Serialized Form

Package edu.columbia.cs.cg.prdualrank.model

Class edu.columbia.cs.cg.prdualrank.model.PRDualRankModel extends Model implements Serializable

Serialized Fields

sPatterns

java.util.SortedSet<E> sPatterns

ePatterns

java.util.SortedSet<E> ePatterns

sTuples

java.util.SortedSet<E> sTuples

eTuples

java.util.SortedSet<E> eTuples

Package edu.columbia.cs.ref.algorithm.feature.generation

Class edu.columbia.cs.ref.algorithm.feature.generation.CandidateSentenceFeatureGenerator extends FeatureGenerator<E extends FeatureSet> implements Serializable

Class edu.columbia.cs.ref.algorithm.feature.generation.FeatureGenerator extends java.lang.Object implements Serializable

Serialized Fields

fgs

java.util.List<E> fgs

The fgs.

Class edu.columbia.cs.ref.algorithm.feature.generation.SentenceFeatureGenerator extends FeatureGenerator<E extends FeatureSet> implements Serializable

Package edu.columbia.cs.ref.algorithm.feature.generation.impl

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.EntityBasedChunkingFG extends CandidateSentenceFeatureGenerator<SequenceFS<Span>> implements Serializable

Serialized Fields

tokenizer

FeatureGenerator<E extends FeatureSet> tokenizer

The tokenizer.

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.EntitySplitsFG extends CandidateSentenceFeatureGenerator<SequenceFS<Span>> implements Serializable

Serialized Fields

tokenizer

FeatureGenerator<E extends FeatureSet> tokenizer

The tokenizer.

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.GenericPartOfSpeechFG extends CandidateSentenceFeatureGenerator<SequenceFS<java.lang.String>> implements Serializable

Serialized Fields

posTagger

FeatureGenerator<E extends FeatureSet> posTagger

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.KnowItAllChunkingFG extends CandidateSentenceFeatureGenerator<SequenceFS<java.lang.String>> implements Serializable

Serialized Fields

tokenizer

FeatureGenerator<E extends FeatureSet> tokenizer

posTagger

FeatureGenerator<E extends FeatureSet> posTagger

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.OpenInformationExtractionFG extends CandidateSentenceFeatureGenerator<WekaInstanceFS> implements Serializable

Serialized Fields

tokenizer

FeatureGenerator<E extends FeatureSet> tokenizer

posTagger

FeatureGenerator<E extends FeatureSet> posTagger

chunker

FeatureGenerator<E extends FeatureSet> chunker

sectionSplit

FeatureGenerator<E extends FeatureSet> sectionSplit

IEfeatures

AlternativeOpenIEFeatures IEfeatures

numFeatures

int numFeatures

attributes

weka.core.FastVector attributes

dataset

weka.core.Instances dataset

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.OpenNLPPartOfSpeechFG extends CandidateSentenceFeatureGenerator<SequenceFS<java.lang.String>> implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Throws:

java.io.IOException

Serialized Fields

tokenizer

FeatureGenerator<E extends FeatureSet> tokenizer

path

java.lang.String path

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.OpenNLPTokenizationFG extends SentenceFeatureGenerator<SequenceFS<Span>> implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Throws:

java.io.IOException

Serialized Fields

path

java.lang.String path

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.SpansToStringsConvertionFG extends CandidateSentenceFeatureGenerator<SequenceFS<java.lang.String>> implements Serializable

Serialized Fields

tokenizer

FeatureGenerator<E extends FeatureSet> tokenizer

Class edu.columbia.cs.ref.algorithm.feature.generation.impl.StanfordNLPDependencyGraphFG extends CandidateSentenceFeatureGenerator<GraphFS<java.lang.Integer,java.lang.String>> implements Serializable

Serialized Fields

parser

edu.stanford.nlp.parser.lexparser.LexicalizedParser parser

tokenizer

FeatureGenerator<E extends FeatureSet> tokenizer

depParses

java.util.Map<K,V> depParses

Package edu.columbia.cs.ref.model

Class edu.columbia.cs.ref.model.CandidateSentence extends FeaturableObject implements Serializable

serialVersionUID: 90249725464599185L

Serialized Fields

sentence

Sentence sentence

entities

java.util.List<E> entities

id

java.lang.String id

relationships

java.util.Map<K,V> relationships

Class edu.columbia.cs.ref.model.Document extends java.lang.Object implements Serializable

serialVersionUID: -743800420105471562L

Serialized Fields

path

java.lang.String path

fileName

java.lang.String fileName

text

java.util.List<E> text

entities

java.util.Map<K,V> entities

relationships

java.util.Map<K,V> relationships

Class edu.columbia.cs.ref.model.Segment extends java.lang.Object implements Serializable

serialVersionUID: 6170689330249545921L

Serialized Fields

value

java.lang.String value

offset

int offset

Class edu.columbia.cs.ref.model.Sentence extends FeaturableObject implements Serializable

Serialized Fields

d

Document d

The d.

offset

int offset

The offset.

length

int length

The length.

Class edu.columbia.cs.ref.model.StructureConfiguration extends java.lang.Object implements Serializable

Serialized Fields

userFg

java.util.List<E> userFg

The user fg.

classificationCore

Core classificationCore

The classification core.

userFgKeys

java.util.List<E> userFgKeys

The user fg keys.

Class edu.columbia.cs.ref.model.TokenizedDocument extends Document implements Serializable

Serialized Fields

detectedSpans

Span[] detectedSpans

detectedString

java.lang.String[] detectedString

entitySpanTable

java.util.Map<K,V> entitySpanTable

Package edu.columbia.cs.ref.model.constraint.relationship

Package edu.columbia.cs.ref.model.constraint.relationship.impl

Class edu.columbia.cs.ref.model.constraint.relationship.impl.AndRelationshipConstraint extends java.lang.Object implements Serializable

Serialized Fields

constraints

RelationshipConstraint[] constraints

The constraints.

Class edu.columbia.cs.ref.model.constraint.relationship.impl.DistanceBetweenEntitiesConstraint extends java.lang.Object implements Serializable

Serialized Fields

k

int k

The k.

Class edu.columbia.cs.ref.model.constraint.relationship.impl.DummyRelationshipConstraint extends java.lang.Object implements Serializable

Class edu.columbia.cs.ref.model.constraint.relationship.impl.EntitiesOrderNotRelevantConstraint extends java.lang.Object implements Serializable

Serialized Fields

previousElements

java.util.Set<E> previousElements

The previous elements.

Class edu.columbia.cs.ref.model.constraint.relationship.impl.OrRelationshipConstraint extends java.lang.Object implements Serializable

Serialized Fields

constraints

RelationshipConstraint[] constraints

The constraints.

Class edu.columbia.cs.ref.model.constraint.relationship.impl.WordDistanceBetweenEntities extends java.lang.Object implements Serializable

Serialized Fields

tokenizer

Tokenizer tokenizer

The tokenizer.

Maxdistance

int Maxdistance

The Maxdistance.

activateCache

boolean activateCache

The activate cache.

Package edu.columbia.cs.ref.model.constraint.role

Package edu.columbia.cs.ref.model.constraint.role.impl

Class edu.columbia.cs.ref.model.constraint.role.impl.AndRoleConstraint extends java.lang.Object implements Serializable

Serialized Fields

constraints

RoleConstraint[] constraints

The constraints.

Class edu.columbia.cs.ref.model.constraint.role.impl.EntityTypeConstraint extends java.lang.Object implements Serializable

Serialized Fields

type

java.lang.String type

The type.

Class edu.columbia.cs.ref.model.constraint.role.impl.IsOptionalConstraint extends java.lang.Object implements Serializable

Class edu.columbia.cs.ref.model.constraint.role.impl.MatchRoleConstraint extends java.lang.Object implements Serializable

Serialized Fields

entityMatcher

EntityMatcher entityMatcher

The entity matcher.

original

Entity original

The original.

Class edu.columbia.cs.ref.model.constraint.role.impl.NoConstraint extends java.lang.Object implements Serializable

Class edu.columbia.cs.ref.model.constraint.role.impl.OrRoleConstraint extends java.lang.Object implements Serializable

Serialized Fields

constraints

RoleConstraint[] constraints

The constraints.

Package edu.columbia.cs.ref.model.core

Class edu.columbia.cs.ref.model.core.Core extends java.lang.Object implements Serializable

Serialized Fields

mandatoryFG

java.util.List<E> mandatoryFG

Class edu.columbia.cs.ref.model.core.Kernel extends Core implements Serializable

Package edu.columbia.cs.ref.model.core.impl

Class edu.columbia.cs.ref.model.core.impl.BagOfNGramsKernel extends Kernel implements Serializable

Serialized Fields

m_bCache

boolean m_bCache

m_bNorm

boolean m_bNorm

m_mapStoK

java.util.Map<K,V> m_mapStoK

Class edu.columbia.cs.ref.model.core.impl.DependencyGraphsKernel extends Kernel implements Serializable

Serialized Fields

m_lambda

double m_lambda

util

SimpleGraphUtils util

m_bCache

boolean m_bCache

m_mapStoK

java.util.Map<K,V> m_mapStoK

m_bNorm

boolean m_bNorm

innerKernel

LocalizedDependencyGraphsKernel innerKernel

outerKernel

LocalizedDependencyGraphsKernel outerKernel

fullKernel

LocalizedDependencyGraphsKernel fullKernel

Class edu.columbia.cs.ref.model.core.impl.LocalizedDependencyGraphsKernel extends java.lang.Object implements Serializable

Serialized Fields

m_lambda

double m_lambda

util

SimpleGraphUtils util

m_bCache

boolean m_bCache

m_bNorm

boolean m_bNorm

Class edu.columbia.cs.ref.model.core.impl.OpenInformationExtractionCore extends Core implements Serializable

Class edu.columbia.cs.ref.model.core.impl.ShortestPathKernel extends Kernel implements Serializable

Serialized Fields

m_lambda

double m_lambda

m_bCache

boolean m_bCache

m_mapStoK

java.util.Map<K,V> m_mapStoK

m_bNorm

boolean m_bNorm

Class edu.columbia.cs.ref.model.core.impl.SubsequencesKernel extends Kernel implements Serializable

Serialized Fields

m_nFore

int m_nFore

m_nIntra

int m_nIntra

m_nAfter

int m_nAfter

m_lambda

double m_lambda

m_bCache

boolean m_bCache

m_bNorm

boolean m_bNorm

m_mapStoK

java.util.Map<K,V> m_mapStoK

Package edu.columbia.cs.ref.model.core.structure

Class edu.columbia.cs.ref.model.core.structure.OperableStructure extends java.lang.Object implements Serializable

Serialized Fields

candidateSentence

CandidateSentence candidateSentence

featuresTable

java.util.Hashtable<K,V> featuresTable

Package edu.columbia.cs.ref.model.core.structure.impl

Class edu.columbia.cs.ref.model.core.structure.impl.OpenInformationExtractionOS extends OperableStructure implements Serializable

serialVersionUID: -2183612647555553754L

Serialized Fields

tokens

java.lang.String tokens

pos

java.lang.String pos

chunks

java.lang.String chunks

first

java.lang.String first

firstIndexes

java.lang.String firstIndexes

middle

java.lang.String middle

middleIndexes

java.lang.String middleIndexes

second

java.lang.String second

secondIndexes

java.lang.String secondIndexes

string

java.lang.String string

instance

weka.core.Instance instance

Class edu.columbia.cs.ref.model.core.structure.impl.RelationOperableStructure extends OperableStructure implements Serializable

serialVersionUID: 1L

Serialized Fields

relation

Relationship relation

Class edu.columbia.cs.ref.model.core.structure.impl.TaggedBagOfNgrams extends OperableStructure implements Serializable

Serialized Fields

ngramsB

java.util.Map<K,V>[] ngramsB

ngramsFB

java.util.Map<K,V>[] ngramsFB

ngramsBA

java.util.Map<K,V>[] ngramsBA

featLeft

java.util.List<E>[] featLeft

featRight

java.util.List<E>[] featRight

entity1Type

java.lang.String entity1Type

entity2Type

java.lang.String entity2Type

entity1Index

int entity1Index

entity2Index

int entity2Index

startFB

int startFB

endFB

int endFB

startB

int startB

endB

int endB

startBA

int startBA

endBA

int endBA

sizeNgrams

int sizeNgrams

sizeWindow

int sizeWindow

Class edu.columbia.cs.ref.model.core.structure.impl.TaggedGraph extends OperableStructure implements Serializable

Serialized Fields

graph

DependencyGraph graph

entity1Index

int entity1Index

entity2Index

int entity2Index

entity1Type

java.lang.String entity1Type

entity2Type

java.lang.String entity2Type

Class edu.columbia.cs.ref.model.core.structure.impl.TaggedSequence extends OperableStructure implements Serializable

Serialized Fields

startFB

int startFB

endFB

int endFB

startB

int startB

endB

int endB

startBA

int startBA

endBA

int endBA

entity1Index

int entity1Index

entity2Index

int entity2Index

fb

java.util.List<E>[] fb

b

java.util.List<E>[] b

ba

java.util.List<E>[] ba

entity1

java.util.List<E> entity1

entity2

java.util.List<E> entity2

entity1Type

java.lang.String entity1Type

entity2Type

java.lang.String entity2Type

Package edu.columbia.cs.ref.model.entity

Class edu.columbia.cs.ref.model.entity.Entity extends java.lang.Object implements Serializable

serialVersionUID: 3840011584730968663L

Serialized Fields

id

java.lang.String id

The id.

entityType

java.lang.String entityType

The entity type.

offset

int offset

The offset.

length

int length

The length.

value

java.lang.String value

The value.

document

Document document

The document.

Package edu.columbia.cs.ref.model.feature

Class edu.columbia.cs.ref.model.feature.FeatureSet extends java.lang.Object implements Serializable

Package edu.columbia.cs.ref.model.feature.impl

Class edu.columbia.cs.ref.model.feature.impl.GraphFS extends FeatureSet implements Serializable

Serialized Fields

graph

SimpleGraph<T,U extends java.io.Serializable> graph

Class edu.columbia.cs.ref.model.feature.impl.SequenceFS extends FeatureSet implements Serializable

Serialized Fields

sequence

java.io.Serializable[] sequence

Class edu.columbia.cs.ref.model.feature.impl.WekaInstanceFS extends FeatureSet implements Serializable

Serialized Fields

instance

weka.core.Instance instance

Package edu.columbia.cs.ref.model.matcher

Package edu.columbia.cs.ref.model.matcher.impl

Class edu.columbia.cs.ref.model.matcher.impl.AndEntityMatcher extends java.lang.Object implements Serializable

Serialized Fields

entityMatchers

EntityMatcher[] entityMatchers

The entity matchers.

Class edu.columbia.cs.ref.model.matcher.impl.DictionaryEntityMatcher extends java.lang.Object implements Serializable

Serialized Fields

dictionary

Dictionary dictionary

The dictionary.

Class edu.columbia.cs.ref.model.matcher.impl.EqualsEntityMatcher extends java.lang.Object implements Serializable

Class edu.columbia.cs.ref.model.matcher.impl.OrEntityMatcher extends java.lang.Object implements Serializable

Serialized Fields

entityMatchers

EntityMatcher[] entityMatchers

The entity matchers.

Package edu.columbia.cs.ref.model.re

Class edu.columbia.cs.ref.model.re.Model extends java.lang.Object implements Serializable

Serialized Fields

currentPredictionProperties

java.util.Map<K,V> currentPredictionProperties

Package edu.columbia.cs.ref.model.re.impl

Class edu.columbia.cs.ref.model.re.impl.JLibsvmBinaryModel extends Model implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Throws:

java.io.IOException

Serialized Fields

lastPositiveProbability

double lastPositiveProbability

lastNegativeProbability

double lastNegativeProbability

lastConfidence

double lastConfidence

trueLabel

java.lang.String trueLabel

falseLabel

java.lang.String falseLabel

conf

StructureConfiguration conf

relationshipType

java.util.Set<E> relationshipType

Class edu.columbia.cs.ref.model.re.impl.JLibsvmCompositeBinaryModel extends Model implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Throws:

java.io.IOException

Serialized Fields

models

java.util.Set<E> models

conf

StructureConfiguration conf

relationshipTypes

java.util.Set<E> relationshipTypes

Class edu.columbia.cs.ref.model.re.impl.JLibsvmModelInformation extends java.lang.Object implements Serializable

Serialized Fields

numSV

int numSV

supportVectors

OperableStructure[] supportVectors

alpha

double[] alpha

rho

float rho

kernel

edu.berkeley.compbio.jlibsvm.kernel.KernelFunction<P> kernel

trueLabel

java.lang.String trueLabel

falseLabel

java.lang.String falseLabel

Class edu.columbia.cs.ref.model.re.impl.JLibsvmMulticlassModelModel extends Model implements Serializable

serialVersionUID: -5785782738918799493L

Serialized Fields

conf

StructureConfiguration conf

relationshipTypes

java.util.Set<E> relationshipTypes

Class edu.columbia.cs.ref.model.re.impl.WekaClassifierModel extends Model implements Serializable

Serialized Fields

classifier

weka.classifiers.Classifier classifier

positiveLabel

java.lang.String positiveLabel

conf

StructureConfiguration conf

relationshipTypes

java.util.Set<E> relationshipTypes

Package edu.columbia.cs.ref.model.relationship

Class edu.columbia.cs.ref.model.relationship.Relationship extends java.lang.Object implements Serializable

serialVersionUID: -455430781191582505L

Serialized Fields

hashCode

int hashCode

The hash code.

id

java.lang.String id

The id.

type

RelationshipType type

The type.

entities

Entity[] entities

The entities.

label

java.lang.String label

The label.

Class edu.columbia.cs.ref.model.relationship.RelationshipType extends java.lang.Object implements Serializable

serialVersionUID: 4327250318382126824L

Serialized Fields

type

java.lang.String type

The type.

indexes

java.util.Hashtable<K,V> indexes

The indexes.

numberEntities

int numberEntities

The number entities.

roleConstraints

RoleConstraint[] roleConstraints

The role constraints.

entityMatchers

EntityMatcher[] entityMatchers

The entity matchers.

relConstraints

RelationshipConstraint relConstraints

The rel constraints.

Package edu.columbia.cs.utils

Class edu.columbia.cs.utils.AlternativeOpenIEFeatures extends java.lang.Object implements Serializable

Serialized Fields

featureMap

java.util.HashMap<K,V> featureMap

VERB

java.lang.String VERB

Each of the private methods below defines a feature.

WORD

java.lang.String WORD

PREP

java.lang.String PREP

Class edu.columbia.cs.utils.DependencyGraph extends SimpleGraph<TokenInformation,java.lang.String> implements Serializable

serialVersionUID: 1429362502044671798L

Serialized Fields

nodesInitialProb

double[] nodesInitialProb

edgesProb

double[][] edgesProb

inShortestPath

boolean[][] inShortestPath

nodesFinalProb

double[] nodesFinalProb

numNodes

int numNodes

entityN1

int entityN1

entityN2

int entityN2

shortestPathEdges

java.util.List<E> shortestPathEdges

w

double w

Class edu.columbia.cs.utils.Pair extends java.lang.Object implements Serializable

Serialized Fields

mA

java.lang.Object mA

mB

java.lang.Object mB

Class edu.columbia.cs.utils.SimpleGraph extends java.lang.Object implements Serializable

serialVersionUID: 6195178378668015263L

Serialized Fields

numNodes

int numNodes

nodes

SimpleGraphNode<T>[] nodes

A

int[][] A

X

java.lang.Object[][] X

edges

java.util.List<E> edges

numEdges

int numEdges

Class edu.columbia.cs.utils.SimpleGraphNode extends java.lang.Object implements Serializable

serialVersionUID: -3982299438910566239L

Serialized Fields

label

java.lang.Object label

Class edu.columbia.cs.utils.SimpleGraphUtils extends java.lang.Object implements Serializable

Serialized Fields

cacheIdentities

java.util.HashMap<K,V> cacheIdentities

Class edu.columbia.cs.utils.Span extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

Class edu.columbia.cs.utils.TokenInformation extends java.lang.Object implements Serializable

serialVersionUID: -2805314937535969201L

Serialized Fields

features

java.util.List<E> features

isInShortestPath

boolean isInShortestPath

isEntity1

boolean isEntity1

isEntity2

boolean isEntity2