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

A

ABS1 - Static variable in class driver.AppletDriver

absurdist-Jul-17-2003: Sum(alpha*R-chi*I)=0

ARROW - Static variable in class gui.RelationLink

Absurdist - class absurdist.Absurdist.

Class Absurdist provides the ABSURDIST II graph matching algorithms to compute the correspondence between two concept systems, and finds the optimal mappings between them.

Absurdist() - Constructor for class absurdist.Absurdist

Creates an empty absurdist system.

Absurdist(ConceptSystem, ConceptSystem) - Constructor for class absurdist.Absurdist

Creates an absurdist system containing the source and target concept systems and random external similarities.

Absurdist.AllBest - class absurdist.Absurdist.AllBest.

An auxiliary class used during the randm tie-breaking process in find2WayMap

Absurdist.AllBest(double) - Constructor for class absurdist.Absurdist.AllBest

Absurdist.AllBest.BestPair - class absurdist.Absurdist.AllBest.BestPair.

A pair of (row,column) indexes

Absurdist.AllBest.BestPair(int, int) - Constructor for class absurdist.Absurdist.AllBest.BestPair

Absurdist.CoefMode - class absurdist.Absurdist.CoefMode.

Various ways of setting Beta and Chi.

Absurdist.CoefMode() - Constructor for class absurdist.Absurdist.CoefMode

Absurdist.Results - class absurdist.Absurdist.Results.

Used for reporting.

Absurdist.Results() - Constructor for class absurdist.Absurdist.Results

Alert - class gui.Alert.

An auxiliary dialog window, convenient to pop up a debug window and wait for the user to respond.

AppletDriver - class driver.AppletDriver.

Class AppletDriver is the Applet to run ABSURDIST II in a interactive GUI.

AppletDriver() - Constructor for class driver.AppletDriver

AppletDriver.AnimationThread - class driver.AppletDriver.AnimationThread.

AppletDriver.AnimationThread() - Constructor for class driver.AppletDriver.AnimationThread

AppletDriver.ComputationThread - class driver.AppletDriver.ComputationThread.

AppletDriver.ComputationThread(AppletDriver.AnimationThread) - Constructor for class driver.AppletDriver.ComputationThread

ApplicDriver - class driver.ApplicDriver.

Class ApplicDriver is used to run AppletDriver as an application, rather than an applet.

ApplicDriver() - Constructor for class driver.ApplicDriver

absurdist - package absurdist

The main graph matching algorithm.

absurdist - Variable in class bnb.BranchAndBound

absurdist - Variable in class driver.AppletDriver

absurdist - Variable in class gui.GraphPanel

accuracy - Variable in class absurdist.Absurdist.Results

Mapping accuracy based on internal similarity.

accuracy - Variable in class absurdist.Measures.Quality

accuracy - Variable in class penalty.PenaltyMinimizer

accuracy2 - Variable in class absurdist.Absurdist.Results

Squares of the averaged values; maintained so that we can compute standard deviation

accuracyDev - Variable in class absurdist.Absurdist.Results

Standard deviations

actionPerformed(ActionEvent) - Method in class driver.AppletDriver

add(Absurdist.Results) - Method in class absurdist.Absurdist.Results

Adds the results of one more experiment.

addAnchor(int, String) - Method in class absurdist.ConceptSystem

Adds another "anchor" (information about formerly attached leaf) to the inner node.

addCategory(String) - Method in class absurdist.ConceptSystem

Adds a concept category.

addConcept(Concept) - Method in class absurdist.ConceptSystem

Adds a concept.

addModel(RelationModel) - Method in class absurdist.ConceptSystem

Adds a relation model.

addNoise(double) - Method in class absurdist.Concept

Adds some noise to this concept's feature values.

addNoise(double, double, double, double) - Method in class absurdist.ConceptSystem

Adds some noise to this system.

addNoise(double) - Method in class absurdist.Relation

Adds some noise to the relation's weight.

adjBest - Static variable in class absurdist.Absurdist

If true, we'll find the optimal permutation (this may be very expensive!) and compare the quality of our permutation to it

adjustCoeff() - Method in class absurdist.Absurdist

Initial setting of the beta and chi coefficients according to the node number and edge fullness of the graph.

adjustCoeff() - Method in class penalty.PenaltyMinimizer

alert(String) - Static method in class gui.Alert

Blocking methiod: Pops up a message window, and hangs there until the "continue" button is pressed.

algCombo - Variable in class driver.AppletDriver

allAnchorCnt() - Method in class absurdist.ConceptSystem

How many anchors are in this system?

allBest - Variable in class absurdist.Absurdist.AllBest

A vector of BestPair instances, listing all occurrences of the best value in the currently analyzed submatrix.

allKeysDifferent(NodeInfo[]) - Static method in class graph.NodeInfo

Do all elements in the sorted array have the same comparison key?

allSum() - Method in class common.CorrespondenceVector

alpha - Variable in class absurdist.Absurdist

Coefficients for external similarity.

alpha - Variable in class test.Test45b

alpha - Variable in class test.Test45c

alphaLabel - Variable in class driver.AppletDriver

alphaShare - Static variable in class absurdist.Absurdist

This flag determines the alpha/(alpha+beta) ratio to be used in adjustCoeff(); it only is used if useAlphaShare is true, and is ignored otherwise.

alphaSlider - Variable in class driver.AppletDriver

anchorOverlap(ConceptSystem, int, int) - Method in class absurdist.ConceptSystem

How many achors do Concept i of this system and Concept iother of the other system have in common? This can be used in external similarity computations

anchors - Variable in class absurdist.ConceptSystem

This is a vector that is either null (if no anchors are in use), or is of the same length as "concepts".

animThread - Variable in class driver.AppletDriver.ComputationThread

averaged - Variable in class absurdist.Absurdist.Results

averages() - Method in class absurdist.Absurdist.Results

Computes averages and standard deviations

B

BranchAndBound - class bnb.BranchAndBound.

Finding an optimal permutation (one miniimizing the "mismatched relation" measure, i.e.

BranchAndBound(Absurdist) - Constructor for class bnb.BranchAndBound

bestMap - Variable in class bnb.BranchAndBound

bestMisRel - Variable in class bnb.BranchAndBound

beta - Variable in class absurdist.Absurdist

Coefficients for activation.

betaLabel - Variable in class driver.AppletDriver

betaSlider - Variable in class driver.AppletDriver

bnb - package bnb

C

CONVERGED - Static variable in class absurdist.Absurdist

Concept systems mapping iteration converged.

CREATED - Static variable in class absurdist.Absurdist

Concept system created.

CSGI - class common.CSGI.

Concept System Graph Interface (CSGI) allows us to access the information about a ConceptSystem as if it were a standard graph.

CSGI(ConceptSystem) - Constructor for class common.CSGI

Creates a CSGI representation for a ConceptSystem

CmpDriver - class driver.CmpDriver.

Class SimpleDriver: The main class for a program that runs Absurdist on two specified concept systems read from input files

CmpDriver() - Constructor for class driver.CmpDriver

Concept - class absurdist.Concept.

Class Concept specifies the data structure for a concept, which contains its name and some features.

Concept() - Constructor for class absurdist.Concept

Creates an empty concept.

Concept(int, String) - Constructor for class absurdist.Concept

Creates a concept with specified index and category and default features.

Concept(int, Vector, boolean, boolean) - Constructor for class absurdist.Concept

Creates a concept with specified index and random features if indicated.

Concept(String, String, int, double, double) - Constructor for class absurdist.Concept

Creates a concept with full features.

Concept(Concept) - Constructor for class absurdist.Concept

Creates a copy of a concept.

Concept(Concept, double) - Constructor for class absurdist.Concept

Creates a copy of a concept with some noise added to the feature values.

ConceptGraph - class gui.ConceptGraph.

Class ConceptGraph: Visual representation of a concept system as a graph.

ConceptGraph(ConceptSystem, int, int, int, int) - Constructor for class gui.ConceptGraph

Creates a concept graph from a concept system.

ConceptNode - class gui.ConceptNode.

Class ConceptNode: Visual representation of a concept in a concept system graph.

ConceptNode(Concept, ConceptSystem, ConceptGraph) - Constructor for class gui.ConceptNode

Creates a concept node by encoding its concept features.

ConceptSystem - class absurdist.ConceptSystem.

Class ConceptSystem is the data model for a concept system specifying the semantic network between the concepts.

ConceptSystem() - Constructor for class absurdist.ConceptSystem

Creates an empty concept system.

ConceptSystem(String, Vector, Vector, Vector, Hashtable) - Constructor for class absurdist.ConceptSystem

Creates a concept systems with specified contents.

ConceptSystem(Graph) - Constructor for class absurdist.ConceptSystem

Creates a concept system from a graph instance.

ConceptSystem(int, double) - Constructor for class absurdist.ConceptSystem

Creates a concept system represented as a random simple graph, with default concepts and default relations.

ConceptSystem(int, int, boolean, boolean, double, int, int, boolean) - Constructor for class absurdist.ConceptSystem

Creates a concept system represented as a random graph, categorized/randked/valued, directed/weighted/labeled as indicated, with concepts of random categories and ranks, and randomly weighted/labeled relations.

ConceptSystem(ConceptSystem) - Constructor for class absurdist.ConceptSystem

Creates a copy of a concept system.

ConceptSystem(ConceptSystem, double, double, double, double) - Constructor for class absurdist.ConceptSystem

Creates another concept system by adding some noise to an existing system.

CorrespondenceVector - class common.CorrespondenceVector.

An instance of this class can be used to store a correspondence matrix between the two systems, or any other object of the same dimension

CorrespondenceVector(int, int) - Constructor for class common.CorrespondenceVector

Creates a CorrepspondenceVector structure of the specified sizes

CorrespondenceVector(double[][]) - Constructor for class common.CorrespondenceVector

Creates a CorrepspondenceVector structure "wrapped around" an existing data array.

cInit - Static variable in class absurdist.Absurdist

Intitial value for correspondence matrix.

cPlot - Variable in class gui.PlotPanel

calcLinkSim(int, int, int, int) - Method in class absurdist.Absurdist

Computes the similarity between link (io, jo) in systemO and (in, jn) in systemN.

calcLinkSim(Link, Link) - Method in class absurdist.Absurdist

Computes the similarity between the two links.

cat2color(String, Vector) - Static method in class gui.ConceptNode

Encodes concept type into node color.

categories - Variable in class absurdist.ConceptSystem

All concept categories involved in the system.

category - Variable in class absurdist.Concept

Nominal attribute, can be used to restrict mapping range.

ccnLabel - Variable in class driver.AppletDriver

ccnSlider - Variable in class driver.AppletDriver

chi - Variable in class absurdist.Absurdist

Coefficients for inhibition.

cinLabel - Variable in class driver.AppletDriver

cinSlider - Variable in class driver.AppletDriver

clone() - Method in class common.CorrespondenceVector

Prepares a copy of this matrix

coefMode - Static variable in class absurdist.Absurdist

This parameter controls how chi and beta are initially set, and whether they are reset during the iterative process.

colSum() - Method in class common.CorrespondenceVector

Lazy evaluation for f(b)=C(All,b)=sum_a{C(a,b)}

color - Variable in class gui.ConceptNode

color - Variable in class gui.RelationLink

colors - Static variable in class gui.ConceptNode

olor set for mapping concept categories

colors - Static variable in class gui.RelationLink

color set for mapping relation label types

common - package common

Data representation classes used in both absurdist and penalty packages.

compareTo(Relation) - Method in class absurdist.Relation

Compares the lexicographical order of this relation and the specified one, according to their label.

compareTo(RelationModel) - Method in class absurdist.RelationModel

Compares the ordering between this model and the specified one, according to their label.

compareTo(Object) - Method in class graph.NodeInfo

Used to sort entries by key

concepts - Variable in class absurdist.ConceptSystem

All concepts in the system.

concepts - Variable in class absurdist.Relation

Concepts involved in this relation.

copyButton - Variable in class driver.AppletDriver

copyPanel - Variable in class driver.AppletDriver

correspond - Variable in class absurdist.Absurdist

Correspondence matrix C[step][row][col].

correspond - Variable in class penalty.PenaltyMinimizer

cvgThresh - Static variable in class absurdist.Absurdist

Threshold for iteration convergence.

D

D - Static variable in class gui.ConceptNode

DIRECTED - Static variable in class absurdist.ConceptSystem

Direction mode for directed relation models.

DT - Static variable in class driver.AppletDriver

DX - Variable in class gui.Plot

Number of pixels each step (on x-axis) or value unit (on y-axis) occupies

DY - Variable in class gui.Plot

d - Variable in class common.CorrespondenceVector

d1 - Variable in class absurdist.Concept

2D normalized values; can be extended to n-ary attribute vector.

d2 - Variable in class absurdist.Concept

2D normalized values; can be extended to n-ary attribute vector.

dampingMode - Static variable in class absurdist.Absurdist

Damping mode.

dash - Static variable in class gui.GraphPanel

daxpy(double, CorrespondenceVector) - Method in class common.CorrespondenceVector

this += alpha * v

debug(String) - Static method in class driver.AppletDriver

debug(String) - Static method in class driver.ApplicDriver

debug(String) - Static method in class driver.CmpDriver

debug(String) - Static method in class driver.RandomDriver

debug(String) - Static method in class driver.SimpleDriver

debug - Static variable in class graph.Graph

debug - Static variable in class graph.NodeInfo

debug - Static variable in class penalty.PenaltyMinimizer

debug(String) - Static method in class test.TestBase

debugAll - Static variable in class test.TestBase

If the derived class sets this to true, absurdist.print() will be triggered, printing both systems etc

debugMode - Static variable in class driver.AppletDriver

debugMode - Static variable in class driver.ApplicDriver

debugMode - Static variable in class driver.CmpDriver

debugMode - Static variable in class driver.RandomDriver

debugMode - Static variable in class driver.SimpleDriver

debugMode - Static variable in class test.TestBase

debugln(String) - Static method in class driver.AppletDriver

debugln(String) - Static method in class driver.ApplicDriver

debugln(String) - Static method in class driver.CmpDriver

debugln(String) - Static method in class driver.RandomDriver

debugln(String) - Static method in class driver.SimpleDriver

debugln(String) - Static method in class test.TestBase

degree(int) - Method in class common.CSGI

The degree of node j

degree() - Method in class graph.Graph.Node

How many neighbors?

describe() - Method in class absurdist.Absurdist

Prints out ABSURDIST parameters (if fixed), or rules for adjusting them (if adjustable)

dfa - Static variable in class test.TestBase

difWeight(Relation) - Method in class absurdist.Relation

Return the difference between the weight of this relation and the specified one.

dim2pos(double, int, int) - Static method in class gui.ConceptNode

Encodes concept dimension value into node position coordinates.

direct2style(boolean) - Static method in class gui.RelationLink

Encodes relation direction into link style.

directCombo - Variable in class driver.AppletDriver

directMode - Variable in class test.Test45a

directMode - Variable in class test.Test45b

directMode - Variable in class test.Test45c

directMode - Variable in class test.Test5

directed - Variable in class absurdist.RelationModel

Whether the relation is directed.

displayEquiv(NodeInfo[]) - Method in class graph.Graph

Show how the nodes are divided into classes of equivalency

distance(Concept) - Method in class absurdist.Concept

Computes the normalized semantic distance between this concept and the specified one.

distance(Concept) - Method in class absurdist.FeatureVectorConcept

Computes the normalized semantic distance between this concept and the specified one.

distance(ConceptNode) - Method in class gui.ConceptNode

Computes the geometric distance between this node and the specified one.

done - Variable in class gui.Alert

dp(CorrespondenceVector) - Method in class common.CorrespondenceVector

Dot product

drawArrow(Graphics, int, int, int, int, int, double) - Static method in class gui.RelationLink

Draws an arrow from point P1(x1, y1) to point P2(x2, y2).

driver - package driver

The main classes for the several versions of the graph matching program (in a separate application with or without a GUI, or as an applet).

E

EMPTY - Static variable in class absurdist.Link

Special value; used to form keys for storing "similarity with an empty link".

EXP - Static variable in class driver.AppletDriver

exponential

enforce1to1map - Static variable in class absurdist.Absurdist

If true, 1-1 mapping will be enforced.

equals(Object) - Method in class absurdist.Link

(Looks like you got to have your own equals() if you use this class as a Hashtable key.)

equals(Object) - Method in class absurdist.LinkPair

Returns true if the specified linkpair is the same as this one.

error(String) - Static method in class driver.AppletDriver

error(String) - Static method in class driver.CmpDriver

error(String) - Static method in class driver.RandomDriver

error(String) - Static method in class driver.SimpleDriver

error(String) - Static method in class test.TestBase

evalMap() - Method in class absurdist.Absurdist

Evaluates the quality of the mapping in mapON[].

evalMap(Absurdist, int[], double[][]) - Static method in class absurdist.Measures

Evaluates the quality of the mapping given in mapON[].

evalMap() - Method in class penalty.PenaltyMinimizer

Computes the accuracy of the mapping.

evalMap2() - Method in class penalty.PenaltyMinimizer

An alternative way to evaluate the accuracy of the mapping.

exSim - Variable in class absurdist.Absurdist

External similarity E[row][col].

F

FIXED_GIVEN - Static variable in class absurdist.Absurdist.CoefMode

Use the values passed in via -Dbeta=...

FIXED_N_2 - Static variable in class absurdist.Absurdist.CoefMode

Fixed values: beta as given, chi=beta*(n-2).

FIXED_YF2003 - Static variable in class absurdist.Absurdist.CoefMode

Fixed values set by Ying Feng's early 2003 code

FeatureVectorConcept - class absurdist.FeatureVectorConcept.

This is a special subclass of Concept, in which each instance contains an internal feature vector used to compute external similarity.

FeatureVectorConcept(String, String, int, Vector) - Constructor for class absurdist.FeatureVectorConcept

FeatureVectorConcept.IVPair - class absurdist.FeatureVectorConcept.IVPair.

An index-value pair; used as a component of fv.

FeatureVectorConcept.IVPair(int, double) - Constructor for class absurdist.FeatureVectorConcept.IVPair

fastInSim(CorrespondenceVector) - Method in class absurdist.Absurdist

Computes the internal similarity matrix fast (in O(N^2*D^2) time), for an unlabeled unweighted graph.

fastInSimGeneral(CorrespondenceVector) - Method in class absurdist.Absurdist

Fast similarity calculation for a general graph.

fastInhib(CorrespondenceVector) - Method in class absurdist.Absurdist

inhib(q,x) = ( C(All-q,x) + C(q, All-x) ) /(n+m-2)

fileDir - Variable in class driver.ApplicDriver

Directory from/to which the user last read/wrote files.

find(int) - Method in class graph.Graph.Node

At which position is x in the neighbor list?

find1WayMap() - Method in class absurdist.Absurdist

Find the one-way O-N and N-O mapping using the strongest correspondence in each row/column.

find2WayMap() - Method in class absurdist.Absurdist

Finds the symmetrical two-way mapping using the N global strongest valid correspondences.

findMapping() - Method in class penalty.PenaltyMinimizer

Finds the strongest valid correspondence as successful mappings.

finished - Variable in class driver.AppletDriver.AnimationThread

flush() - Method in class common.CorrespondenceVector

Flushes the "cached" values of row and column sums.

fullLabel - Variable in class driver.AppletDriver

fullSlider - Variable in class driver.AppletDriver

fullness - Variable in class test.TestBase

fv - Variable in class absurdist.FeatureVectorConcept

The fv vector contained in each FeatureVectorConcept is used to determine "distance" between concepts, instead of the (d1,d2) pair in the parent Concept class.

G

GenGraphs - class graph.GenGraphs.

The main program for a test driver.

GenGraphs() - Constructor for class graph.GenGraphs

Graph - class graph.Graph.

An un-directed graph

Graph(int, double) - Constructor for class graph.Graph

Constructs a random graph with N nodes and (N*D)/2 edges

Graph.Node - class graph.Graph.Node.

An instance of this class represents one node of the graph

Graph.Node() - Constructor for class graph.Graph.Node

GraphPanel - class gui.GraphPanel.

Class GraphPanel: The panel on which the concept system graphs are painted.

GraphPanel() - Constructor for class gui.GraphPanel

GraphPanel(Absurdist) - Constructor for class gui.GraphPanel

gbConstr - Variable in class driver.AppletDriver

gbLayout - Variable in class driver.AppletDriver

genAsymGraph(int, double) - Static method in class graph.GenGraphs

Tries to generate a random asymmetric graphs.

genButton - Variable in class driver.AppletDriver

genPanel - Variable in class driver.AppletDriver

get(Link, Link) - Method in interface absurdist.LinkSimCache

Retrieves the value representing Sim(lo,ln), or NaN if none was stored)

get(Link, Link) - Method in class absurdist.LinkSimCacheArray

Retrieves the value representing Sim(lo,ln), or NaN if none was stored)

get(Link, Link) - Method in class absurdist.LinkSimCacheHash

Retrieves the value representing Sim(lo,ln), or NaN if none was stored)

getCategory(int) - Method in class absurdist.ConceptSystem

Gets the ith concept category.

getCategoryIndex(String) - Method in class absurdist.ConceptSystem

Gets the index of a concept category in the system.

getCategoryNum() - Method in class absurdist.ConceptSystem

Gets the total number of concept categories in the system.

getConcept(int) - Method in class absurdist.ConceptSystem

Gets the ith concept.

getConcept(String) - Method in class absurdist.ConceptSystem

Gets the concept with the specified name

getConcept1() - Method in class absurdist.Relation

Returns the 1st concept in the relation.

getConcept2() - Method in class absurdist.Relation

Returns the 2nd concept in the relation.

getConceptIndex(Concept) - Method in class absurdist.ConceptSystem

Gets the index of a concept in the system.

getConceptIndex(String) - Method in class absurdist.ConceptSystem

Gets the index of a concept with the specified name.

getConceptNum() - Method in class absurdist.ConceptSystem

Gets the total number of concepts in the system.

getKey(int, int) - Static method in class absurdist.ConceptSystem

Gets the key for the relations between concept i and j.

getLabel() - Method in class absurdist.Relation

Returns the label of the relation.

getLeft() - Method in class gui.ConceptNode

Gets the x position of left-top corner.

getLeftTop() - Method in class gui.ConceptNode

Gets the left-top point.

getLink(int, int, String) - Method in class gui.ConceptGraph

Gets the relation link of the specified label between concept node i and concept node j.

getLinks(int, int) - Method in class gui.ConceptGraph

Gets the relation link list between concept node i and concept node j.

getMap() - Method in class bnb.BranchAndBound

getMatrix() - Method in class common.CorrespondenceVector

getMaxDgrConceptIdx() - Method in class common.CSGI

The index of the node that has the largest degree.

getMinDgrConceptIdx() - Method in class common.CSGI

The index of the node that has the lowest degree.

getModel(int) - Method in class absurdist.ConceptSystem

Gets the ith relation model.

getModel(String) - Method in class absurdist.ConceptSystem

Gets the relation model with the specified label.

getModelIndex(RelationModel) - Method in class absurdist.ConceptSystem

Gets the index of a relation model in the system.

getModelIndex(String) - Method in class absurdist.ConceptSystem

Gets the index of a relation model with the specified label.

getModelNum() - Method in class absurdist.ConceptSystem

Gets the total number of relation models in the system.

getNei(int) - Method in class common.CSGI

Returns the sorted list of nodes connected to the node j

getNeiPlus(int) - Method in class common.CSGI

Returns the sorted list of nodes connected to the node j, plus j itself

getNode(int) - Method in class gui.ConceptGraph

Gets the ith concept node.

getNode1() - Method in class gui.RelationLink

Returns the 1st concept in the relation.

getNode2() - Method in class gui.RelationLink

Returns the 2nd concept in the relation.

getNodeDegree(int) - Method in class graph.Graph

getNodeNeigh(int, int) - Method in class graph.Graph

getNodeNum() - Method in class graph.Graph

getOption(String, String) - Method in class common.ParseConfig

Gets the requested value from the hash table or from the Java system property aName The Java system property, if given, overrides the value from the hash table.

getOption(String, int) - Method in class common.ParseConfig

gets the requested integer value from the hash table or from the Java system property aName

getOption(String, boolean) - Method in class common.ParseConfig

Gets the requested integer value from the hash table or from the Java system property aName

getOptionDouble(String, double) - Method in class common.ParseConfig

gets the requested double value from the hash table or from the Java system property aName

getParameter(String) - Method in class common.ParseConfig

Gets the requested value from the hash table.

getRange() - Method in class gui.Plot

Returns a pair numbers that encloses the entire range of var[][][]

getRelListNum() - Method in class absurdist.ConceptSystem

Gets the total number of relation lists in the system.

getRelation(int, int, String) - Method in class absurdist.ConceptSystem

Gets the relation of the specified label between concept i and concept j.

getRelation(Vector, String) - Static method in class absurdist.ConceptSystem

Gets the relation of the specified label in a relation list.

getRelations(int, int) - Method in class absurdist.ConceptSystem

Gets the relation list between concept i and concept j.

getSysN(ConceptSystem) - Method in class test.Test45a

Creates the noisy system.

getSysN(ConceptSystem) - Method in class test.Test45b

Creates the noisy system.

getSysN(ConceptSystem) - Method in class test.Test45c

Creates the noisy system.

getSysN(ConceptSystem) - Method in class test.Test5

Creates the noisy system.

getSysN(ConceptSystem) - Method in class test.TestBase

Creates the noisy system.

getSysN(ConceptSystem) - Method in class test.TestNoiseRCRI

Creates the noisy system.

getSysO() - Method in class test.Test45a

Creates the base system.

getSysO() - Method in class test.Test45b

Creates the base system.

getSysO() - Method in class test.Test45c

Creates the base system.

getSysO() - Method in class test.Test5

Creates the base system.

getSysO() - Method in class test.TestBase

Creates the base system.

getSysO() - Method in class test.TestNoiseRCRI

Creates the base system.

getTop() - Method in class gui.ConceptNode

Gets the y position of left-top corner.

gradMatchingPenalty(CorrespondenceVector) - Method in class penalty.PenaltyMinimizer

gradNormPenalty(CorrespondenceVector) - Method in class penalty.PenaltyMinimizer

gradTotalPenalty(CorrespondenceVector) - Method in class penalty.PenaltyMinimizer

graph - package graph

Code for generating asymmetric graphs (graphs without non-trivial homomorphisms).

graphPanel - Variable in class driver.AppletDriver

gui - package gui

Graphical user interface for displaying the graph matching process, and the best match found.

H

hashArray(Integer[]) - Static method in class graph.NodeInfo

Converts an array of integers into a single "fingerprint" integer, using a hash function

hashCode() - Method in class absurdist.Link

Just something...

hashCode() - Method in class absurdist.LinkPair

Just something...

height - Variable in class gui.ConceptGraph

width and height of its bound

height - Variable in class gui.Plot

I

INITIAL - Static variable in class absurdist.Absurdist

Initial status without concept system created.

ITERATING - Static variable in class absurdist.Absurdist

Concept systems in mapping iteration.

i - Variable in class absurdist.Link

iPlot - Variable in class gui.PlotPanel

id - Variable in class graph.NodeInfo

Node id; Graph.node[id] is the appropriate entry in the graph

idx - Variable in class absurdist.FeatureVectorConcept.IVPair

importSourceFile() - Method in class driver.ApplicDriver

Imports one ("Original") concept system from text data file, and creates the second ("Noisy") based on it.

importSourceSystem(String) - Method in class driver.AppletDriver

Import the source concept system from a text file.

importTargetFile() - Method in class driver.ApplicDriver

Import the second ("noisy") concept system from text data file.

importTargetSystem(String) - Method in class driver.AppletDriver

Imports the target concept system from a text file.

in - Variable in class absurdist.LinkPair

inSim - Variable in class absurdist.Absurdist

Internal similarity, also called activator, R[step][row][col].

inhib - Variable in class absurdist.Absurdist

Inhibitor I[step][row][col].

init() - Method in class driver.AppletDriver

initExSim() - Method in class absurdist.Absurdist

Initialize external similarity matrix to all 0's.

initRandom() - Method in class penalty.PenaltyMinimizer

Creates a ranomly-initialized vector.

insertIfNotThere(int) - Method in class graph.Graph.Node

Insertx x into the neighbor list, if it is not there yet

intLoop - Static variable in class absurdist.Absurdist

Sampling interval for plots.

inv - Variable in class graph.Graph.Node

Some invariants used for sorting nodes according to their topological properties

invNext - Variable in class graph.Graph.Node

Some invariants used for sorting nodes according to their topological properties

io - Variable in class absurdist.LinkPair

isCategorized() - Method in class absurdist.ConceptSystem

Checks whether this concept system is categorized, i.e.

isConverged() - Method in class absurdist.Absurdist

Returns true if the network iteration is converged; otherwise false.

isCreated() - Method in class absurdist.Absurdist

Returns true if the two systems are already created; otherwise false.

isDirected() - Method in class absurdist.ConceptSystem

Checks whether this concept system contains any directed relation models.

isDirected() - Method in class absurdist.Relation

Checks whether this relation is directed.

isInitial() - Method in class absurdist.Absurdist

Returns true if the two systems have not yet been created; otherwise false.

isIterating() - Method in class absurdist.Absurdist

Returns true if the network iteration is going on; otherwise false.

isLabeled() - Method in class absurdist.ConceptSystem

Checks whether this concept system is labeled, i.e.

isMapped() - Method in class absurdist.Absurdist

Returns true if the two systems are already mapped; otherwise false.

isRanked() - Method in class absurdist.Concept

Checks whether this concept is ranked, i.e.

isRanked() - Method in class absurdist.ConceptSystem

Checks whether any of the concept in this concept system is ranked.

isSimple() - Method in class absurdist.ConceptSystem

Checks whether this is a simple system, i.e.

isValued() - Method in class absurdist.Concept

Checks whether this concept is valued, i.e.

isValued() - Method in class absurdist.ConceptSystem

Checks whether any of the concept in this concept system is valued.

isWeighted() - Method in class absurdist.ConceptSystem

Checks whether any of the relation in this concept system is weighted.

isWeighted() - Method in class absurdist.Relation

Checks whether this relation is weighted.

iterCnt - Variable in class absurdist.Absurdist.Results

How many iterations have actually been performed by the end of the iterative process

iterCnt2 - Variable in class absurdist.Absurdist.Results

Squares of the averaged values; maintained so that we can compute standard deviation

iterCntDev - Variable in class absurdist.Absurdist.Results

Standard deviations

iterateNet() - Method in class absurdist.Absurdist

Iterate the network to comppute correspondence between unit pairs.

iterateNet() - Method in class penalty.PenaltyMinimizer

Iterates, using the steepest descent method, to find a correspondence between two concept systems minimizing the penalty functional.

J

j - Variable in class absurdist.Link

jn - Variable in class absurdist.LinkPair

jo - Variable in class absurdist.LinkPair

K

K1 - Variable in class penalty.PenaltyMinimizer

K1 and K3 are the mapping penalty parameters.

K2 - Variable in class penalty.PenaltyMinimizer

K1 and K3 are the mapping penalty parameters.

K3 - Variable in class penalty.PenaltyMinimizer

K1 and K3 are the mapping penalty parameters.

kappa - Variable in class penalty.PenaltyMinimizer

Kappa is the normzlization penalty parameter.

key - Variable in class graph.NodeInfo

Sorting key; is made from composing all topological invariants that we have tried so far

L

Link - class absurdist.Link.

Node pair (i,j).

Link(int, int) - Constructor for class absurdist.Link

LinkPair - class absurdist.LinkPair.

An auxiliary class used to form keys in the link similarity cache in Absurdist.

LinkPair(Link, Link) - Constructor for class absurdist.LinkPair

LinkPair(int, int, Link) - Constructor for class absurdist.LinkPair

A convenience constructor

LinkPair(Link, int, int) - Constructor for class absurdist.LinkPair

A convenience constructor

LinkSimCache - interface absurdist.LinkSimCache.

The interface for a structure used to cache information about link similarity.

LinkSimCacheArray - class absurdist.LinkSimCacheArray.

LinkSimCache implemented as a rectangular array.

LinkSimCacheArray() - Constructor for class absurdist.LinkSimCacheArray

LinkSimCacheHash - class absurdist.LinkSimCacheHash.

LinkSimCache implemented as a Hashtable

LinkSimCacheHash() - Constructor for class absurdist.LinkSimCacheHash

lRate - Static variable in class absurdist.Absurdist

Learning rate (this may be adjusted if resetL=true).

label - Variable in class absurdist.RelationModel

Identifier of this RelationModel.

label2color(RelationModel, Vector) - Static method in class gui.RelationLink

Encodes relation label into link color.

linkedTo(int) - Method in class graph.Graph.Node

Is this node linked to node x?

loadSystems(String, int, int) - Static method in class absurdist.Absurdist

Creates a new instance of Absurdist initialized with the 2 systems read from a file containing Java serialized objects.

loadSystems(String) - Method in class driver.AppletDriver

Initializes Absurdist with two ConceptSystems loaded from a file

lookupLinkSim(Link, Link) - Method in class absurdist.Absurdist

Access function for linkSimCache; retrieves the cached link similarity value.

M

MAPPED - Static variable in class absurdist.Absurdist

Concept systems mapping completed.

MIXED - Static variable in class absurdist.ConceptSystem

Direction mode for a mixture of directed and undirected relation models.

Measures - class absurdist.Measures.

Mapping quality measurements

Measures() - Constructor for class absurdist.Measures

Measures.Quality - class absurdist.Measures.Quality.

Return type for evalMap()

Measures.Quality() - Constructor for class absurdist.Measures.Quality

m - Variable in class common.CorrespondenceVector

main(String[]) - Static method in class common.ParseConfig

Purely for testing

main(String[]) - Static method in class driver.ApplicDriver

main(String[]) - Static method in class driver.CmpDriver

main(String[]) - Static method in class driver.RandomDriver

main(String[]) - Static method in class driver.SimpleDriver

main(String[]) - Static method in class graph.GenGraphs

Generates a specified number of random asymmetric graphs.

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

Converts a Graph to a ConceptSystem.

main(String[]) - Static method in class gui.Alert

main(String[]) - Static method in class test.Test45a

main(String[]) - Static method in class test.Test45b

main(String[]) - Static method in class test.Test45c

main(String[]) - Static method in class test.Test5

main(String[]) - Static method in class test.TestExSimMode

main(String[]) - Static method in class test.TestExSimNum

main(String[]) - Static method in class test.TestLoopDensity

main(String[]) - Static method in class test.TestLoopSize

main(String[]) - Static method in class test.TestNoiseDegree

main(String[]) - Static method in class test.TestNoiseDensity

main(String[]) - Static method in class test.TestNoiseRCRI

main(String[]) - Static method in class test.TestNoiseSize

main(String[]) - Static method in class test.TestNoiseSizeDgr

mainCall(String[]) - Method in class test.Test45a

mainCall(String[]) - Method in class test.Test45b

mainCall(String[]) - Method in class test.Test45c

mainCall(String[]) - Method in class test.Test5

mainCall(String[]) - Method in class test.TestExSimMode

mainCall(String[]) - Method in class test.TestExSimNum

mainCall(String[]) - Method in class test.TestNoiseRCRI

mainLoop(int, double, double, int, PrintStream) - Method in class test.TestBase

Create a system with a specified number of nodes and "relation fulness", and its noisy copy with a specified noise level; match them; repeat NRuns times.

map - Variable in class bnb.BranchAndBound

mapButton - Variable in class driver.AppletDriver

mapNO - Variable in class absurdist.Absurdist

Mappings from systemN to systemO, recording indices of matched concepts.

mapNO - Variable in class penalty.PenaltyMinimizer

mapON - Variable in class absurdist.Absurdist

Mappings from systemO to systemN, recording indices of matched concepts.

mapON - Variable in class penalty.PenaltyMinimizer

mapPanel - Variable in class driver.AppletDriver

mapSystem() - Method in class absurdist.Absurdist

Maps orginal concept system to the one with added noise, using exponenital/linear activator/inhibitor.

mapSystem(ConceptSystem, ConceptSystem) - Method in class penalty.PenaltyMinimizer

Maps orginal concept system to the one with added noise.

mapSystem(ConceptSystem, ConceptSystem) - Method in interface penalty.SystemMatcher

Finds a correspondence between two concept systems.

mapT - Variable in class penalty.PenaltyMinimizer

mapThresh - Static variable in class absurdist.Absurdist

Threshold for valid mapping.

matchingPenalty(CorrespondenceVector, CorrespondenceVector) - Method in class penalty.PenaltyMinimizer

max - Variable in class absurdist.Absurdist.AllBest

The currently best value

maxL - Static variable in class absurdist.Absurdist

The ceiling for adjustable learning rate.

maxLoop - Static variable in class absurdist.Absurdist

Maximum number of iterations.

mayBeSymmetric() - Method in class graph.Graph

Tests whether this graph may have some symmetry, by means of looking at N topological invariants of the vertices.

mayBeSymmetric(int) - Method in class graph.Graph

Tests whether this graph may have some symmetry, by means of looking at topological invariants of the vertices.

minus(CorrespondenceVector) - Method in class common.CorrespondenceVector

this -= v

misCon - Variable in class absurdist.Absurdist.Results

Total number of mismapped concepts.

misCon - Variable in class absurdist.Measures.Quality

misCon2 - Variable in class absurdist.Absurdist.Results

Squares of the averaged values; maintained so that we can compute standard deviation

misConDev - Variable in class absurdist.Absurdist.Results

Standard deviations

misRel - Variable in class absurdist.Absurdist.Results

Sum of mismapped relations (i.e.

misRel - Variable in class absurdist.Measures.Quality

misRel2 - Variable in class absurdist.Absurdist.Results

Squares of the averaged values; maintained so that we can compute standard deviation

misRelAdjId - Variable in class absurdist.Absurdist.Results

Sum of mismapped relations adjusted by subtracting the sum of mismapped relations for the identity mapping

misRelAdjId2 - Variable in class absurdist.Absurdist.Results

Squares of the averaged values; maintained so that we can compute standard deviation

misRelAdjIdDev - Variable in class absurdist.Absurdist.Results

Standard deviations

misRelAdjOp - Variable in class absurdist.Absurdist.Results

Same thing, but adjusted by the misrel for the optimal mapping

misRelAdjOp2 - Variable in class absurdist.Absurdist.Results

Squares of the averaged values; maintained so that we can compute standard deviation

misRelAdjOpDev - Variable in class absurdist.Absurdist.Results

Standard deviations

misRelDev - Variable in class absurdist.Absurdist.Results

Standard deviations

mn - Variable in class absurdist.Absurdist.AllBest.BestPair

mo - Variable in class absurdist.Absurdist.AllBest.BestPair

model - Variable in class absurdist.Relation

Relation model of this relation.

models - Variable in class absurdist.ConceptSystem

All relation models used in the system.

mouseClicked(MouseEvent) - Method in class driver.AppletDriver

mouseDragged(MouseEvent) - Method in class driver.AppletDriver

mouseEntered(MouseEvent) - Method in class driver.AppletDriver

mouseExited(MouseEvent) - Method in class driver.AppletDriver

mouseMoved(MouseEvent) - Method in class driver.AppletDriver

mousePressed(MouseEvent) - Method in class driver.AppletDriver

mouseReleased(MouseEvent) - Method in class driver.AppletDriver

N

NRuns - Static variable in class test.TestBase

NodeInfo - class graph.NodeInfo.

Is used for sorting nodes with respect to topological invariants

NodeInfo(int) - Constructor for class graph.NodeInfo

n - Variable in class common.CorrespondenceVector

n - Variable in class test.TestBase

Local copies of important variables.

nCatField - Variable in class driver.AppletDriver

nCatLabel - Variable in class driver.AppletDriver

nConField - Variable in class driver.AppletDriver

nConLabel - Variable in class driver.AppletDriver

nLabel - Variable in class test.Test45a

nLabel - Variable in class test.Test45b

nLabel - Variable in class test.Test45c

nLabel - Variable in class test.Test5

nLabelField - Variable in class driver.AppletDriver

nLabelLabel - Variable in class driver.AppletDriver

nLoop - Variable in class penalty.PenaltyMinimizer

Maximum number of iterations.

nPlot - Variable in class gui.PlotPanel

nStep - Variable in class absurdist.Absurdist

Actual number of steps being recorded during network iteration.

nStep - Variable in class gui.Plot

name - Variable in class absurdist.Concept

Unique identifier of this concept.

name - Variable in class absurdist.ConceptSystem

Identifier of the system.

neigh(int) - Method in class graph.Graph.Node

The k-th neighbor

neighbors - Variable in class graph.Graph.Node

Sorted list of nodes connected to this node.

netIn - Variable in class absurdist.Absurdist

Network input N[step][row][col].

nn - Variable in class bnb.BranchAndBound

no - Variable in class bnb.BranchAndBound

node - Variable in class graph.Graph

The nodes of the graph.

noise - Variable in class test.TestBase

normPenalty(CorrespondenceVector, double) - Method in class penalty.PenaltyMinimizer

Computes the normalization penalty |B*c-z*b|^2

normPenalty(CorrespondenceVector, double, CorrespondenceVector, double) - Method in class penalty.PenaltyMinimizer

Computes the dot product of two vector combinations.

O

OX - Static variable in class gui.Plot

OY1 - Static variable in class gui.Plot

OY2 - Static variable in class gui.Plot

openFile() - Method in class driver.ApplicDriver

out - Variable in class test.TestBase

P

PEN - Static variable in class driver.AppletDriver

penalty

PLAIN - Static variable in class gui.RelationLink

line styles to indicate relation direction

ParseConfig - class common.ParseConfig.

This class is used to obtain configuration paramters, from a configuration file or from Java System Properties.

ParseConfig() - Constructor for class common.ParseConfig

Creates an empty hashtable.

ParseConfig(String) - Constructor for class common.ParseConfig

Creates a hashtable that contains the parsed contents of the specified configuration file.

ParseConfig(Reader) - Constructor for class common.ParseConfig

Creates a hashtable that contains the parsed data obtained from an open reader (which may, for example, be associated with an open file), and then closes the reader.

PenaltyMinimizer - class penalty.PenaltyMinimizer.

This algorithm tries to compute the correspondence between two concept systems that minimizes a certain penalty function.

PenaltyMinimizer() - Constructor for class penalty.PenaltyMinimizer

Plot - class gui.Plot.

Class Plot: Visual representation of a plot for an Absurdist variable.

Plot(double[][][], int, int, int, int, int) - Constructor for class gui.Plot

Creates a plot from a variable array.

PlotPanel - class gui.PlotPanel.

Class PlotPanel: The panel on which the concept system variable plots are painted.

PlotPanel() - Constructor for class gui.PlotPanel

PlotPanel(Absurdist) - Constructor for class gui.PlotPanel

paint(Graphics2D) - Method in class gui.ConceptGraph

Paints the object.

paint(Graphics2D) - Method in class gui.ConceptNode

Paints the object.

paint(Graphics2D) - Method in class gui.Plot

Paints the object.

paint(Graphics2D) - Method in class gui.RelationLink

Paints the object.

paintComponent(Graphics) - Method in class gui.GraphPanel

Paints the component.

paintComponent(Graphics) - Method in class gui.PlotPanel

Paints the component.

paintCorrespond(Graphics2D, int, int, int) - Method in class gui.GraphPanel

Paints the correspondence link at a certain step between concept node pair (io, in) in two systems.

penalmin - Variable in class driver.AppletDriver

penalty - package penalty

This package implements a graph matching method based on the minimization of a certain "penalty functional".

perfectCnt - Variable in class absurdist.Absurdist.Results

How many runs resulted in an identity permutation

permute(int[]) - Method in class graph.Graph.Node

permute(int[]) - Method in class graph.Graph

Permutes the graph.

pickOne() - Method in class absurdist.Absurdist.AllBest

Random tie-breaking.

plotPanel - Variable in class driver.AppletDriver

plus(CorrespondenceVector) - Method in class common.CorrespondenceVector

this += v

prefix - Static variable in class common.ParseConfig

print() - Method in class absurdist.Absurdist

Prints the source and target concept systems, the correspondence matrix, and the final mappings.

print(boolean) - Method in class penalty.PenaltyMinimizer

Prints the original and noisy concept systems, the correspondence matrix, and the final mappings.

print(boolean) - Method in interface penalty.SystemMatcher

Prints the two systems being matched (the original and noisy concept systems, the correspondence matrix, and the final mappings.

printCorrespond() - Method in class absurdist.Absurdist

Prints the correspondence matrix to the standard output.

printCorrespond(PrintWriter) - Method in class penalty.PenaltyMinimizer

printExSim() - Method in class absurdist.Absurdist

Prints the external similarity matrix to the standard output.

printMap() - Method in class absurdist.Absurdist

Prints the mapping between systemO and systemN to the standard output.

printMapping(PrintWriter) - Method in class penalty.PenaltyMinimizer

printMatrix(double[][], PrintWriter) - Method in class penalty.PenaltyMinimizer

printStats(int, double, double, int, Absurdist.Results, PrintStream) - Static method in class test.TestBase

printSystem(PrintWriter) - Method in class penalty.PenaltyMinimizer

printSystems() - Method in class absurdist.Absurdist

Prints the two systems to the standard output.

prop - Static variable in class absurdist.Absurdist

An empty property list -- just an interface to system properties

put(Link, Link, double) - Method in interface absurdist.LinkSimCache

Stores the value representing Sim(lo,ln).

put(Link, Link, double) - Method in class absurdist.LinkSimCacheArray

Stores the value representing Sim(lo,ln).

put(Link, Link, double) - Method in class absurdist.LinkSimCacheHash

Stores the value representing Sim(lo,ln).

putRelation(int, int, Relation) - Method in class absurdist.ConceptSystem

Adds the specified relation to the relation list between concept i and concept j.

putRelation(Vector, Relation) - Static method in class absurdist.ConceptSystem

Adds the specified relation to a relation list.

putRelations(int, int, Vector) - Method in class absurdist.ConceptSystem

Puts the relation list between concept i and concept j.

R

RESET_BALANCE - Static variable in class absurdist.Absurdist.CoefMode

Fixed beta.

RandomDriver - class driver.RandomDriver.

Class RandomDriver: The main class to run a simple test for ABSURDIST (no GUI).

RandomDriver() - Constructor for class driver.RandomDriver

Relation - class absurdist.Relation.

Class Relation Specifies the data structure for a relation, which contains its involved concepts and some features.

Relation() - Constructor for class absurdist.Relation

Creates an empty relation.

Relation(RelationModel, Concept, Concept) - Constructor for class absurdist.Relation

Creates a relation of the specified model with default weight between two concepts.

Relation(RelationModel, Concept, Concept, boolean) - Constructor for class absurdist.Relation

Creates a relation of the specified model with random weight if weighted between two concepts.

Relation(RelationModel, Concept, Concept, double) - Constructor for class absurdist.Relation

Creates a relation with full features between two concepts.

Relation(Relation) - Constructor for class absurdist.Relation

Creates a copy of a relation sharing the same concepts.