def buildAdjacencyMatrixWithShortestPaths(tokenElements, dependencyElements, entityElements, pairElement, directed = True, weight_by_distance = False):
#Punctuation dependencies are mostly junk
dependencyElements = removeDependencies(dependencyElements, ["punct"])
parseGraph = ParseGraph.ParseGraph(tokenElements, dependencyElements)
parseGraph.markNamedEntities(entityElements)
e1Id = pairElement.get("e1")
e2Id = pairElement.get("e2")
entity1TokenIds = parseGraph.getNamedEntityTokenIds( [e1Id] )
entity2TokenIds = parseGraph.getNamedEntityTokenIds( [e2Id] )
binaryPaths = parseGraph.buildBinaryPaths(entity1TokenIds, entity2TokenIds)
shortestPaths = ParseGraph.getShortestPaths(binaryPaths)
parseGraph.setAllDependencyWeights(0.3)
parseGraph.setDependencyWeightsByPath(shortestPaths, 0.9)
if weight_by_distance:
parseGraph.reduceWeightByDistance(0.9, 0.5)
parseGraph.setPPIPrefixForDependencies("sp", 0.9) # shortest path prefix
parseGraph.maskNames(e1Id, e2Id)
parseGraph.addPositionTags(entity1TokenIds, entity2TokenIds)
if pairElement.get("interaction") == "True":
output = 1.
else:
output = -1.
adjMatrix, labels = parseGraph.buildAdjacencyMatrix(floattype)
return adjMatrix, labels, output
def buildAdjacencyMatrixWithShortestPaths(tokenElements,
dependencyElements,
entityElements,
pairElement,
directed=True,
weight_by_distance=False):
#Punctuation dependencies are mostly junk
dependencyElements = removeDependencies(dependencyElements, ["punct"])
parseGraph = ParseGraph.ParseGraph(tokenElements, dependencyElements)
parseGraph.markNamedEntities(entityElements)
e1Id = pairElement.get("e1")
e2Id = pairElement.get("e2")
entity1TokenIds = parseGraph.getNamedEntityTokenIds([e1Id])
entity2TokenIds = parseGraph.getNamedEntityTokenIds([e2Id])
binaryPaths = parseGraph.buildBinaryPaths(entity1TokenIds, entity2TokenIds)
shortestPaths = ParseGraph.getShortestPaths(binaryPaths)
parseGraph.setAllDependencyWeights(0.3)
parseGraph.setDependencyWeightsByPath(shortestPaths, 0.9)
if weight_by_distance:
parseGraph.reduceWeightByDistance(0.9, 0.5)
parseGraph.setPPIPrefixForDependencies("sp", 0.9) # shortest path prefix
parseGraph.maskNames(e1Id, e2Id)
parseGraph.addPositionTags(entity1TokenIds, entity2TokenIds)
if pairElement.get("interaction") == "True":
output = 1.
else:
output = -1.
adjMatrix, labels = parseGraph.buildAdjacencyMatrix(floattype)
return adjMatrix, labels, output
