class RelationClassifier:
"""
Manages binary classifier(s) for relation classification.
"""
def __init__(self,
classifierType='SVM',
tfidf=True,
features=None,
threshold=None,
acceptedEntityPairs=None):
"""
Constructor for the RelationClassifier class
:param classifierType: Which classifier to use (must be 'SVM' or 'LogisticRegression')
:param tfidf: Whether to use tfidf for the vectorizer
:param features: A list of specific features. Valid features are "entityTypes","unigramsBetweenEntities","bigrams","dependencyPathEdges","dependencyPathEdgesNearEntities"
:param threshold: A specific threshold to use for classification (which will then use a logistic regression classifier)
:param acceptedEntityPairs: Pairs of entities that relations must match. None will match allow relations of any entity types.
:type classifierType: str
:type tfidf: bool
:type features: list of str
:type threshold: float
:type acceptedEntityPairs: list of tuples
"""
assert classifierType in [
'SVM', 'LogisticRegression'
], "classifierType must be 'SVM' or 'LogisticRegression'"
assert classifierType == 'LogisticRegression' or threshold is None, "Threshold can only be used when classifierType is 'LogisticRegression'"
self.isTrained = False
self.classifierType = classifierType
self.tfidf = tfidf
self.acceptedEntityPairs = acceptedEntityPairs
self.chosenFeatures = [
"entityTypes", "unigramsBetweenEntities", "bigrams",
"dependencyPathEdges", "dependencyPathEdgesNearEntities"
]
if not features is None:
assert isinstance(features, list)
self.chosenFeatures = features
self.threshold = threshold
def train(self, corpus):
"""
Trains the classifier using this corpus. All relations in the corpus will be used for training.
:param corpus: Corpus to use for training
:type corpus: kindred.Corpus
"""
assert isinstance(corpus, kindred.Corpus)
self.candidateBuilder = CandidateBuilder(
acceptedEntityPairs=self.acceptedEntityPairs)
self.candidateBuilder.fit_transform(corpus)
candidateRelations = corpus.getCandidateRelations()
candidateClasses = corpus.getCandidateClasses()
if len(candidateRelations) == 0:
raise RuntimeError(
"No candidate relations found in corpus for training")
self.relTypeToValidEntityTypes = defaultdict(set)
for d in corpus.documents:
for r in d.getRelations():
entityIDsToEntities = d.getEntityIDsToEntities()
relationEntities = [
entityIDsToEntities[eID] for eID in r.entityIDs
]
validEntityTypes = tuple(
[e.entityType for e in relationEntities])
relKey = tuple([r.relationType] + r.argNames)
self.relTypeToValidEntityTypes[relKey].add(validEntityTypes)
self.classToRelType = {
(i + 1): relType
for i, relType in enumerate(corpus.relationTypes)
}
# Get the set of valid classes
relationtypeCount = len(corpus.relationTypes)
allClasses = list(range(1, relationtypeCount + 1))
self.allClasses = allClasses
simplifiedClasses = []
# TODO: Try sparse matrix rep
for candidateRelation, candidateClassGroup in zip(
candidateRelations, candidateClasses):
simplifiedClasses.append(candidateClassGroup[0])
self.vectorizer = Vectorizer(featureChoice=self.chosenFeatures,
tfidf=self.tfidf)
trainVectors = self.vectorizer.fit_transform(corpus)
assert trainVectors.shape[0] == len(candidateClasses)
self.clf = None
if self.classifierType == 'SVM':
self.clf = svm.LinearSVC(class_weight='balanced', random_state=1)
elif self.classifierType == 'LogisticRegression' and self.threshold is None:
self.clf = LogisticRegression(class_weight='balanced',
random_state=1)
elif self.classifierType == 'LogisticRegression' and not self.threshold is None:
self.clf = kindred.LogisticRegressionWithThreshold(self.threshold)
self.clf.fit(trainVectors, simplifiedClasses)
self.isTrained = True
def predict(self, corpus):
"""
Use the relation classifier to predict new relations for a corpus. The new relations will be added to the Corpus.
:param corpus: Corpus to make predictions on
:type corpus: kindred.Corpus
"""
assert self.isTrained, "Classifier must be trained using train() before predictions can be made"
assert isinstance(corpus, kindred.Corpus)
self.candidateBuilder.transform(corpus)
candidateRelations = corpus.getCandidateRelations()
# Check if there are any candidate relations to classify in this corpus
if len(candidateRelations) == 0:
return
entityIDsToType = {}
for doc in corpus.documents:
for e in doc.getEntities():
entityIDsToType[e.entityID] = e.entityType
predictedRelations = []
tmpMatrix = self.vectorizer.transform(corpus)
predictedClasses = self.clf.predict(tmpMatrix)
for predictedClass, candidateRelation in zip(predictedClasses,
candidateRelations):
if predictedClass != 0:
relKey = self.classToRelType[predictedClass]
relType = relKey[0]
argNames = relKey[1:]
candidateRelationEntityTypes = tuple([
entityIDsToType[eID] for eID in candidateRelation.entityIDs
])
if not tuple(candidateRelationEntityTypes
) in self.relTypeToValidEntityTypes[relKey]:
continue
predictedRelation = kindred.Relation(
relType, candidateRelation.entityIDs, argNames=argNames)
predictedRelations.append(predictedRelation)
# Add the predicted relations into the corpus
entitiesToDoc = {}
for i, doc in enumerate(corpus.documents):
for e in doc.getEntities():
entitiesToDoc[e.entityID] = i
for predictedRelation in predictedRelations:
docIDs = [
entitiesToDoc[eID] for eID in predictedRelation.entityIDs
]
docIDs = list(set(docIDs))
assert len(
docIDs
) > 0, "Predicted relation contains entities that don't match any documents in corpus"
assert len(
docIDs
) == 1, "Predicted relation contains entities that are spread across documents"
docID = docIDs[0]
corpus.documents[docID].addRelation(predictedRelation)
def train(self,corpus):
"""
Trains the classifier using this corpus. All relations in the corpus will be used for training.
:param corpus: Corpus to use for training
:type corpus: kindred.Corpus
"""
assert isinstance(corpus,kindred.Corpus)
if not corpus.parsed:
parser = kindred.Parser(model=self.model)
parser.parse(corpus)
self.candidateBuilder = CandidateBuilder(entityCount=self.entityCount,acceptedEntityTypes=self.acceptedEntityTypes)
candidateRelations = self.candidateBuilder.build(corpus)
if len(candidateRelations) == 0:
raise RuntimeError("No candidate relations found in corpus for training. Does the corpus contain text and entity annotations with at least one sentence containing %d entities." % (self.entityCount))
candidateRelationKeys = set()
for cr in candidateRelations:
assert isinstance(cr,kindred.CandidateRelation)
for knownType,knownArgNames in cr.knownTypesAndArgNames:
relKey = tuple([knownType] + knownArgNames)
candidateRelationKeys.add(relKey)
# Create mappings from the class index to a relation type and back again
self.colToRelType = sorted(list(candidateRelationKeys))
self.relTypeToCol = { relationType:i for i,relationType in enumerate(self.colToRelType) }
Y = np.zeros((len(candidateRelations),len(self.colToRelType)),np.int32)
candidateClasses = []
for i,cr in enumerate(candidateRelations):
for knownType,knownArgNames in cr.knownTypesAndArgNames:
relKey = tuple([knownType] + knownArgNames)
col = self.relTypeToCol[relKey]
Y[i,col] = 1
entityCountsInRelations = set([ len(r.entities) for r in corpus.getRelations() ])
entityCountsInRelations = sorted(list(set(entityCountsInRelations)))
assert self.entityCount in entityCountsInRelations, "Relation classifier is expecting to train on relations with %d entities (entityCount=%d). But the known relations in the corpus contain relations with the following entity counts: %s. Perhaps the entityCount parameter should be changed or there is a problem with the training corpus." % (self.entityCount,self.entityCount,str(entityCountsInRelations))
self.relTypeToValidEntityTypes = defaultdict(set)
for d in corpus.documents:
for r in d.relations:
validEntityTypes = tuple([ e.entityType for e in r.entities ])
relKey = tuple([r.relationType] + r.argNames)
self.relTypeToValidEntityTypes[relKey].add(validEntityTypes)
self.vectorizer = Vectorizer(entityCount=self.entityCount,featureChoice=self.chosenFeatures,tfidf=self.tfidf)
trainVectors = self.vectorizer.fit_transform(candidateRelations)
assert trainVectors.shape[0] == Y.shape[0]
posCount = Y.sum()
negCount = Y.shape[0]*Y.shape[1] - posCount
assert negCount > 0, "Must have at least one negative candidate relation in set for training"
assert posCount > 0, "Must have at least one positive candidate relation in set for training"
self.clf = None
if self.classifierType == 'SVM':
self.clf = kindred.MultiLabelClassifier(svm.LinearSVC,class_weight='balanced',random_state=1,max_iter=10000)
elif self.classifierType == 'LogisticRegression' and self.threshold is None:
self.clf = kindred.MultiLabelClassifier(LogisticRegression,class_weight='balanced',random_state=1,solver='liblinear',multi_class='ovr')
elif self.classifierType == 'LogisticRegression' and not self.threshold is None:
self.clf = kindred.MultiLabelClassifier(kindred.LogisticRegressionWithThreshold,threshold=self.threshold)
self.clf.fit(trainVectors,Y)
self.isTrained = True
def train(self, corpus):
"""
Trains the classifier using this corpus. All relations in the corpus will be used for training.
:param corpus: Corpus to use for training
:type corpus: kindred.Corpus
"""
assert isinstance(corpus, kindred.Corpus)
self.candidateBuilder = CandidateBuilder(
acceptedEntityPairs=self.acceptedEntityPairs)
self.candidateBuilder.fit_transform(corpus)
candidateRelations = corpus.getCandidateRelations()
candidateClasses = corpus.getCandidateClasses()
if len(candidateRelations) == 0:
raise RuntimeError(
"No candidate relations found in corpus for training")
self.relTypeToValidEntityTypes = defaultdict(set)
for d in corpus.documents:
for r in d.getRelations():
entityIDsToEntities = d.getEntityIDsToEntities()
relationEntities = [
entityIDsToEntities[eID] for eID in r.entityIDs
]
validEntityTypes = tuple(
[e.entityType for e in relationEntities])
relKey = tuple([r.relationType] + r.argNames)
self.relTypeToValidEntityTypes[relKey].add(validEntityTypes)
self.classToRelType = {
(i + 1): relType
for i, relType in enumerate(corpus.relationTypes)
}
# Get the set of valid classes
relationtypeCount = len(corpus.relationTypes)
allClasses = list(range(1, relationtypeCount + 1))
self.allClasses = allClasses
simplifiedClasses = []
# TODO: Try sparse matrix rep
for candidateRelation, candidateClassGroup in zip(
candidateRelations, candidateClasses):
simplifiedClasses.append(candidateClassGroup[0])
self.vectorizer = Vectorizer(featureChoice=self.chosenFeatures,
tfidf=self.tfidf)
trainVectors = self.vectorizer.fit_transform(corpus)
assert trainVectors.shape[0] == len(candidateClasses)
self.clf = None
if self.classifierType == 'SVM':
self.clf = svm.LinearSVC(class_weight='balanced', random_state=1)
elif self.classifierType == 'LogisticRegression' and self.threshold is None:
self.clf = LogisticRegression(class_weight='balanced',
random_state=1)
elif self.classifierType == 'LogisticRegression' and not self.threshold is None:
self.clf = kindred.LogisticRegressionWithThreshold(self.threshold)
self.clf.fit(trainVectors, simplifiedClasses)
self.isTrained = True
class RelationClassifier:
"""
Manages binary classifier(s) for relation classification.
:param classifierType: Which classifier is used ('SVM' or 'LogisticRegression')
:param tfidf: Whether it will use tfidf for the vectorizer
:param features: A list of specific features. Valid features are "entityTypes", "unigramsBetweenEntities", "bigrams", "dependencyPathEdges", "dependencyPathEdgesNearEntities"
:param threshold: A specific threshold to use for classification (which will then use a logistic regression classifier)
:param entityCount: Number of entities in each relation (default=2). Passed to the CandidateBuilder (if needed)
:param acceptedEntityTypes: Tuples of entity types that relations must match. None will match allow relations of any entity types. Passed to the CandidateBuilder (if needed)
:param isTrained: Whether the classifier has been trained yet. Will throw an error if predict is called before it is trained.
"""
def __init__(self,classifierType='SVM',tfidf=True,features=None,threshold=None,entityCount=2,acceptedEntityTypes=None,model='en'):
"""
Constructor for the RelationClassifier class
:param classifierType: Which classifier to use (must be 'SVM' or 'LogisticRegression')
:param tfidf: Whether to use tfidf for the vectorizer
:param features: A list of specific features. Valid features are "entityTypes", "unigramsBetweenEntities", "bigrams", "dependencyPathEdges", "dependencyPathEdgesNearEntities"
:param threshold: A specific threshold to use for classification (which will then use a logistic regression classifier)
:param entityCount: Number of entities in each relation (default=2). Passed to the CandidateBuilder (if needed)
:param acceptedEntityTypes: Tuples of entity types that relations must match. None will match allow relations of any entity types. Passed to the CandidateBuilder (if needed)
:param model: Name of an available Spacy language model for any parsing needed (e.g. en/de/es/pt/fr/it/nl)
:type classifierType: str
:type tfidf: bool
:type features: list of str
:type threshold: float
:type entityCount: int
:type acceptedEntityTypes: list of tuples
:type model: str
"""
assert classifierType in ['SVM','LogisticRegression'], "classifierType must be 'SVM' or 'LogisticRegression'"
assert classifierType == 'LogisticRegression' or threshold is None, "Threshold can only be used when classifierType is 'LogisticRegression'"
assert isinstance(tfidf,bool)
assert threshold is None or isinstance(threshold,float)
assert isinstance(entityCount,int)
assert acceptedEntityTypes is None or isinstance(acceptedEntityTypes,list)
self.isTrained = False
self.classifierType = classifierType
self.tfidf = tfidf
self.entityCount = entityCount
self.acceptedEntityTypes = acceptedEntityTypes
self.chosenFeatures = ["entityTypes","unigramsBetweenEntities","bigrams","dependencyPathEdges","dependencyPathEdgesNearEntities"]
if not features is None:
assert isinstance(features,list)
self.chosenFeatures = features
self.threshold = threshold
self.model = model
def train(self,corpus):
"""
Trains the classifier using this corpus. All relations in the corpus will be used for training.
:param corpus: Corpus to use for training
:type corpus: kindred.Corpus
"""
assert isinstance(corpus,kindred.Corpus)
if not corpus.parsed:
parser = kindred.Parser(model=self.model)
parser.parse(corpus)
self.candidateBuilder = CandidateBuilder(entityCount=self.entityCount,acceptedEntityTypes=self.acceptedEntityTypes)
candidateRelations = self.candidateBuilder.build(corpus)
if len(candidateRelations) == 0:
raise RuntimeError("No candidate relations found in corpus for training. Does the corpus contain text and entity annotations with at least one sentence containing %d entities." % (self.entityCount))
candidateRelationKeys = set()
for cr in candidateRelations:
assert isinstance(cr,kindred.CandidateRelation)
for knownType,knownArgNames in cr.knownTypesAndArgNames:
relKey = tuple([knownType] + knownArgNames)
candidateRelationKeys.add(relKey)
# Create mappings from the class index to a relation type and back again
self.colToRelType = sorted(list(candidateRelationKeys))
self.relTypeToCol = { relationType:i for i,relationType in enumerate(self.colToRelType) }
Y = np.zeros((len(candidateRelations),len(self.colToRelType)),np.int32)
candidateClasses = []
for i,cr in enumerate(candidateRelations):
for knownType,knownArgNames in cr.knownTypesAndArgNames:
relKey = tuple([knownType] + knownArgNames)
col = self.relTypeToCol[relKey]
Y[i,col] = 1
entityCountsInRelations = set([ len(r.entities) for r in corpus.getRelations() ])
entityCountsInRelations = sorted(list(set(entityCountsInRelations)))
assert self.entityCount in entityCountsInRelations, "Relation classifier is expecting to train on relations with %d entities (entityCount=%d). But the known relations in the corpus contain relations with the following entity counts: %s. Perhaps the entityCount parameter should be changed or there is a problem with the training corpus." % (self.entityCount,self.entityCount,str(entityCountsInRelations))
self.relTypeToValidEntityTypes = defaultdict(set)
for d in corpus.documents:
for r in d.relations:
validEntityTypes = tuple([ e.entityType for e in r.entities ])
relKey = tuple([r.relationType] + r.argNames)
self.relTypeToValidEntityTypes[relKey].add(validEntityTypes)
self.vectorizer = Vectorizer(entityCount=self.entityCount,featureChoice=self.chosenFeatures,tfidf=self.tfidf)
trainVectors = self.vectorizer.fit_transform(candidateRelations)
assert trainVectors.shape[0] == Y.shape[0]
posCount = Y.sum()
negCount = Y.shape[0]*Y.shape[1] - posCount
assert negCount > 0, "Must have at least one negative candidate relation in set for training"
assert posCount > 0, "Must have at least one positive candidate relation in set for training"
self.clf = None
if self.classifierType == 'SVM':
self.clf = kindred.MultiLabelClassifier(svm.LinearSVC,class_weight='balanced',random_state=1,max_iter=10000)
elif self.classifierType == 'LogisticRegression' and self.threshold is None:
self.clf = kindred.MultiLabelClassifier(LogisticRegression,class_weight='balanced',random_state=1,solver='liblinear',multi_class='ovr')
elif self.classifierType == 'LogisticRegression' and not self.threshold is None:
self.clf = kindred.MultiLabelClassifier(kindred.LogisticRegressionWithThreshold,threshold=self.threshold)
self.clf.fit(trainVectors,Y)
self.isTrained = True
def predict(self,corpus):
"""
Use the relation classifier to predict new relations for a corpus. The new relations will be added to the Corpus.
:param corpus: Corpus to make predictions on
:type corpus: kindred.Corpus
"""
assert self.isTrained, "Classifier must be trained using train() before predictions can be made"
assert isinstance(corpus,kindred.Corpus)
if not corpus.parsed:
parser = kindred.Parser(model=self.model)
parser.parse(corpus)
candidateRelations = self.candidateBuilder.build(corpus)
# Check if there are any candidate relations to classify in this corpus
if len(candidateRelations) == 0:
return
predictedRelations = []
testVectors = self.vectorizer.transform(candidateRelations)
classMatrix = self.clf.predict(testVectors)
if self.clf.has_predict_proba():
probMatrix = self.clf.predict_proba(testVectors)
else:
probMatrix = None
predictedProb = None
for matrixRow,matrixCol in zip(*classMatrix.nonzero()):
candidateRelation = candidateRelations[matrixRow]
if probMatrix is not None:
predictedProb = probMatrix[matrixRow,matrixCol]
relKey = self.colToRelType[matrixCol]
relType = relKey[0]
argNames = relKey[1:]
candidateRelationEntityTypes = tuple( [ e.entityType for e in candidateRelation.entities ] )
if not tuple(candidateRelationEntityTypes) in self.relTypeToValidEntityTypes[relKey]:
continue
predictedRelation = kindred.Relation(relType,candidateRelation.entities,argNames=argNames,probability=predictedProb)
predictedRelations.append(predictedRelation)
# Add the predicted relations into the corpus
entitiesToDoc = {}
for i,doc in enumerate(corpus.documents):
for e in doc.entities:
entitiesToDoc[e] = i
for predictedRelation in predictedRelations:
docIDs = [ entitiesToDoc[e] for e in predictedRelation.entities ]
docIDs = list(set(docIDs))
assert len(docIDs) > 0, "Predicted relation contains entities that don't match any documents in corpus"
assert len(docIDs) == 1, "Predicted relation contains entities that are spread across documents"
docID = docIDs[0]
if not predictedRelation in corpus.documents[docID].relations:
corpus.documents[docID].addRelation(predictedRelation)