnc.inducers.TANInducer

Timer - class jbnc.util.Timer.

Measures time intervals in milliseconds.

Timer() - Constructor for class jbnc.util.Timer

Creates and start the timer.

TreeAugmenter - class jbnc.operators.TreeAugmenter.

Constructs Tree Augmented Naive Bayes classifier (TAN).

TreeAugmenter() - Constructor for class jbnc.operators.TreeAugmenter

tStart - Variable in class jbnc.util.Timer

tStop - Variable in class jbnc.util.Timer

tableName - Variable in class jbnc.Classifier

test(BayesNet, DatasetInt, boolean) - Method in class jbnc.CrossVal

Bayesian network classifier testing wrapper.

test(BayesNet, Dataset) - Method in class jbnc.util.BNCTester

testClassifier(BayesNet) - Method in class jbnc.util.BNCTester

testClassifier_old() - Method in class jbnc.util.BNCTester

testDataset - Variable in class jbnc.measures.QualityMeasureLCV

testFileName - Variable in class jbnc.Classifier

testSets - Variable in class jbnc.measures.QualityMeasureLCV

test_old(BayesNet, Dataset) - Method in class jbnc.util.BNCTester

test_old(InferenceGraph, Dataset) - Method in class jbnc.util.BNCTester

toString() - Method in class jbnc.dataset.AttributeSpecs

Description of the attribute type or list of attribute states (in type is DISCRETE).

toString() - Method in class jbnc.dataset.AttributeType

toString() - Method in class jbnc.graphs.Edge

Description of the Method

toString() - Method in class jbnc.graphs.EdgeWithWeight

Description of the Method

toString() - Method in class jbnc.graphs.Vertex

Description of the Method

train(BayesianInducer, FrequencyCalc, boolean, double) - Method in class jbnc.CrossVal

Bayesian network classifier training wrapper.

train(FrequencyCalc) - Method in class jbnc.inducers.BayesianInducer

Construct bayesian network from the training data

train(FrequencyCalc, boolean, double) - Method in class jbnc.inducers.BayesianInducer

Construct bayesian network from the training data

train(FrequencyCalc, boolean, double) - Method in class jbnc.inducers.FANInducer

Construct FAN network from the training data.

train(FrequencyCalc, boolean, double) - Method in class jbnc.inducers.NaiveBayesInducer

Construct a naive-Bayes network from the training data.

train(FrequencyCalc, boolean, double) - Method in class jbnc.inducers.SFANInducer

Construct SFAN network from the training data

train(FrequencyCalc, boolean, double) - Method in class jbnc.inducers.STANInducer

Construct STAN network from the training data

train(FrequencyCalc, boolean, double) - Method in class jbnc.inducers.TANInducer

Construct TAN network from the training data

train(List, List, FrequencyCalc, QualityMeasure, boolean, double) - Method in class jbnc.operators.Augmenter

train(List, List, FrequencyCalc, QualityMeasure, boolean, double) - Method in class jbnc.operators.ForestAugmenter

Description of the Method

train(FrequencyCalc, QualityMeasure, Augmenter, boolean, double) - Method in class jbnc.operators.SAN

Description of the Method

train(List, List, FrequencyCalc, QualityMeasure, boolean, double) - Method in class jbnc.operators.TreeAugmenter

It is assumed that 'gamma' and 'lambda' have no elements in common.

trainDataset - Variable in class jbnc.measures.QualityMeasureLCV

trainFileName - Variable in class jbnc.Classifier

U

union(Object, Object) - Method in class jbnc.graphs.DisjointSets

Unites the dynamic sets that contain x and y , say S _x and S_y , into a new set that is the union of these sets.

usageMsg - Static variable in class jbnc.Classifier

usePriors - Variable in class jbnc.measures.QualityMeasure

Flag indicating use of priors.

useTimer - Variable in class jbnc.Classifier

useTimer - Variable in class jbnc.util.BNCTester

V

Vertex - class jbnc.graphs.Vertex.

Description of the Class

Vertex(String, int) - Constructor for class jbnc.graphs.Vertex

Constructor for the Vertex object

variables - Variable in class jbnc.graphs.BNCInference

Variables for each of the probability function.

verifyDataset(DatasetInt) - Method in class jbnc.inducers.BayesianInducer

Check validity of the dataset.

verifyDatasetVsNetwork() - Method in class jbnc.util.BNCTester

vertices - Variable in class jbnc.graphs.Graph

W

weight - Variable in class jbnc.graphs.EdgeWithWeight

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