def __init__(self,
style=["typed", "directed"],
length=None,
types=[],
featureSet=None,
classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert (classSet.getId("neg") == 1)
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
if style.find(",") != -1:
style = style.split(",")
self.styles = style
self.negFrac = None
self.posPairGaz = POSPairGazetteer()
for s in style:
if s.find("negFrac") != -1:
self.negFrac = float(s.split("_")[-1])
print >> sys.stderr, "Downsampling negatives to", self.negFrac
self.negRand = random.Random(15)
elif s.find("posPairGaz") != -1:
self.posPairGaz = POSPairGazetteer(
loadFrom=s.split("_", 1)[-1])
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
if "graph_kernel" in self.styles:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(
self.featureSet)
if "noAnnType" in self.styles:
self.multiEdgeFeatureBuilder.noAnnType = True
if "noMasking" in self.styles:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if "maxFeatures" in self.styles:
self.multiEdgeFeatureBuilder.maximum = True
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if "ontology" in self.styles:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(
self.featureSet)
if "nodalida" in self.styles:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(
self.featureSet)
#IF LOCAL
if "bioinfer_limits" in self.styles:
self.bioinferOntologies = OntologyUtils.getBioInferTempOntology()
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
#ENDIF
self.pathLengths = length
assert (self.pathLengths == None)
self.types = types
if "random" in self.styles:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
def __init__(self, style=["typed","directed"], length=None, types=[], featureSet=None, classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert( classSet.getId("neg") == 1 )
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
if style.find(",") != -1:
style = style.split(",")
self.styles = style
self.negFrac = None
self.posPairGaz = POSPairGazetteer()
for s in style:
if s.find("negFrac") != -1:
self.negFrac = float(s.split("_")[-1])
print >> sys.stderr, "Downsampling negatives to", self.negFrac
self.negRand = random.Random(15)
elif s.find("posPairGaz") != -1:
self.posPairGaz = POSPairGazetteer(loadFrom=s.split("_", 1)[-1])
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
if "graph_kernel" in self.styles:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(self.featureSet)
if "noAnnType" in self.styles:
self.multiEdgeFeatureBuilder.noAnnType = True
if "noMasking" in self.styles:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if "maxFeatures" in self.styles:
self.multiEdgeFeatureBuilder.maximum = True
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if "ontology" in self.styles:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(self.featureSet)
if "nodalida" in self.styles:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(self.featureSet)
#IF LOCAL
if "bioinfer_limits" in self.styles:
self.bioinferOntologies = OntologyUtils.getBioInferTempOntology()
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
#ENDIF
self.pathLengths = length
assert(self.pathLengths == None)
self.types = types
if "random" in self.styles:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
def __init__(self,
style=None,
classSet=None,
featureSet=None,
gazetteerFileName=None,
skiplist=None):
if classSet == None:
classSet = IdSet(1)
assert (classSet.getId("neg") == 1)
if featureSet == None:
featureSet = IdSet()
ExampleBuilder.__init__(self, classSet, featureSet)
#gazetteerFileName="/usr/share/biotext/GeniaChallenge/SharedTaskTriggerTest/gazetteer-train"
if gazetteerFileName != None:
self.gazetteer = Gazetteer.loadGztr(gazetteerFileName)
print >> sys.stderr, "Loaded gazetteer from", gazetteerFileName
else:
print >> sys.stderr, "No gazetteer loaded"
self.gazetteer = None
self.styles = style
self.skiplist = set()
if skiplist != None:
f = open(skiplist, "rt")
for line in f.readlines():
self.skiplist.add(line.strip())
f.close()
self.styles = [
"trigger_features", "typed", "directed", "no_linear", "entities",
"genia_limits", "noMasking", "maxFeatures"
]
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
if "graph_kernel" in self.styles:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(
self.featureSet)
if "noAnnType" in self.styles:
self.multiEdgeFeatureBuilder.noAnnType = True
if "noMasking" in self.styles:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if "maxFeatures" in self.styles:
self.multiEdgeFeatureBuilder.maximum = True
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
def __init__(self, style=None, length=None, types=[], featureSet=None, classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert( classSet.getId("neg") == 1 or (len(classSet.Ids)== 2 and classSet.getId("neg") == -1) )
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
self.styles = self.getParameters(style, [
"typed", "directed", "headsOnly", "graph_kernel", "noAnnType", "noMasking", "maxFeatures",
"genia_limits", "epi_limits", "id_limits", "rel_limits", "bb_limits", "bi_limits", "co_limits",
"genia_task1", "ontology", "nodalida", "bacteria_renaming", "trigger_features", "rel_features",
"ddi_features", "evex", "giuliano", "random", "themeOnly", "causeOnly", "no_path", "entities",
"skip_extra_triggers", "headsOnly", "graph_kernel", "trigger_features", "no_task", "no_dependency",
"disable_entity_features", "disable_terminus_features", "disable_single_element_features",
"disable_ngram_features", "disable_path_edge_features", "no_linear", "subset", "binary", "pos_only",
"entity_type"
])
if style == None: # no parameters given
style["typed"] = style["directed"] = style["headsOnly"] = True
# self.styles = style
# if "selftrain_group" in self.styles:
# self.selfTrainGroups = set()
# if "selftrain_group-1" in self.styles:
# self.selfTrainGroups.add("-1")
# if "selftrain_group0" in self.styles:
# self.selfTrainGroups.add("0")
# if "selftrain_group1" in self.styles:
# self.selfTrainGroups.add("1")
# if "selftrain_group2" in self.styles:
# self.selfTrainGroups.add("2")
# if "selftrain_group3" in self.styles:
# self.selfTrainGroups.add("3")
# print >> sys.stderr, "Self-train-groups:", self.selfTrainGroups
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
# NOTE Temporarily re-enabling predicted range
#self.multiEdgeFeatureBuilder.definePredictedValueRange([], None)
if self.styles["graph_kernel"]:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(self.featureSet)
if self.styles["noAnnType"]:
self.multiEdgeFeatureBuilder.noAnnType = True
if self.styles["noMasking"]:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if self.styles["maxFeatures"]:
self.multiEdgeFeatureBuilder.maximum = True
if self.styles["genia_task1"]:
self.multiEdgeFeatureBuilder.filterAnnTypes.add("Entity")
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if self.styles["ontology"]:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(self.featureSet)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(self.featureSet)
if self.styles["bacteria_renaming"]:
self.bacteriaRenamingFeatureBuilder = BacteriaRenamingFeatureBuilder(self.featureSet)
if self.styles["trigger_features"]:
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder.useNonNameEntities = True
if self.styles["genia_task1"]:
self.triggerFeatureBuilder.filterAnnTypes.add("Entity")
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
if self.styles["rel_features"]:
self.relFeatureBuilder = RELFeatureBuilder(featureSet)
if self.styles["ddi_features"]:
self.drugFeatureBuilder = DrugFeatureBuilder(featureSet)
if self.styles["evex"]:
self.evexFeatureBuilder = EVEXFeatureBuilder(featureSet)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder = GiulianoFeatureBuilder(featureSet)
self.pathLengths = length
assert(self.pathLengths == None)
self.types = types
if self.styles["random"]:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
class MultiEdgeExampleBuilder(ExampleBuilder):
"""
This example builder makes edge examples, i.e. examples describing
the event arguments.
"""
def __init__(self, style=None, length=None, types=[], featureSet=None, classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert( classSet.getId("neg") == 1 or (len(classSet.Ids)== 2 and classSet.getId("neg") == -1) )
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
self.styles = self.getParameters(style, [
"typed", "directed", "headsOnly", "graph_kernel", "noAnnType", "noMasking", "maxFeatures",
"genia_limits", "epi_limits", "id_limits", "rel_limits", "bb_limits", "bi_limits", "co_limits",
"genia_task1", "ontology", "nodalida", "bacteria_renaming", "trigger_features", "rel_features",
"ddi_features", "evex", "giuliano", "random", "themeOnly", "causeOnly", "no_path", "entities",
"skip_extra_triggers", "headsOnly", "graph_kernel", "trigger_features", "no_task", "no_dependency",
"disable_entity_features", "disable_terminus_features", "disable_single_element_features",
"disable_ngram_features", "disable_path_edge_features", "no_linear", "subset", "binary", "pos_only",
"entity_type"
])
if style == None: # no parameters given
style["typed"] = style["directed"] = style["headsOnly"] = True
# self.styles = style
# if "selftrain_group" in self.styles:
# self.selfTrainGroups = set()
# if "selftrain_group-1" in self.styles:
# self.selfTrainGroups.add("-1")
# if "selftrain_group0" in self.styles:
# self.selfTrainGroups.add("0")
# if "selftrain_group1" in self.styles:
# self.selfTrainGroups.add("1")
# if "selftrain_group2" in self.styles:
# self.selfTrainGroups.add("2")
# if "selftrain_group3" in self.styles:
# self.selfTrainGroups.add("3")
# print >> sys.stderr, "Self-train-groups:", self.selfTrainGroups
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
# NOTE Temporarily re-enabling predicted range
#self.multiEdgeFeatureBuilder.definePredictedValueRange([], None)
if self.styles["graph_kernel"]:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(self.featureSet)
if self.styles["noAnnType"]:
self.multiEdgeFeatureBuilder.noAnnType = True
if self.styles["noMasking"]:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if self.styles["maxFeatures"]:
self.multiEdgeFeatureBuilder.maximum = True
if self.styles["genia_task1"]:
self.multiEdgeFeatureBuilder.filterAnnTypes.add("Entity")
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if self.styles["ontology"]:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(self.featureSet)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(self.featureSet)
if self.styles["bacteria_renaming"]:
self.bacteriaRenamingFeatureBuilder = BacteriaRenamingFeatureBuilder(self.featureSet)
if self.styles["trigger_features"]:
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder.useNonNameEntities = True
if self.styles["genia_task1"]:
self.triggerFeatureBuilder.filterAnnTypes.add("Entity")
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
if self.styles["rel_features"]:
self.relFeatureBuilder = RELFeatureBuilder(featureSet)
if self.styles["ddi_features"]:
self.drugFeatureBuilder = DrugFeatureBuilder(featureSet)
if self.styles["evex"]:
self.evexFeatureBuilder = EVEXFeatureBuilder(featureSet)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder = GiulianoFeatureBuilder(featureSet)
self.pathLengths = length
assert(self.pathLengths == None)
self.types = types
if self.styles["random"]:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
def definePredictedValueRange(self, sentences, elementName):
self.multiEdgeFeatureBuilder.definePredictedValueRange(sentences, elementName)
def getPredictedValueRange(self):
return self.multiEdgeFeatureBuilder.predictedRange
def filterEdgesByType(self, edges, typesToInclude):
if len(typesToInclude) == 0:
return edges
edgesToKeep = []
for edge in edges:
if edge.get("type") in typesToInclude:
edgesToKeep.append(edge)
return edgesToKeep
def getCategoryNameFromTokens(self, sentenceGraph, t1, t2, directed=True):
"""
Example class. Multiple overlapping edges create a merged type.
"""
types = set()
# if sentenceGraph.interactionGraph.has_edge(t1, t2):
# intEdges = sentenceGraph.interactionGraph.get_edge_data(t1, t2, default={})
# # NOTE: Only works if keys are ordered integers
# for i in range(len(intEdges)):
# types.add(intEdges[i]["element"].get("type"))
# if (not directed) and sentenceGraph.interactionGraph.has_edge(t2, t1):
# intEdges = sentenceGraph.interactionGraph.get_edge(t2, t1, default={})
# # NOTE: Only works if keys are ordered integers
# for i in range(len(intEdges)):
# types.add(intEdges[i]["element"].get("type"))
intEdges = sentenceGraph.interactionGraph.getEdges(t1, t2)
if (not directed):
intEdges = intEdges + sentenceGraph.interactionGraph.getEdges(t2, t1)
for intEdge in intEdges:
types.add(intEdge[2].get("type"))
types = list(types)
types.sort()
categoryName = ""
for name in types:
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def getCategoryName(self, sentenceGraph, e1, e2, directed=True, duplicateEntities=None):
"""
Example class. Multiple overlapping edges create a merged type.
"""
# interactions = []
# e1s = [e1]
# if duplicateEntities != None and e1 in duplicateEntities:
# e1s += duplicateEntities[e1]
# e2s = [e2]
# if duplicateEntities != None and e2 in duplicateEntities:
# e2s += duplicateEntities[e2]
# for entity1 in e1s:
# for entity2 in e2s:
# interactions = interactions + sentenceGraph.getInteractions(entity1, entity2)
# if not directed:
# interactions = interactions + sentenceGraph.getInteractions(entity2, entity1)
interactions = sentenceGraph.getInteractions(e1, e2, True)
#print interactions
types = set()
for interaction in interactions:
types.add(interaction[2].get("type"))
types = list(types)
types.sort()
categoryName = ""
for name in types:
if self.styles["causeOnly"] and name != "Cause":
continue
if self.styles["themeOnly"] and name != "Theme":
continue
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def isPotentialRELInteraction(self, e1, e2):
if e1.get("type") == "Protein" and e2.get("type") == "Entity":
return True
else:
return False
def isPotentialBBInteraction(self, e1, e2, sentenceGraph):
#if e1.get("type") == "Bacterium" and e2.get("type") in ["Host", "HostPart", "Geographical", "Environmental", "Food", "Medical", "Soil", "Water"]:
# Note: "Environment" type is misspelled as "Environmental" in the BB-task documentation
if e1.get("type") == "Bacterium" and e2.get("type") in ["Host", "HostPart", "Geographical", "Environment", "Food", "Medical", "Soil", "Water"]:
return True
elif e1.get("type") == "Host" and e2.get("type") == "HostPart":
return True
else:
return False
def getBISuperType(self, eType):
if eType in ["GeneProduct", "Protein", "ProteinFamily", "PolymeraseComplex"]:
return "ProteinEntity"
elif eType in ["Gene", "GeneFamily", "GeneComplex", "Regulon", "Site", "Promoter"]:
return "GeneEntity"
else:
return None
def isPotentialBIInteraction(self, e1, e2, sentenceGraph, stats):
e1Type = e1.get("type")
e1SuperType = self.getBISuperType(e1Type)
e2Type = e2.get("type")
e2SuperType = self.getBISuperType(e2Type)
tag = "(" + e1Type + "/" + e2Type + ")"
if e1Type == "Regulon":
if e2SuperType in ["GeneEntity", "ProteinEntity"]:
return True
if e1SuperType == "ProteinEntity":
if e2Type in ["Site", "Promoter", "Gene", "GeneComplex"]:
return True
if e1Type in ["Action", "Transcription", "Expression"]:
return True
if e1Type == "Site":
if e2SuperType == "GeneEntity":
return True
if e1Type == "Promoter":
if e2SuperType in ["GeneEntity", "ProteinEntity"]:
return True
if e1SuperType in ["GeneEntity", "ProteinEntity"]:
if e2SuperType in ["GeneEntity", "ProteinEntity"]:
return True
stats.filter("bi_limits") #+tag)
return False
def isPotentialEPIInteraction(self, e1, e2, sentenceGraph):
if e1.get("type") != "Catalysis":
if e1.get("type") in ["Protein", "Entity"]:
return False
elif e2.get("type") in ["Protein", "Entity"]:
return True
else:
return False
else: # Catalysis
if e2.get("type") != "Entity":
return True
else:
return False
assert False, (e1.get("type"), e2.get("type"))
def isPotentialIDInteraction(self, e1, e2, sentenceGraph):
e1Type = e1.get("type")
e2Type = e2.get("type")
e1IsCore = e1Type in ["Protein", "Regulon-operon", "Two-component-system", "Chemical", "Organism"]
e2IsCore = e2Type in ["Protein", "Regulon-operon", "Two-component-system", "Chemical", "Organism"]
if e1IsCore:
return False
elif e1Type in ["Gene_expression", "Transcription"]:
if e2Type in ["Protein", "Regulon-operon"]:
return True
else:
return False
elif e1Type in ["Protein_catabolism", "Phosphorylation"]:
if e2Type == "Protein":
return True
else:
return False
elif e1Type == "Localization":
if e2IsCore or e2Type == "Entity":
return True
else:
return False
elif e1Type in ["Binding", "Process"]:
if e2IsCore:
return True
else:
return False
elif "egulation" in e1Type:
if e2Type != "Entity":
return True
else:
return False
elif e1Type == "Entity":
if e2IsCore:
return True
else:
return False
assert False, (e1Type, e2Type)
def isPotentialCOInteraction(self, e1, e2, sentenceGraph):
if e1.get("type") == "Exp" and e2.get("type") == "Exp":
anaphoraTok = sentenceGraph.entityHeadTokenByEntity[e1]
antecedentTok = sentenceGraph.entityHeadTokenByEntity[e2]
antecedentTokenFound = False
for token in sentenceGraph.tokens:
if token == antecedentTok:
antecedentTokenFound = True
if token == anaphoraTok: # if, not elif, to take into accoutn cases where e1Tok == e2Tok
if antecedentTokenFound:
return True
else:
return False
assert False
elif e1.get("type") == "Exp" and e2.get("type") == "Protein":
return True
else:
return False
def isPotentialGeniaInteraction(self, e1, e2):
e1Type = e1.get("type")
e2Type = e2.get("type")
if e1Type == "Protein":
return False
elif e1Type in ["Entity", "Gene_expression", "Transcription", "Protein_catabolism", "Phosphorylation", "Binding"]:
if e2Type == "Protein":
return True
else:
return False
elif e1Type == "Localization":
if e2Type in ["Protein", "Entity"]:
return True
else:
return False
elif "egulation" in e1Type:
if e2Type != "Entity":
return True
else:
return False
assert False, (e1Type, e2Type)
def getGoldCategoryName(self, goldGraph, entityToGold, e1, e2, directed=True):
if len(entityToGold[e1]) > 0 and len(entityToGold[e2]) > 0:
return self.getCategoryName(goldGraph, entityToGold[e1][0], entityToGold[e2][0], directed=directed)
else:
return "neg"
def buildExamplesFromGraph(self, sentenceGraph, outfile, goldGraph = None):
"""
Build examples for a single sentence. Returns a list of examples.
See Core/ExampleUtils for example format.
"""
#examples = []
exampleIndex = 0
if self.styles["trigger_features"]:
self.triggerFeatureBuilder.initSentence(sentenceGraph)
if self.styles["evex"]:
self.evexFeatureBuilder.initSentence(sentenceGraph)
# Filter entities, if needed
#mergedIds = None
#duplicateEntities = None
#entities = sentenceGraph.entities
#entities, mergedIds, duplicateEntities = self.mergeEntities(sentenceGraph, False) # "no_duplicates" in self.styles)
sentenceGraph.mergeInteractionGraph(True)
entities = sentenceGraph.mergedEntities
entityToDuplicates = sentenceGraph.mergedEntityToDuplicates
self.exampleStats.addValue("Duplicate entities skipped", len(sentenceGraph.entities) - len(entities))
# Connect to optional gold graph
if goldGraph != None:
entityToGold = EvaluateInteractionXML.mapEntities(entities, goldGraph.entities)
paths = None
if not self.styles["no_path"]:
##undirected = sentenceGraph.getUndirectedDependencyGraph()
#undirected = self.nxMultiDiGraphToUndirected(sentenceGraph.dependencyGraph)
###undirected = sentenceGraph.dependencyGraph.to_undirected()
####undirected = NX10.MultiGraph(sentenceGraph.dependencyGraph) This didn't work
undirected = sentenceGraph.dependencyGraph.toUndirected()
#paths = NX10.all_pairs_shortest_path(undirected, cutoff=999)
paths = undirected
#for edge in sentenceGraph.dependencyGraph.edges:
# assert edge[2] != None
#for edge in undirected.edges:
# assert edge[2] != None
#if sentenceGraph.sentenceElement.get("id") == "GENIA.d70.s5":
# print [(x[0].get("id"), x[1].get("id"), x[2].get("id")) for x in sentenceGraph.dependencyGraph.edges]
# Generate examples based on interactions between entities or interactions between tokens
if self.styles["entities"]:
loopRange = len(entities)
else:
loopRange = len(sentenceGraph.tokens)
for i in range(loopRange-1):
for j in range(i+1,loopRange):
eI = None
eJ = None
if self.styles["entities"]:
eI = entities[i]
eJ = entities[j]
tI = sentenceGraph.entityHeadTokenByEntity[eI]
tJ = sentenceGraph.entityHeadTokenByEntity[eJ]
#if "no_ne_interactions" in self.styles and eI.get("isName") == "True" and eJ.get("isName") == "True":
# continue
if eI.get("type") == "neg" or eJ.get("type") == "neg":
continue
if self.styles["skip_extra_triggers"]:
if eI.get("source") != None or eJ.get("source") != None:
continue
else:
tI = sentenceGraph.tokens[i]
tJ = sentenceGraph.tokens[j]
# only consider paths between entities (NOTE! entities, not only named entities)
if self.styles["headsOnly"]:
if (len(sentenceGraph.tokenIsEntityHead[tI]) == 0) or (len(sentenceGraph.tokenIsEntityHead[tJ]) == 0):
continue
if self.styles["directed"]:
# define forward
if self.styles["entities"]:
categoryName = self.getCategoryName(sentenceGraph, eI, eJ, True)
if goldGraph != None:
categoryName = self.getGoldCategoryName(goldGraph, entityToGold, eI, eJ, True)
else:
categoryName = self.getCategoryNameFromTokens(sentenceGraph, tI, tJ, True)
# make forward
self.exampleStats.beginExample(categoryName)
makeExample = True
if self.styles["genia_limits"] and not self.isPotentialGeniaInteraction(eI, eJ):
makeExample = False
self.exampleStats.filter("genia_limits")
if self.styles["genia_task1"] and (eI.get("type") == "Entity" or eJ.get("type") == "Entity"):
makeExample = False
self.exampleStats.filter("genia_task1")
if self.styles["rel_limits"] and not self.isPotentialRELInteraction(eI, eJ):
makeExample = False
self.exampleStats.filter("rel_limits")
if self.styles["co_limits"] and not self.isPotentialCOInteraction(eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("co_limits")
if self.styles["bb_limits"] and not self.isPotentialBBInteraction(eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("bb_limits")
if categoryName != "neg":
self.exampleStats.filter("bb_limits(" + categoryName + ":" + eI.get("type") + "/" + eJ.get("type") + ")")
if self.styles["bi_limits"] and not self.isPotentialBIInteraction(eI, eJ, sentenceGraph, self.exampleStats):
makeExample = False
#self.exampleStats.filter("bi_limits")
if self.styles["epi_limits"] and not self.isPotentialEPIInteraction(eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("epi_limits")
if self.styles["id_limits"] and not self.isPotentialIDInteraction(eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("id_limits")
# if self.styles["selftrain_limits"] and (eI.get("selftrain") == "False" or eJ.get("selftrain") == "False"):
# makeExample = False
# self.exampleStats.filter("selftrain_limits")
# if self.styles["selftrain_group"] and (eI.get("selftraingroup") not in self.selfTrainGroups or eJ.get("selftraingroup") not in self.selfTrainGroups):
# makeExample = False
# self.exampleStats.filter("selftrain_group")
if self.styles["pos_only"] and categoryName == "neg":
makeExample = False
self.exampleStats.filter("pos_only")
if makeExample:
#examples.append( self.buildExample(tI, tJ, paths, sentenceGraph, categoryName, exampleIndex, eI, eJ) )
ExampleUtils.appendExamples([self.buildExample(tI, tJ, paths, sentenceGraph, categoryName, exampleIndex, eI, eJ)], outfile)
exampleIndex += 1
self.exampleStats.endExample()
# define reverse
if self.styles["entities"]:
categoryName = self.getCategoryName(sentenceGraph, eJ, eI, True)
if goldGraph != None:
categoryName = self.getGoldCategoryName(goldGraph, entityToGold, eJ, eI, True)
else:
categoryName = self.getCategoryNameFromTokens(sentenceGraph, tJ, tI, True)
# make reverse
self.exampleStats.beginExample(categoryName)
makeExample = True
if self.styles["genia_limits"] and not self.isPotentialGeniaInteraction(eJ, eI):
makeExample = False
self.exampleStats.filter("genia_limits")
if self.styles["genia_task1"] and (eI.get("type") == "Entity" or eJ.get("type") == "Entity"):
makeExample = False
self.exampleStats.filter("genia_task1")
if self.styles["rel_limits"] and not self.isPotentialRELInteraction(eJ, eI):
makeExample = False
self.exampleStats.filter("rel_limits")
if self.styles["co_limits"] and not self.isPotentialCOInteraction(eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("co_limits")
if self.styles["bb_limits"] and not self.isPotentialBBInteraction(eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("bb_limits")
if categoryName != "neg":
self.exampleStats.filter("bb_limits(" + categoryName + ":" + eJ.get("type") + "/" + eI.get("type") + ")")
if self.styles["bi_limits"] and not self.isPotentialBIInteraction(eJ, eI, sentenceGraph, self.exampleStats):
makeExample = False
#self.exampleStats.filter("bi_limits")
if self.styles["epi_limits"] and not self.isPotentialEPIInteraction(eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("epi_limits")
if self.styles["id_limits"] and not self.isPotentialIDInteraction(eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("id_limits")
# if self.styles["selftrain_limits"] and (eI.get("selftrain") == "False" or eJ.get("selftrain") == "False"):
# makeExample = False
# self.exampleStats.filter("selftrain_limits")
# if self.styles["selftrain_group"] and (eI.get("selftraingroup") not in self.selfTrainGroups or eJ.get("selftraingroup") not in self.selfTrainGroups):
# makeExample = False
# self.exampleStats.filter("selftrain_group")
if self.styles["pos_only"] and categoryName == "neg":
makeExample = False
self.exampleStats.filter("pos_only")
if makeExample:
#examples.append( self.buildExample(tJ, tI, paths, sentenceGraph, categoryName, exampleIndex, eJ, eI) )
ExampleUtils.appendExamples([self.buildExample(tJ, tI, paths, sentenceGraph, categoryName, exampleIndex, eJ, eI)], outfile)
exampleIndex += 1
self.exampleStats.endExample()
else:
if self.styles["entities"]:
categoryName = self.getCategoryName(sentenceGraph, eI, eJ, False)
else:
categoryName = self.getCategoryNameFromTokens(sentenceGraph, tI, tJ, False)
self.exampleStats.beginExample(categoryName)
forwardExample = self.buildExample(tI, tJ, paths, sentenceGraph, categoryName, exampleIndex, eI, eJ)
if not self.styles["graph_kernel"]:
reverseExample = self.buildExample(tJ, tI, paths, sentenceGraph, categoryName, exampleIndex, eJ, eI)
forwardExample[2].update(reverseExample[2])
#examples.append(forwardExample)
ExampleUtils.appendExamples([forwardExample], outfile)
exampleIndex += 1
self.exampleStats.endExample()
#return examples
return exampleIndex
def buildExample(self, token1, token2, paths, sentenceGraph, categoryName, exampleIndex, entity1=None, entity2=None):
"""
Build a single directed example for the potential edge between token1 and token2
"""
# dummy return for speed testing
#return (sentenceGraph.getSentenceId()+".x"+str(exampleIndex),1,{},{})
# define features
features = {}
if True: #token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
#if token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
# path = paths[token1][token2]
#else:
# path = [token1, token2]
if not self.styles["no_path"]:
# directedPath reduces performance by 0.01 pp
#directedPath = sentenceGraph.dependencyGraph.getPaths(token1, token2)
#if len(directedPath) == 0:
# directedPath = sentenceGraph.dependencyGraph.getPaths(token2, token1)
# for dp in directedPath:
# dp.reverse()
#if len(directedPath) == 0:
# path = paths.getPaths(token1, token2)
#else:
# path = directedPath
path = paths.getPaths(token1, token2)
if len(path) > 0:
#if len(path) > 1:
# print len(path)
path = path[0]
pathExists = True
else:
path = [token1, token2]
pathExists = False
else:
path = [token1, token2]
pathExists = False
#print token1.get("id"), token2.get("id")
assert(self.pathLengths == None)
if self.pathLengths == None or len(path)-1 in self.pathLengths:
# if not "no_ontology" in self.styles:
# self.ontologyFeatureBuilder.setFeatureVector(features)
# self.ontologyFeatureBuilder.buildOntologyFeaturesForPath(sentenceGraph, path)
# self.ontologyFeatureBuilder.setFeatureVector(None)
if self.styles["trigger_features"]: # F 85.52 -> 85.55
self.triggerFeatureBuilder.setFeatureVector(features)
self.triggerFeatureBuilder.tag = "trg1_"
self.triggerFeatureBuilder.buildFeatures(token1)
self.triggerFeatureBuilder.tag = "trg2_"
self.triggerFeatureBuilder.buildFeatures(token2)
self.triggerFeatureBuilder.setFeatureVector(None)
# REL features
if self.styles["rel_features"] and not self.styles["no_task"]:
self.relFeatureBuilder.setFeatureVector(features)
self.relFeatureBuilder.tag = "rel1_"
self.relFeatureBuilder.buildAllFeatures(sentenceGraph.tokens, sentenceGraph.tokens.index(token1))
self.relFeatureBuilder.tag = "rel2_"
self.relFeatureBuilder.buildAllFeatures(sentenceGraph.tokens, sentenceGraph.tokens.index(token2))
self.relFeatureBuilder.setFeatureVector(None)
if self.styles["bacteria_renaming"] and not self.styles["no_task"]:
self.bacteriaRenamingFeatureBuilder.setFeatureVector(features)
self.bacteriaRenamingFeatureBuilder.buildPairFeatures(entity1, entity2)
#self.bacteriaRenamingFeatureBuilder.buildSubstringFeatures(entity1, entity2) # decreases perf. 74.76 -> 72.41
self.bacteriaRenamingFeatureBuilder.setFeatureVector(None)
if self.styles["co_limits"] and not self.styles["no_task"]:
e1Offset = Range.charOffsetToSingleTuple(entity1.get("charOffset"))
e2Offset = Range.charOffsetToSingleTuple(entity2.get("charOffset"))
if Range.contains(e1Offset, e2Offset):
features[self.featureSet.getId("e1_contains_e2")] = 1
if entity2.get("isName") == "True":
features[self.featureSet.getId("e1_contains_e2name")] = 1
if Range.contains(e2Offset, e1Offset):
features[self.featureSet.getId("e2_contains_e1")] = 1
if entity1.get("isName") == "True":
features[self.featureSet.getId("e2_contains_e1name")] = 1
if self.styles["ddi_features"]:
self.drugFeatureBuilder.setFeatureVector(features)
self.drugFeatureBuilder.tag = "ddi_"
self.drugFeatureBuilder.buildPairFeatures(entity1, entity2)
if self.styles["ddi_mtmx"]:
self.drugFeatureBuilder.buildMTMXFeatures(entity1, entity2)
self.drugFeatureBuilder.setFeatureVector(None)
#if "graph_kernel" in self.styles or not "no_dependency" in self.styles:
# #print "Getting edges"
# if token1 != token2 and pathExists:
# #print "g1"
# edges = self.multiEdgeFeatureBuilder.getEdges(sentenceGraph.dependencyGraph, path)
# #print "g2"
# else:
# edges = None
if self.styles["graph_kernel"]:
self.graphKernelFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.graphKernelFeatureBuilder.buildGraphKernelFeatures(sentenceGraph, path)
self.graphKernelFeatureBuilder.setFeatureVector(None)
if self.styles["entity_type"]:
features[self.featureSet.getId("e1_"+entity1.get("type"))] = 1
features[self.featureSet.getId("e2_"+entity2.get("type"))] = 1
features[self.featureSet.getId("distance_"+str(len(path)))] = 1
if not self.styles["no_dependency"]:
#print "Dep features"
self.multiEdgeFeatureBuilder.setFeatureVector(features, entity1, entity2)
#self.multiEdgeFeatureBuilder.buildStructureFeatures(sentenceGraph, paths) # remove for fast
if not self.styles["disable_entity_features"]:
self.multiEdgeFeatureBuilder.buildEntityFeatures(sentenceGraph)
self.multiEdgeFeatureBuilder.buildPathLengthFeatures(path)
if not self.styles["disable_terminus_features"]:
self.multiEdgeFeatureBuilder.buildTerminusTokenFeatures(path, sentenceGraph) # remove for fast
if not self.styles["disable_single_element_features"]:
self.multiEdgeFeatureBuilder.buildSingleElementFeatures(path, sentenceGraph)
if not self.styles["disable_ngram_features"]:
#print "NGrams"
self.multiEdgeFeatureBuilder.buildPathGrams(2, path, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(3, path, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(4, path, sentenceGraph) # remove for fast
#self.buildEdgeCombinations(path, edges, sentenceGraph, features) # remove for fast
#if edges != None:
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[0], edges[0][1]+edges[1][0], "t1", sentenceGraph) # remove for fast
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[-1], edges[len(path)-1][len(path)-2]+edges[len(path)-2][len(path)-1], "t2", sentenceGraph) # remove for fast
if not self.styles["disable_path_edge_features"]:
self.multiEdgeFeatureBuilder.buildPathEdgeFeatures(path, sentenceGraph)
self.multiEdgeFeatureBuilder.buildSentenceFeatures(sentenceGraph)
self.multiEdgeFeatureBuilder.setFeatureVector(None)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder.setFeatureVector(features, entity1, entity2)
shortestPaths = self.nodalidaFeatureBuilder.buildShortestPaths(sentenceGraph.dependencyGraph, path)
print shortestPaths
if len(shortestPaths) > 0:
self.nodalidaFeatureBuilder.buildNGrams(shortestPaths, sentenceGraph)
self.nodalidaFeatureBuilder.setFeatureVector(None)
if not self.styles["no_linear"]:
self.tokenFeatureBuilder.setFeatureVector(features)
for i in range(len(sentenceGraph.tokens)):
if sentenceGraph.tokens[i] == token1:
token1Index = i
if sentenceGraph.tokens[i] == token2:
token2Index = i
linearPreTag = "linfw_"
if token1Index > token2Index:
token1Index, token2Index = token2Index, token1Index
linearPreTag = "linrv_"
self.tokenFeatureBuilder.buildLinearOrderFeatures(token1Index, sentenceGraph, 2, 2, preTag="linTok1")
self.tokenFeatureBuilder.buildLinearOrderFeatures(token2Index, sentenceGraph, 2, 2, preTag="linTok2")
# Before, middle, after
# self.tokenFeatureBuilder.buildTokenGrams(0, token1Index-1, sentenceGraph, "bf")
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, "bw")
# self.tokenFeatureBuilder.buildTokenGrams(token2Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, "af")
# before-middle, middle, middle-after
# self.tokenFeatureBuilder.buildTokenGrams(0, token2Index-1, sentenceGraph, linearPreTag+"bf", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, linearPreTag+"bw", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, linearPreTag+"af", max=2)
self.tokenFeatureBuilder.setFeatureVector(None)
if self.styles["random"]:
self.randomFeatureBuilder.setFeatureVector(features)
self.randomFeatureBuilder.buildRandomFeatures(100, 0.01)
self.randomFeatureBuilder.setFeatureVector(None)
if self.styles["genia_limits"] and not self.styles["no_task"]:
e1Type = entity1.get("type")
e2Type = entity2.get("type")
assert(entity1.get("isName") == "False")
if entity2.get("isName") == "True":
features[self.featureSet.getId("GENIA_target_protein")] = 1
else:
features[self.featureSet.getId("GENIA_nested_event")] = 1
if e1Type.find("egulation") != -1: # leave r out to avoid problems with capitalization
if entity2.get("isName") == "True":
features[self.featureSet.getId("GENIA_regulation_of_protein")] = 1
else:
features[self.featureSet.getId("GENIA_regulation_of_event")] = 1
if self.styles["bi_limits"]:
# Make features based on entity types
e1Type = entity1.get("type")
e2Type = entity2.get("type")
e1SuperType = str(self.getBISuperType(e1Type))
e2SuperType = str(self.getBISuperType(e2Type))
features[self.featureSet.getId("BI_e1_"+e1Type)] = 1
features[self.featureSet.getId("BI_e2_"+e2Type)] = 1
features[self.featureSet.getId("BI_e1sup_"+e1SuperType)] = 1
features[self.featureSet.getId("BI_e2sup_"+e2SuperType)] = 1
features[self.featureSet.getId("BI_e1e2_"+e1Type+"_"+e2Type)] = 1
features[self.featureSet.getId("BI_e1e2sup_"+e1SuperType+"_"+e2SuperType)] = 1
if self.styles["evex"]:
self.evexFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.evexFeatureBuilder.buildEdgeFeatures(entity1, entity2, token1, token2, path, sentenceGraph)
self.evexFeatureBuilder.setFeatureVector(None)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.giulianoFeatureBuilder.buildEdgeFeatures(entity1, entity2, token1, token2, path, sentenceGraph)
self.giulianoFeatureBuilder.setFeatureVector(None)
else:
features[self.featureSet.getId("always_negative")] = 1
if self.styles["subset"]:
features[self.featureSet.getId("out_of_scope")] = 1
else:
features[self.featureSet.getId("always_negative")] = 1
if self.styles["subset"]:
features[self.featureSet.getId("out_of_scope")] = 1
path = [token1, token2]
# define extra attributes
#if int(path[0].get("id").split("_")[-1]) < int(path[-1].get("id").split("_")[-1]):
if int(path[0].get("charOffset").split("-")[0]) < int(path[-1].get("charOffset").split("-")[0]):
#extra = {"xtype":"edge","type":"i","t1":path[0],"t2":path[-1]}
extra = {"xtype":"edge","type":"i","t1":path[0].get("id"),"t2":path[-1].get("id")}
extra["deprev"] = False
else:
#extra = {"xtype":"edge","type":"i","t1":path[-1],"t2":path[0]}
extra = {"xtype":"edge","type":"i","t1":path[-1].get("id"),"t2":path[0].get("id")}
extra["deprev"] = True
if entity1 != None:
#extra["e1"] = entity1
extra["e1"] = entity1.get("id")
if sentenceGraph.mergedEntityToDuplicates != None:
#extra["e1GoldIds"] = mergedEntityIds[entity1]
extra["e1DuplicateIds"] = ",".join([x.get("id") for x in sentenceGraph.mergedEntityToDuplicates[entity1]])
if entity2 != None:
#extra["e2"] = entity2
extra["e2"] = entity2.get("id")
if sentenceGraph.mergedEntityToDuplicates != None:
extra["e2DuplicateIds"] = ",".join([x.get("id") for x in sentenceGraph.mergedEntityToDuplicates[entity2]])
#extra["e2GoldIds"] = mergedEntityIds[entity2]
extra["categoryName"] = categoryName
if self.styles["bacteria_renaming"]:
if entity1.get("text") != None and entity1.get("text") != "":
extra["e1t"] = entity1.get("text").replace(" ", "---").replace(":","-COL-")
if entity2.get("text") != None and entity2.get("text") != "":
extra["e2t"] = entity2.get("text").replace(" ", "---").replace(":","-COL-")
sentenceOrigId = sentenceGraph.sentenceElement.get("origId")
if sentenceOrigId != None:
extra["SOID"] = sentenceOrigId
# make example
if self.styles["binary"]:
if categoryName != "neg":
category = 1
else:
category = -1
categoryName = "i"
else:
category = self.classSet.getId(categoryName)
# NOTE: temporarily disable for replicating 110310 experiment
#features[self.featureSet.getId("extra_constant")] = 1
return (sentenceGraph.getSentenceId()+".x"+str(exampleIndex),category,features,extra)
def __init__(self, style=None, types=[], featureSet=None, classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
assert( classSet.getId("neg") == 1 or (len(classSet.Ids)== 2 and classSet.getId("neg") == -1) )
# Basic style = trigger_features:typed:directed:no_linear:entities:auto_limits:noMasking:maxFeatures
self._setDefaultParameters([
"directed", "undirected", "headsOnly", "graph_kernel", "noAnnType", "mask_nodes", "limit_features",
"no_auto_limits", "co_features", "genia_features", "bi_features", #"genia_limits", "epi_limits", "id_limits", "rel_limits", "bb_limits", "bi_limits", "co_limits",
"genia_task1", "ontology", "nodalida", "bacteria_renaming", "no_trigger_features", "rel_features",
"drugbank_features", "ddi_mtmx", "evex", "giuliano", "random", "themeOnly", "causeOnly", "no_path", "token_nodes",
"skip_extra_triggers", "headsOnly", "graph_kernel", "no_task", "no_dependency",
"disable_entity_features", "disable_terminus_features", "disable_single_element_features",
"disable_ngram_features", "disable_path_edge_features", "linear_features", "subset", "binary", "pos_only",
"entity_type", "filter_shortest_path", "maskTypeAsProtein", "keep_neg", "metamap",
"sdb_merge", "sdb_features", "ontobiotope_features", "no_self_loops", "full_entities",
"no_features", "wordnet", "wordvector", "se10t8_undirected", "filter_types", "doc_extra",
"entity_extra"])
self.styles = self.getParameters(style)
#if style == None: # no parameters given
# style["typed"] = style["directed"] = style["headsOnly"] = True
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet, self.styles)
# NOTE Temporarily re-enabling predicted range
#self.multiEdgeFeatureBuilder.definePredictedValueRange([], None)
if self.styles["graph_kernel"]:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(self.featureSet)
if self.styles["noAnnType"]:
self.multiEdgeFeatureBuilder.noAnnType = True
if self.styles["mask_nodes"]:
self.multiEdgeFeatureBuilder.maskNamedEntities = True
else:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if not self.styles["limit_features"]:
self.multiEdgeFeatureBuilder.maximum = True
if self.styles["genia_task1"]:
self.multiEdgeFeatureBuilder.filterAnnTypes.add("Entity")
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if self.styles["ontology"]:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(self.featureSet)
if self.styles["ontobiotope_features"]:
self.ontobiotopeFeatureBuilder = OntoBiotopeFeatureBuilder(self.featureSet)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(self.featureSet)
if self.styles["bacteria_renaming"]:
self.bacteriaRenamingFeatureBuilder = BacteriaRenamingFeatureBuilder(self.featureSet)
if not self.styles["no_trigger_features"]:
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet, self.styles)
self.triggerFeatureBuilder.useNonNameEntities = True
if self.styles["noAnnType"]:
self.triggerFeatureBuilder.noAnnType = True
if self.styles["genia_task1"]:
self.triggerFeatureBuilder.filterAnnTypes.add("Entity")
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
if self.styles["rel_features"]:
self.relFeatureBuilder = RELFeatureBuilder(featureSet)
if self.styles["drugbank_features"]:
self.drugFeatureBuilder = DrugFeatureBuilder(featureSet)
if self.styles["evex"]:
self.evexFeatureBuilder = EVEXFeatureBuilder(featureSet)
if self.styles["wordnet"]:
self.wordNetFeatureBuilder = WordNetFeatureBuilder(featureSet)
if self.styles["wordvector"]:
self.wordVectorFeatureBuilder = WordVectorFeatureBuilder(featureSet, self.styles)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder = GiulianoFeatureBuilder(featureSet)
self.types = types
if self.styles["random"]:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
class EdgeExampleBuilder(ExampleBuilder):
"""
This example builder makes edge examples, i.e. examples describing
the event arguments.
"""
def __init__(self, style=None, types=[], featureSet=None, classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
assert( classSet.getId("neg") == 1 or (len(classSet.Ids)== 2 and classSet.getId("neg") == -1) )
# Basic style = trigger_features:typed:directed:no_linear:entities:auto_limits:noMasking:maxFeatures
self._setDefaultParameters([
"directed", "undirected", "headsOnly", "graph_kernel", "noAnnType", "mask_nodes", "limit_features",
"no_auto_limits", "co_features", "genia_features", "bi_features", #"genia_limits", "epi_limits", "id_limits", "rel_limits", "bb_limits", "bi_limits", "co_limits",
"genia_task1", "ontology", "nodalida", "bacteria_renaming", "no_trigger_features", "rel_features",
"drugbank_features", "ddi_mtmx", "evex", "giuliano", "random", "themeOnly", "causeOnly", "no_path", "token_nodes",
"skip_extra_triggers", "headsOnly", "graph_kernel", "no_task", "no_dependency",
"disable_entity_features", "disable_terminus_features", "disable_single_element_features",
"disable_ngram_features", "disable_path_edge_features", "linear_features", "subset", "binary", "pos_only",
"entity_type", "filter_shortest_path", "maskTypeAsProtein", "keep_neg", "metamap",
"sdb_merge", "sdb_features", "ontobiotope_features", "no_self_loops", "full_entities",
"no_features", "wordnet", "wordvector", "se10t8_undirected", "filter_types", "doc_extra",
"entity_extra"])
self.styles = self.getParameters(style)
#if style == None: # no parameters given
# style["typed"] = style["directed"] = style["headsOnly"] = True
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet, self.styles)
# NOTE Temporarily re-enabling predicted range
#self.multiEdgeFeatureBuilder.definePredictedValueRange([], None)
if self.styles["graph_kernel"]:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(self.featureSet)
if self.styles["noAnnType"]:
self.multiEdgeFeatureBuilder.noAnnType = True
if self.styles["mask_nodes"]:
self.multiEdgeFeatureBuilder.maskNamedEntities = True
else:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if not self.styles["limit_features"]:
self.multiEdgeFeatureBuilder.maximum = True
if self.styles["genia_task1"]:
self.multiEdgeFeatureBuilder.filterAnnTypes.add("Entity")
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if self.styles["ontology"]:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(self.featureSet)
if self.styles["ontobiotope_features"]:
self.ontobiotopeFeatureBuilder = OntoBiotopeFeatureBuilder(self.featureSet)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(self.featureSet)
if self.styles["bacteria_renaming"]:
self.bacteriaRenamingFeatureBuilder = BacteriaRenamingFeatureBuilder(self.featureSet)
if not self.styles["no_trigger_features"]:
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet, self.styles)
self.triggerFeatureBuilder.useNonNameEntities = True
if self.styles["noAnnType"]:
self.triggerFeatureBuilder.noAnnType = True
if self.styles["genia_task1"]:
self.triggerFeatureBuilder.filterAnnTypes.add("Entity")
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
if self.styles["rel_features"]:
self.relFeatureBuilder = RELFeatureBuilder(featureSet)
if self.styles["drugbank_features"]:
self.drugFeatureBuilder = DrugFeatureBuilder(featureSet)
if self.styles["evex"]:
self.evexFeatureBuilder = EVEXFeatureBuilder(featureSet)
if self.styles["wordnet"]:
self.wordNetFeatureBuilder = WordNetFeatureBuilder(featureSet)
if self.styles["wordvector"]:
self.wordVectorFeatureBuilder = WordVectorFeatureBuilder(featureSet, self.styles)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder = GiulianoFeatureBuilder(featureSet)
self.types = types
if self.styles["random"]:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
def definePredictedValueRange(self, sentences, elementName):
self.multiEdgeFeatureBuilder.definePredictedValueRange(sentences, elementName)
def getPredictedValueRange(self):
return self.multiEdgeFeatureBuilder.predictedRange
def filterEdgesByType(self, edges, typesToInclude):
if len(typesToInclude) == 0:
return edges
edgesToKeep = []
for edge in edges:
if edge.get("type") in typesToInclude:
edgesToKeep.append(edge)
return edgesToKeep
def getCategoryNameFromTokens(self, sentenceGraph, t1, t2, directed=True):
"""
Example class. Multiple overlapping edges create a merged type.
"""
types = set()
intEdges = sentenceGraph.interactionGraph.getEdges(t1, t2)
if not directed:
intEdges = intEdges + sentenceGraph.interactionGraph.getEdges(t2, t1)
for intEdge in intEdges:
types.add(intEdge[2].get("type"))
types = list(types)
types.sort()
categoryName = ""
for name in types:
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def getCategoryName(self, sentenceGraph, e1, e2, directed=True):
"""
Example class. Multiple overlapping edges create a merged type.
"""
interactions = sentenceGraph.getInteractions(e1, e2, True)
if not directed and not self.styles["se10t8_undirected"]:
interactions = interactions + sentenceGraph.getInteractions(e2, e1, True)
types = set()
for interaction in interactions:
types.add(interaction[2].get("type"))
types = list(types)
types.sort()
categoryName = ""
for name in types:
if self.styles["causeOnly"] and name != "Cause":
continue
if self.styles["themeOnly"] and name != "Theme":
continue
if categoryName != "":
categoryName += "---"
if self.styles["sdb_merge"]:
name = self.mergeForSeeDev(name, self.structureAnalyzer)
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def getBISuperType(self, eType):
if eType in ["GeneProduct", "Protein", "ProteinFamily", "PolymeraseComplex"]:
return "ProteinEntity"
elif eType in ["Gene", "GeneFamily", "GeneComplex", "Regulon", "Site", "Promoter"]:
return "GeneEntity"
else:
return None
def getSeeDevSuperTypes(self, eType):
if eType in ("Gene", "Gene_Family", "Box", "Promoter"):
return ("DNA", "Molecule")
elif eType == "RNA":
return ("RNA", "DNA_Product", "Molecule")
elif eType in ("Protein", "Protein_Family", "Protein_Complex", "Protein_Domain"):
return ("Amino_acid_sequence", "DNA_Product", "Molecule")
elif eType == "Hormone":
return ("Molecule",)
elif eType in ("Regulatory_Network", "Pathway"):
return ("Dynamic_process",)
elif eType in ("Genotype", "Tissue", "Development_Phase"):
return ("Biological_context", "Context")
elif eType == "Environmental_Factor":
return ("Context",)
else:
raise Exception("Unknown SeeDev type '" + str(eType) + "'")
def mergeForSeeDev(self, categoryName, structureAnalyzer):
if categoryName in structureAnalyzer.typeMap["forward"]:
return structureAnalyzer.typeMap["forward"][categoryName]
return categoryName
# for tag in ("Regulates", "Exists", "Interacts", "Is", "Occurs"):
# if categoryName.startswith(tag):
# categoryName = tag
# break
# return categoryName
def processCorpus(self, input, output, gold=None, append=False, allowNewIds=True, structureAnalyzer=None):
if self.styles["sdb_merge"]:
structureAnalyzer.determineNonOverlappingTypes()
self.structureAnalyzer = structureAnalyzer
ExampleBuilder.processCorpus(self, input, output, gold, append, allowNewIds, structureAnalyzer)
def isValidInteraction(self, e1, e2, structureAnalyzer,forceUndirected=False):
return len(structureAnalyzer.getValidEdgeTypes(e1.get("type"), e2.get("type"), forceUndirected=forceUndirected)) > 0
def getGoldCategoryName(self, goldGraph, entityToGold, e1, e2, directed=True):
if len(entityToGold[e1]) > 0 and len(entityToGold[e2]) > 0:
return self.getCategoryName(goldGraph, entityToGold[e1][0], entityToGold[e2][0], directed=directed)
else:
return "neg"
def filterEdge(self, edge, edgeTypes):
import types
assert edgeTypes != None
if type(edgeTypes) not in [types.ListType, types.TupleType]:
edgeTypes = [edgeTypes]
if edge[2].get("type") in edgeTypes:
return True
else:
return False
def keepExample(self, e1, e2, categoryName, isDirected, structureAnalyzer):
makeExample = True
if (not self.styles["no_auto_limits"]) and not self.isValidInteraction(e1, e2, structureAnalyzer, forceUndirected=not isDirected):
makeExample = False
self.exampleStats.filter("auto_limits")
if self.styles["genia_task1"] and (e1.get("type") == "Entity" or e2.get("type") == "Entity"):
makeExample = False
self.exampleStats.filter("genia_task1")
if self.styles["pos_only"] and categoryName == "neg":
makeExample = False
self.exampleStats.filter("pos_only")
if self.styles["no_self_loops"] and ((e1 == e2) or (e1.get("headOffset") == e2.get("headOffset"))):
makeExample = False
self.exampleStats.filter("no_self_loops")
return makeExample
def getExampleCategoryName(self, e1=None, e2=None, t1=None, t2=None, sentenceGraph=None, goldGraph=None, entityToGold=None, isDirected=True, structureAnalyzer=None):
if self.styles["token_nodes"]:
categoryName = self.getCategoryNameFromTokens(sentenceGraph, t1, t2, isDirected)
else:
categoryName = self.getCategoryName(sentenceGraph, e1, e2, isDirected)
if goldGraph != None:
categoryName = self.getGoldCategoryName(goldGraph, entityToGold, e1, e2, isDirected)
if self.styles["filter_types"] != None and categoryName in self.styles["filter_types"]:
categoryName = "neg"
if self.styles["se10t8_undirected"]:
assert e1.get("id").endswith(".e1")
assert e2.get("id").endswith(".e2")
#if self.styles["sdb_merge"]:
# categoryName = self.mergeForSeeDev(categoryName, structureAnalyzer)
return categoryName
def buildExamplesFromGraph(self, sentenceGraph, outfile, goldGraph = None, structureAnalyzer=None):
"""
Build examples for a single sentence. Returns a list of examples.
See Core/ExampleUtils for example format.
"""
#examples = []
exampleIndex = 0
# example directionality
if self.styles["directed"] == None and self.styles["undirected"] == None: # determine directedness from corpus
examplesAreDirected = structureAnalyzer.hasDirectedTargets() if structureAnalyzer != None else True
elif self.styles["directed"]:
assert self.styles["undirected"] in [None, False]
examplesAreDirected = True
elif self.styles["undirected"]:
assert self.styles["directed"] in [None, False]
examplesAreDirected = False
if not self.styles["no_trigger_features"]:
self.triggerFeatureBuilder.initSentence(sentenceGraph)
if self.styles["evex"]:
self.evexFeatureBuilder.initSentence(sentenceGraph)
# if self.styles["sdb_merge"]:
# self.determineNonOverlappingTypes(structureAnalyzer)
# Filter entities, if needed
sentenceGraph.mergeInteractionGraph(True)
entities = sentenceGraph.mergedEntities
entityToDuplicates = sentenceGraph.mergedEntityToDuplicates
self.exampleStats.addValue("Duplicate entities skipped", len(sentenceGraph.entities) - len(entities))
# Connect to optional gold graph
entityToGold = None
if goldGraph != None:
entityToGold = EvaluateInteractionXML.mapEntities(entities, goldGraph.entities)
paths = None
if not self.styles["no_path"]:
undirected = sentenceGraph.dependencyGraph.toUndirected()
paths = undirected
if self.styles["filter_shortest_path"] != None: # For DDI use filter_shortest_path=conj_and
paths.resetAnalyses() # just in case
paths.FloydWarshall(self.filterEdge, {"edgeTypes":self.styles["filter_shortest_path"]})
# Generate examples based on interactions between entities or interactions between tokens
if self.styles["token_nodes"]:
loopRange = len(sentenceGraph.tokens)
else:
loopRange = len(entities)
for i in range(loopRange-1):
for j in range(i+1,loopRange):
eI = None
eJ = None
if self.styles["token_nodes"]:
tI = sentenceGraph.tokens[i]
tJ = sentenceGraph.tokens[j]
else:
eI = entities[i]
eJ = entities[j]
tI = sentenceGraph.entityHeadTokenByEntity[eI]
tJ = sentenceGraph.entityHeadTokenByEntity[eJ]
if eI.get("type") == "neg" or eJ.get("type") == "neg":
continue
if self.styles["skip_extra_triggers"]:
if eI.get("source") != None or eJ.get("source") != None:
continue
# only consider paths between entities (NOTE! entities, not only named entities)
if self.styles["headsOnly"]:
if (len(sentenceGraph.tokenIsEntityHead[tI]) == 0) or (len(sentenceGraph.tokenIsEntityHead[tJ]) == 0):
continue
examples = self.buildExamplesForPair(tI, tJ, paths, sentenceGraph, goldGraph, entityToGold, eI, eJ, structureAnalyzer, examplesAreDirected)
for categoryName, features, extra in examples:
# make example
if self.styles["binary"]:
if categoryName != "neg":
category = 1
else:
category = -1
extra["categoryName"] = "i"
else:
category = self.classSet.getId(categoryName)
example = [sentenceGraph.getSentenceId()+".x"+str(exampleIndex), category, features, extra]
ExampleUtils.appendExamples([example], outfile)
exampleIndex += 1
return exampleIndex
def buildExamplesForPair(self, token1, token2, paths, sentenceGraph, goldGraph, entityToGold, entity1=None, entity2=None, structureAnalyzer=None, isDirected=True):
# define forward
categoryName = self.getExampleCategoryName(entity1, entity2, token1, token2, sentenceGraph, goldGraph, entityToGold, isDirected, structureAnalyzer=structureAnalyzer)
# make forward
forwardExample = None
self.exampleStats.beginExample(categoryName)
if self.keepExample(entity1, entity2, categoryName, isDirected, structureAnalyzer):
forwardExample = self.buildExample(token1, token2, paths, sentenceGraph, categoryName, entity1, entity2, structureAnalyzer, isDirected)
if isDirected: # build a separate reverse example (if that is valid)
self.exampleStats.endExample() # end forward example
# define reverse
categoryName = self.getExampleCategoryName(entity2, entity1, token2, token1, sentenceGraph, goldGraph, entityToGold, True, structureAnalyzer=structureAnalyzer)
# make reverse
self.exampleStats.beginExample(categoryName)
reverseExample = None
if self.keepExample(entity2, entity1, categoryName, True, structureAnalyzer):
reverseExample = self.buildExample(token2, token1, paths, sentenceGraph, categoryName, entity2, entity1, structureAnalyzer, isDirected)
self.exampleStats.endExample()
return filter(None, [forwardExample, reverseExample])
elif self.styles["se10t8_undirected"]: # undirected example with a directed type
self.exampleStats.endExample()
return [forwardExample]
elif forwardExample != None: # merge features from the reverse example to the forward one
reverseExample = self.buildExample(token2, token1, paths, sentenceGraph, categoryName, entity2, entity1, structureAnalyzer, isDirected)
forwardExample[1].update(reverseExample[1])
self.exampleStats.endExample() # end merged example
return [forwardExample]
else: # undirected example that was filtered
self.exampleStats.endExample() # end merged example
return []
def buildExample(self, token1, token2, paths, sentenceGraph, categoryName, entity1=None, entity2=None, structureAnalyzer=None, isDirected=True):
"""
Build a single directed example for the potential edge between token1 and token2
"""
# define features
if not self.styles["no_path"]:
path = paths.getPaths(token1, token2)
if len(path) > 0:
path = path[0]
#pathExists = True
else:
path = [token1, token2]
#pathExists = False
else:
path = [token1, token2]
#pathExists = False
features = {}
if not self.styles["no_features"]:
features = self.buildFeatures(sentenceGraph, entity1, entity2, token1, token2, path)
# define extra attributes
if int(path[0].get("charOffset").split("-")[0]) < int(path[-1].get("charOffset").split("-")[0]):
extra = {"xtype":"edge","type":"i","t1":path[0].get("id"),"t2":path[-1].get("id")}
extra["deprev"] = False
else:
extra = {"xtype":"edge","type":"i","t1":path[-1].get("id"),"t2":path[0].get("id")}
extra["deprev"] = True
if entity1 != None:
extra["e1"] = entity1.get("id")
if sentenceGraph.mergedEntityToDuplicates != None:
extra["e1DuplicateIds"] = ",".join([x.get("id") for x in sentenceGraph.mergedEntityToDuplicates[entity1]])
if entity2 != None:
extra["e2"] = entity2.get("id")
if sentenceGraph.mergedEntityToDuplicates != None:
extra["e2DuplicateIds"] = ",".join([x.get("id") for x in sentenceGraph.mergedEntityToDuplicates[entity2]])
extra["categoryName"] = categoryName
if self.styles["bacteria_renaming"]:
if entity1.get("text") != None and entity1.get("text") != "":
extra["e1t"] = entity1.get("text").replace(" ", "---").replace(":","-COL-")
if entity2.get("text") != None and entity2.get("text") != "":
extra["e2t"] = entity2.get("text").replace(" ", "---").replace(":","-COL-")
if self.styles["doc_extra"]:
if hasattr(sentenceGraph, "documentElement") and sentenceGraph.documentElement.get("origId") != None:
extra["DOID"] = sentenceGraph.documentElement.get("origId")
if self.styles["entity_extra"]:
if entity1.get("origId") != None: extra["e1OID"] = entity1.get("origId")
if entity2.get("origId") != None: extra["e2OID"] = entity2.get("origId")
sentenceOrigId = sentenceGraph.sentenceElement.get("origId")
if sentenceOrigId != None:
extra["SOID"] = sentenceOrigId
extra["directed"] = str(isDirected)
if self.styles["sdb_merge"]:
extra["sdb_merge"] = "True"
#print extra
return (categoryName, features, extra)
def buildFeatures(self, sentenceGraph, entity1, entity2, token1, token2, path):
features = {}
if not self.styles["no_trigger_features"]: # F 85.52 -> 85.55
self.triggerFeatureBuilder.setFeatureVector(features)
self.triggerFeatureBuilder.tag = "trg1_"
self.triggerFeatureBuilder.buildFeatures(token1)
self.triggerFeatureBuilder.tag = "trg2_"
self.triggerFeatureBuilder.buildFeatures(token2)
self.triggerFeatureBuilder.setFeatureVector(None)
# REL features
if self.styles["rel_features"] and not self.styles["no_task"]:
self.relFeatureBuilder.setFeatureVector(features)
self.relFeatureBuilder.tag = "rel1_"
self.relFeatureBuilder.buildAllFeatures(sentenceGraph.tokens, sentenceGraph.tokens.index(token1))
self.relFeatureBuilder.tag = "rel2_"
self.relFeatureBuilder.buildAllFeatures(sentenceGraph.tokens, sentenceGraph.tokens.index(token2))
self.relFeatureBuilder.setFeatureVector(None)
if self.styles["bacteria_renaming"] and not self.styles["no_task"]:
self.bacteriaRenamingFeatureBuilder.setFeatureVector(features)
self.bacteriaRenamingFeatureBuilder.buildPairFeatures(entity1, entity2)
#self.bacteriaRenamingFeatureBuilder.buildSubstringFeatures(entity1, entity2) # decreases perf. 74.76 -> 72.41
self.bacteriaRenamingFeatureBuilder.setFeatureVector(None)
if self.styles["co_features"] and not self.styles["no_task"]:
e1Offset = Range.charOffsetToSingleTuple(entity1.get("charOffset"))
e2Offset = Range.charOffsetToSingleTuple(entity2.get("charOffset"))
if Range.contains(e1Offset, e2Offset):
features[self.featureSet.getId("e1_contains_e2")] = 1
if entity2.get("given") == "True":
features[self.featureSet.getId("e1_contains_e2name")] = 1
if Range.contains(e2Offset, e1Offset):
features[self.featureSet.getId("e2_contains_e1")] = 1
if entity1.get("given") == "True":
features[self.featureSet.getId("e2_contains_e1name")] = 1
if self.styles["drugbank_features"]:
self.drugFeatureBuilder.setFeatureVector(features)
self.drugFeatureBuilder.tag = "ddi_"
self.drugFeatureBuilder.buildPairFeatures(entity1, entity2)
if self.styles["ddi_mtmx"]:
self.drugFeatureBuilder.buildMTMXFeatures(entity1, entity2)
self.drugFeatureBuilder.setFeatureVector(None)
if self.styles["graph_kernel"]:
self.graphKernelFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.graphKernelFeatureBuilder.buildGraphKernelFeatures(sentenceGraph, path)
self.graphKernelFeatureBuilder.setFeatureVector(None)
if self.styles["entity_type"]:
e1Type = self.multiEdgeFeatureBuilder.getEntityType(entity1)
e2Type = self.multiEdgeFeatureBuilder.getEntityType(entity2)
features[self.featureSet.getId("e1_"+e1Type)] = 1
features[self.featureSet.getId("e2_"+e2Type)] = 1
features[self.featureSet.getId("distance_"+str(len(path)))] = 1
if not self.styles["no_dependency"]:
#print "Dep features"
self.multiEdgeFeatureBuilder.setFeatureVector(features, entity1, entity2)
#self.multiEdgeFeatureBuilder.buildStructureFeatures(sentenceGraph, paths) # remove for fast
if not self.styles["disable_entity_features"]:
self.multiEdgeFeatureBuilder.buildEntityFeatures(sentenceGraph)
self.multiEdgeFeatureBuilder.buildPathLengthFeatures(path)
if not self.styles["disable_terminus_features"]:
self.multiEdgeFeatureBuilder.buildTerminusTokenFeatures(path, sentenceGraph) # remove for fast
if not self.styles["disable_single_element_features"]:
self.multiEdgeFeatureBuilder.buildSingleElementFeatures(path, sentenceGraph)
if not self.styles["disable_ngram_features"]:
#print "NGrams"
self.multiEdgeFeatureBuilder.buildPathGrams(2, path, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(3, path, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(4, path, sentenceGraph) # remove for fast
#self.buildEdgeCombinations(path, edges, sentenceGraph, features) # remove for fast
#if edges != None:
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[0], edges[0][1]+edges[1][0], "t1", sentenceGraph) # remove for fast
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[-1], edges[len(path)-1][len(path)-2]+edges[len(path)-2][len(path)-1], "t2", sentenceGraph) # remove for fast
if not self.styles["disable_path_edge_features"]:
self.multiEdgeFeatureBuilder.buildPathEdgeFeatures(path, sentenceGraph)
self.multiEdgeFeatureBuilder.buildSentenceFeatures(sentenceGraph)
self.multiEdgeFeatureBuilder.setFeatureVector(None)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder.setFeatureVector(features, entity1, entity2)
shortestPaths = self.nodalidaFeatureBuilder.buildShortestPaths(sentenceGraph.dependencyGraph, path)
print shortestPaths
if len(shortestPaths) > 0:
self.nodalidaFeatureBuilder.buildNGrams(shortestPaths, sentenceGraph)
self.nodalidaFeatureBuilder.setFeatureVector(None)
if self.styles["linear_features"]:
self.tokenFeatureBuilder.setFeatureVector(features)
for i in range(len(sentenceGraph.tokens)):
if sentenceGraph.tokens[i] == token1:
token1Index = i
if sentenceGraph.tokens[i] == token2:
token2Index = i
linearPreTag = "linfw_"
if token1Index > token2Index:
token1Index, token2Index = token2Index, token1Index
linearPreTag = "linrv_"
self.tokenFeatureBuilder.buildLinearOrderFeatures(token1Index, sentenceGraph, 2, 2, preTag="linTok1")
self.tokenFeatureBuilder.buildLinearOrderFeatures(token2Index, sentenceGraph, 2, 2, preTag="linTok2")
# Before, middle, after
# self.tokenFeatureBuilder.buildTokenGrams(0, token1Index-1, sentenceGraph, "bf")
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, "bw")
# self.tokenFeatureBuilder.buildTokenGrams(token2Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, "af")
# before-middle, middle, middle-after
# self.tokenFeatureBuilder.buildTokenGrams(0, token2Index-1, sentenceGraph, linearPreTag+"bf", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, linearPreTag+"bw", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, linearPreTag+"af", max=2)
self.tokenFeatureBuilder.setFeatureVector(None)
if self.styles["random"]:
self.randomFeatureBuilder.setFeatureVector(features)
self.randomFeatureBuilder.buildRandomFeatures(100, 0.01)
self.randomFeatureBuilder.setFeatureVector(None)
if self.styles["genia_features"] and not self.styles["no_task"]:
e1Type = entity1.get("type")
e2Type = entity2.get("type")
assert(entity1.get("given") in (None, "False"))
if entity2.get("given") == "True":
features[self.featureSet.getId("GENIA_target_protein")] = 1
else:
features[self.featureSet.getId("GENIA_nested_event")] = 1
if e1Type.find("egulation") != -1: # leave r out to avoid problems with capitalization
if entity2.get("given") == "True":
features[self.featureSet.getId("GENIA_regulation_of_protein")] = 1
else:
features[self.featureSet.getId("GENIA_regulation_of_event")] = 1
if self.styles["bi_features"]:
# Make features based on entity types
e1Type = entity1.get("type")
e2Type = entity2.get("type")
e1SuperType = str(self.getBISuperType(e1Type))
e2SuperType = str(self.getBISuperType(e2Type))
features[self.featureSet.getId("BI_e1_"+e1Type)] = 1
features[self.featureSet.getId("BI_e2_"+e2Type)] = 1
features[self.featureSet.getId("BI_e1sup_"+e1SuperType)] = 1
features[self.featureSet.getId("BI_e2sup_"+e2SuperType)] = 1
features[self.featureSet.getId("BI_e1e2_"+e1Type+"_"+e2Type)] = 1
features[self.featureSet.getId("BI_e1e2sup_"+e1SuperType+"_"+e2SuperType)] = 1
if self.styles["sdb_features"]:
e1Type = entity1.get("type")
e2Type = entity2.get("type")
features[self.featureSet.getId("SDB_e1_"+e1Type)] = 1
features[self.featureSet.getId("SDB_e2_"+e2Type)] = 1
features[self.featureSet.getId("SDB_e1e2_"+e1Type+"_"+e2Type)] = 1
if e1Type == e2Type:
features[self.featureSet.getId("SDB_e1e2_equal")] = 1
features[self.featureSet.getId("SDB_e1e2_equal_" + e1Type)] = 1
e1SuperTypes = str(self.getSeeDevSuperTypes(e1Type))
e2SuperTypes = str(self.getSeeDevSuperTypes(e2Type))
for e1SuperType in e1SuperTypes:
for e2SuperType in e2SuperTypes:
features[self.featureSet.getId("SDB_e1sup_"+e1SuperType)] = 1
features[self.featureSet.getId("SDB_e2sup_"+e2SuperType)] = 1
features[self.featureSet.getId("SDB_e1e2sup_"+e1SuperType+"_"+e2SuperType)] = 1
if e1SuperType == e2SuperType:
features[self.featureSet.getId("SDB_e1e2sup_equal")] = 1
features[self.featureSet.getId("SDB_e1e2sup_equal_" + e1SuperType)] = 1
if self.styles["ontobiotope_features"]:
self.ontobiotopeFeatureBuilder.setFeatureVector(features)
self.ontobiotopeFeatureBuilder.buildOBOFeaturesForEntityPair(entity1, entity2)
self.ontobiotopeFeatureBuilder.setFeatureVector(None)
if self.styles["full_entities"]:
e1Text = entity1.get("text").lower()
e2Text = entity2.get("text").lower()
features[self.featureSet.getId("FULL_e1_"+e1Text)] = 1
features[self.featureSet.getId("FULL_e2_"+e2Text)] = 1
for ep1 in e1Text.split():
for ep2 in e2Text.split():
features[self.featureSet.getId("FULL_e1_"+ep1)] = 1
features[self.featureSet.getId("FULL_e2_"+ep2)] = 1
features[self.featureSet.getId("FULL_e1e2_"+ep1+"_"+ep2)] = 1
if self.styles["evex"]:
self.evexFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.evexFeatureBuilder.buildEdgeFeatures(entity1, entity2, token1, token2, path, sentenceGraph)
self.evexFeatureBuilder.setFeatureVector(None)
if self.styles["wordnet"]:
self.wordNetFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.wordNetFeatureBuilder.buildFeaturesForEntityPair(token1, token2)
self.wordNetFeatureBuilder.buildLinearFeatures(token1, sentenceGraph.tokens, tag="t1_")
self.wordNetFeatureBuilder.buildLinearFeatures(token2, sentenceGraph.tokens, tag="t2_")
self.wordNetFeatureBuilder.buildPathFeatures(path)
self.wordNetFeatureBuilder.setFeatureVector(None)
if self.styles["wordvector"]:
self.wordVectorFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.wordVectorFeatureBuilder.buildFeatures(token1, "t1_")
self.wordVectorFeatureBuilder.buildFeatures(token2, "t2_")
self.wordVectorFeatureBuilder.buildLinearFeatures(token1, sentenceGraph.tokens, tag="t1_")
self.wordVectorFeatureBuilder.buildLinearFeatures(token2, sentenceGraph.tokens, tag="t2_")
self.wordVectorFeatureBuilder.buildPathFeatures(path)
self.wordVectorFeatureBuilder.buildFBAFeatures(sentenceGraph.tokens, sentenceGraph.tokens.index(token1), sentenceGraph.tokens.index(token2))
self.wordVectorFeatureBuilder.setFeatureVector(None)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.giulianoFeatureBuilder.buildEdgeFeatures(entity1, entity2, token1, token2, path, sentenceGraph)
self.giulianoFeatureBuilder.setFeatureVector(None)
return features
class AsymmetricEventExampleBuilder(ExampleBuilder):
def __init__(self,
style=["typed", "directed"],
length=None,
types=[],
featureSet=None,
classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert (classSet.getId("neg") == 1)
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
if style.find(",") != -1:
style = style.split(",")
self.styles = style
self.negFrac = None
self.posPairGaz = POSPairGazetteer()
for s in style:
if s.find("negFrac") != -1:
self.negFrac = float(s.split("_")[-1])
print >> sys.stderr, "Downsampling negatives to", self.negFrac
self.negRand = random.Random(15)
elif s.find("posPairGaz") != -1:
self.posPairGaz = POSPairGazetteer(
loadFrom=s.split("_", 1)[-1])
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
if "graph_kernel" in self.styles:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(
self.featureSet)
if "noAnnType" in self.styles:
self.multiEdgeFeatureBuilder.noAnnType = True
if "noMasking" in self.styles:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if "maxFeatures" in self.styles:
self.multiEdgeFeatureBuilder.maximum = True
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if "ontology" in self.styles:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(
self.featureSet)
if "nodalida" in self.styles:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(
self.featureSet)
#IF LOCAL
if "bioinfer_limits" in self.styles:
self.bioinferOntologies = OntologyUtils.getBioInferTempOntology()
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
#ENDIF
self.pathLengths = length
assert (self.pathLengths == None)
self.types = types
if "random" in self.styles:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
#self.outFile = open("exampleTempFile.txt","wt")
@classmethod
def run(cls, input, output, parse, tokenization, style, idFileTag=None):
classSet, featureSet = cls.getIdSets(idFileTag)
if style != None:
e = cls(style=style, classSet=classSet, featureSet=featureSet)
else:
e = cls(classSet=classSet, featureSet=featureSet)
sentences = cls.getSentences(input, parse, tokenization)
e.buildExamplesForSentences(sentences, output, idFileTag)
if "printClassIds" in e.styles:
print >> sys.stderr, e.classSet.Ids
def definePredictedValueRange(self, sentences, elementName):
self.multiEdgeFeatureBuilder.definePredictedValueRange(
sentences, elementName)
def getPredictedValueRange(self):
return self.multiEdgeFeatureBuilder.predictedRange
def filterEdgesByType(self, edges, typesToInclude):
if len(typesToInclude) == 0:
return edges
edgesToKeep = []
for edge in edges:
if edge.get("type") in typesToInclude:
edgesToKeep.append(edge)
return edgesToKeep
def getCategoryNameFromTokens(self, sentenceGraph, t1, t2, directed=True):
types = set()
themeE1Types = set()
intEdges = []
if sentenceGraph.interactionGraph.has_edge(t1, t2):
intEdges = sentenceGraph.interactionGraph.get_edge_data(t1,
t2,
default={})
# NOTE: Only works if keys are ordered integers
for i in range(len(intEdges)):
types.add(intEdges[i]["element"].get("type"))
# if (not directed) and sentenceGraph.interactionGraph.has_edge(t2, t1):
# intEdgesReverse = sentenceGraph.interactionGraph.get_edge(t2, t1, default={})
# # NOTE: Only works if keys are ordered integers
# for i in range(len(intEdgesReverse)):
# intElement = intEdgesReverse[i]["element"]
# intType = intElement.get("type")
# types.add(intType)
# intEdges.extend(intEdgesReverse)
for i in range(len(intEdges)):
intElement = intEdges[i]["element"]
intType = intElement.get("type")
if intType == "Theme":
e1Entity = sentenceGraph.entitiesById[intElement.get("e1")]
themeE1Types.add(e1Entity.get("type"))
#types.add(intType)
if len(themeE1Types) != 0:
themeE1Types = list(themeE1Types)
themeE1Types.sort()
categoryName = ""
for name in themeE1Types:
if categoryName != "":
categoryName += "---"
categoryName += name
return categoryName
else:
types = list(types)
types.sort()
categoryName = ""
for name in types:
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def getCategoryName(self, sentenceGraph, e1, e2, directed=True):
interactions = sentenceGraph.getInteractions(e1, e2)
if not directed:
interactions.extend(sentenceGraph.getInteractions(e2, e1))
types = set()
for interaction in interactions:
types.add(interaction.attrib["type"])
types = list(types)
types.sort()
categoryName = ""
for name in types:
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def preProcessExamples(self, allExamples):
# Duplicates cannot be removed here, as they should only be removed from the training set. This is done
# in the classifier.
# if "no_duplicates" in self.styles:
# count = len(allExamples)
# print >> sys.stderr, " Removing duplicates,",
# allExamples = ExampleUtils.removeDuplicates(allExamples)
# print >> sys.stderr, "removed", count - len(allExamples)
if "normalize" in self.styles:
print >> sys.stderr, " Normalizing feature vectors"
ExampleUtils.normalizeFeatureVectors(allExamples)
return allExamples
def isPotentialGeniaInteraction(self, e1, e2):
if e1.get("isName") == "True":
return False
else:
return True
#IF LOCAL
def getBioInferParentType(self, eType):
if eType == "Physical_entity" or OntologyUtils.hasParent(
eType, "Physical_entity", self.bioinferOntologies):
return "Physical"
elif eType == "Property_entity" or OntologyUtils.hasParent(
eType, "Property_entity", self.bioinferOntologies):
return "Property"
elif OntologyUtils.hasParent(eType, "Relationship",
self.bioinferOntologies):
return "Process"
else:
assert False, eType
# if self.bioinferOntologies["Entity"].has_key(eType):
# if OntologyUtils.hasParent(eType, "Physical_entity", self.bioinferOntologies):
# assert not OntologyUtils.hasParent(eType, "Property_entity", self.bioinferOntologies), eType
# return "Physical"
# else:
# assert OntologyUtils.hasParent(eType, "Property_entity", self.bioinferOntologies), eType
# return "Property"
#
# else:
# assert self.bioinferOntologies.has_key(eType), eType
# #assert OntologyUtils.hasParent(eType, "Process_entity", self.bioinferOntologies["Relationship"]), eType
# return "Process"
def isPotentialBioInferInteraction(self, e1, e2, categoryName):
e1Type = self.getBioInferParentType(e1.get("type"))
e2Type = self.getBioInferParentType(e2.get("type"))
if e1Type == "Process" or e1Type == "Property":
return True
elif e1Type == "Physical" and e2Type == "Physical":
return True
elif e1Type == "Physical" and e2Type == "Process": # hack
return True
else:
assert (
categoryName == "neg"
), categoryName + " category for " + e1Type + " and " + e2Type
return False
#ENDIF
def nxMultiDiGraphToUndirected(self, graph):
undirected = NX10.MultiGraph(name=graph.name)
undirected.add_nodes_from(graph)
undirected.add_edges_from(graph.edges_iter())
return undirected
def buildExamples(self, sentenceGraph):
examples = []
exampleIndex = 0
clearGraph = sentenceGraph.getCleared()
#undirected = sentenceGraph.getUndirectedDependencyGraph()
undirected = self.nxMultiDiGraphToUndirected(
sentenceGraph.dependencyGraph)
##undirected = sentenceGraph.dependencyGraph.to_undirected()
###undirected = NX10.MultiGraph(sentenceGraph.dependencyGraph) This didn't work
paths = NX10.all_pairs_shortest_path(undirected, cutoff=999)
self.triggerFeatureBuilder.initSentence(clearGraph)
# Generate examples based on interactions between entities or interactions between tokens
if "entities" in self.styles:
loopRange = len(sentenceGraph.entities)
else:
loopRange = len(sentenceGraph.tokens)
#for i in range(loopRange-1):
for i in range(loopRange): # allow self-interactions
#for j in range(i+1,loopRange):
for j in range(i, loopRange): # allow self-interactions
eI = None
eJ = None
if "entities" in self.styles:
eI = sentenceGraph.entities[i]
eJ = sentenceGraph.entities[j]
tI = sentenceGraph.entityHeadTokenByEntity[eI]
tJ = sentenceGraph.entityHeadTokenByEntity[eJ]
#if "no_ne_interactions" in self.styles and eI.get("isName") == "True" and eJ.get("isName") == "True":
# continue
if eI.get("type") == "neg" or eJ.get("type") == "neg":
continue
else:
tI = sentenceGraph.tokens[i]
tJ = sentenceGraph.tokens[j]
# # only consider paths between entities (NOTE! entities, not only named entities)
# if "headsOnly" in self.styles:
# if (len(sentenceGraph.tokenIsEntityHead[tI]) == 0) or (len(sentenceGraph.tokenIsEntityHead[tJ]) == 0):
# continue
if "directed" in self.styles:
# define forward
if "entities" in self.styles:
categoryName = self.getCategoryName(
sentenceGraph, eI, eJ, True)
else:
categoryName = self.getCategoryNameFromTokens(
sentenceGraph, tI, tJ, True)
self.exampleStats.beginExample(categoryName)
if self.negFrac == None or categoryName != "neg" or (
categoryName == "neg"
and self.negRand.random() < self.negFrac):
makeExample = True
if ("genia_limits" in self.styles
) and not self.isPotentialGeniaInteraction(eI, eJ):
makeExample = False
self.exampleStats.filter("genia_limits")
if self.posPairGaz.getNegFrac(
(tI.get("POS"), tJ.get("POS"))) == 1.0:
makeExample = False
self.exampleStats.filter("pos_pair")
if makeExample:
if not sentenceGraph.tokenIsName[tI]:
examples.append(
self.buildExample(tI, tJ, paths,
clearGraph, categoryName,
exampleIndex, eI, eJ))
exampleIndex += 1
else:
self.exampleStats.filter("genia_token_limits")
else:
self.exampleStats.filter("neg_frac")
self.exampleStats.endExample()
# define reverse
if "entities" in self.styles:
categoryName = self.getCategoryName(
sentenceGraph, eJ, eI, True)
else:
categoryName = self.getCategoryNameFromTokens(
sentenceGraph, tJ, tI, True)
self.exampleStats.beginExample(categoryName)
if self.negFrac == None or categoryName != "neg" or (
categoryName == "neg"
and self.negRand.random() < self.negFrac):
makeExample = True
if ("genia_limits" in self.styles
) and not self.isPotentialGeniaInteraction(eJ, eI):
makeExample = False
self.exampleStats.filter("genia_limits")
if ("bioinfer_limits" in self.styles
) and not self.isPotentialBioInferInteraction(
eJ, eI, categoryName):
makeExample = False
self.exampleStats.filter("bioinfer_limits")
if self.posPairGaz.getNegFrac(
(tJ.get("POS"), tI.get("POS"))) == 1.0:
makeExample = False
self.exampleStats.filter("pos_pair")
if makeExample:
if not sentenceGraph.tokenIsName[tJ]:
examples.append(
self.buildExample(tJ, tI, paths,
clearGraph, categoryName,
exampleIndex, eJ, eI))
exampleIndex += 1
else:
self.exampleStats.filter("genia_token_limits")
else:
self.exampleStats.filter("neg_frac")
self.exampleStats.endExample()
# else:
# if "entities" in self.styles:
# categoryName = self.getCategoryName(sentenceGraph, eI, eJ, False)
# else:
# categoryName = self.getCategoryNameFromTokens(sentenceGraph, tI, tJ, False)
# forwardExample = self.buildExample(tI, tJ, paths, clearGraph, categoryName, exampleIndex, eI, eJ)
# if not "graph_kernel" in self.styles:
# reverseExample = self.buildExample(tJ, tI, paths, clearGraph, categoryName, exampleIndex, eJ, eI)
# forwardExample[2].update(reverseExample[2])
# examples.append(forwardExample)
# exampleIndex += 1
return examples
def buildExample(self,
token1,
token2,
paths,
sentenceGraph,
categoryName,
exampleIndex,
entity1=None,
entity2=None):
# define features
features = {}
if True: #token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
if token1 != token2 and paths.has_key(
token1) and paths[token1].has_key(token2):
path = paths[token1][token2]
else:
path = [token1, token2]
assert (self.pathLengths == None)
if self.pathLengths == None or len(path) - 1 in self.pathLengths:
if not "no_trigger":
self.triggerFeatureBuilder.setFeatureVector(self.features)
self.triggerFeatureBuilder.tag = "trg_t1_"
self.triggerFeatureBuilder.buildFeatures(eventToken)
self.triggerFeatureBuilder.tag = "trg_t2_"
self.triggerFeatureBuilder.buildFeatures(eventToken)
# if not "no_ontology" in self.styles:
# self.ontologyFeatureBuilder.setFeatureVector(features)
# self.ontologyFeatureBuilder.buildOntologyFeaturesForPath(sentenceGraph, path)
# self.ontologyFeatureBuilder.setFeatureVector(None)
if "graph_kernel" in self.styles or not "no_dependency" in self.styles:
if token1 != token2 and paths.has_key(
token1) and paths[token1].has_key(token2):
edges = self.multiEdgeFeatureBuilder.getEdges(
sentenceGraph.dependencyGraph, path)
else:
edges = None
if "graph_kernel" in self.styles:
self.graphKernelFeatureBuilder.setFeatureVector(
features, entity1, entity2)
self.graphKernelFeatureBuilder.buildGraphKernelFeatures(
sentenceGraph, path, edges)
self.graphKernelFeatureBuilder.setFeatureVector(None)
if "entity_type" in self.styles:
features[self.featureSet.getId("e1_" +
entity1.attrib["type"])] = 1
features[self.featureSet.getId("e2_" +
entity2.attrib["type"])] = 1
features[self.featureSet.getId("distance_" +
str(len(path)))] = 1
if not "no_dependency" in self.styles:
if token1 == token2:
features[self.featureSet.getId("tokenSelfLoop")] = 1
self.multiEdgeFeatureBuilder.setFeatureVector(
features, entity1, entity2)
#self.multiEdgeFeatureBuilder.buildStructureFeatures(sentenceGraph, paths) # remove for fast
if not "disable_entity_features" in self.styles:
self.multiEdgeFeatureBuilder.buildEntityFeatures(
sentenceGraph)
self.multiEdgeFeatureBuilder.buildPathLengthFeatures(path)
if not "disable_terminus_features" in self.styles:
self.multiEdgeFeatureBuilder.buildTerminusTokenFeatures(
path, sentenceGraph) # remove for fast
if not "disable_single_element_features" in self.styles:
self.multiEdgeFeatureBuilder.buildSingleElementFeatures(
path, edges, sentenceGraph)
if not "disable_ngram_features" in self.styles:
self.multiEdgeFeatureBuilder.buildPathGrams(
2, path, edges, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(
3, path, edges, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(
4, path, edges, sentenceGraph) # remove for fast
#self.buildEdgeCombinations(path, edges, sentenceGraph, features) # remove for fast
#if edges != None:
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[0], edges[0][1]+edges[1][0], "t1", sentenceGraph) # remove for fast
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[-1], edges[len(path)-1][len(path)-2]+edges[len(path)-2][len(path)-1], "t2", sentenceGraph) # remove for fast
if not "disable_path_edge_features" in self.styles:
self.multiEdgeFeatureBuilder.buildPathEdgeFeatures(
path, edges, sentenceGraph)
self.multiEdgeFeatureBuilder.buildSentenceFeatures(
sentenceGraph)
self.multiEdgeFeatureBuilder.setFeatureVector(None)
if "nodalida" in self.styles:
self.nodalidaFeatureBuilder.setFeatureVector(
features, entity1, entity2)
shortestPaths = self.nodalidaFeatureBuilder.buildShortestPaths(
sentenceGraph.dependencyGraph, path)
print shortestPaths
if len(shortestPaths) > 0:
self.nodalidaFeatureBuilder.buildNGrams(
shortestPaths, sentenceGraph)
self.nodalidaFeatureBuilder.setFeatureVector(None)
if not "no_linear" in self.styles:
self.tokenFeatureBuilder.setFeatureVector(features)
for i in range(len(sentenceGraph.tokens)):
if sentenceGraph.tokens[i] == token1:
token1Index = i
if sentenceGraph.tokens[i] == token2:
token2Index = i
linearPreTag = "linfw_"
if token1Index > token2Index:
token1Index, token2Index = token2Index, token1Index
linearPreTag = "linrv_"
self.tokenFeatureBuilder.buildLinearOrderFeatures(
token1Index, sentenceGraph, 2, 2, preTag="linTok1")
self.tokenFeatureBuilder.buildLinearOrderFeatures(
token2Index, sentenceGraph, 2, 2, preTag="linTok2")
# Before, middle, after
# self.tokenFeatureBuilder.buildTokenGrams(0, token1Index-1, sentenceGraph, "bf")
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, "bw")
# self.tokenFeatureBuilder.buildTokenGrams(token2Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, "af")
# before-middle, middle, middle-after
# self.tokenFeatureBuilder.buildTokenGrams(0, token2Index-1, sentenceGraph, linearPreTag+"bf", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, linearPreTag+"bw", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, linearPreTag+"af", max=2)
self.tokenFeatureBuilder.setFeatureVector(None)
if "random" in self.styles:
self.randomFeatureBuilder.setFeatureVector(features)
self.randomFeatureBuilder.buildRandomFeatures(100, 0.01)
self.randomFeatureBuilder.setFeatureVector(None)
if "genia_limits" in self.styles:
e1Type = entity1.get("type")
e2Type = entity2.get("type")
assert (entity1.get("isName") == "False")
if entity2.get("isName") == "True":
features[self.featureSet.getId(
"GENIA_target_protein")] = 1
else:
features[self.featureSet.getId(
"GENIA_nested_event")] = 1
if e1Type.find(
"egulation"
) != -1: # leave r out to avoid problems with capitalization
if entity2.get("isName") == "True":
features[self.featureSet.getId(
"GENIA_regulation_of_protein")] = 1
else:
features[self.featureSet.getId(
"GENIA_regulation_of_event")] = 1
else:
features[self.featureSet.getId("always_negative")] = 1
if "subset" in self.styles:
features[self.featureSet.getId("out_of_scope")] = 1
else:
features[self.featureSet.getId("always_negative")] = 1
if "subset" in self.styles:
features[self.featureSet.getId("out_of_scope")] = 1
path = [token1, token2]
self.triggerFeatureBuilder.tag = ""
self.triggerFeatureBuilder.setFeatureVector(None)
# define extra attributes
# if int(path[0].attrib["id"].split("_")[-1]) < int(path[-1].attrib["id"].split("_")[-1]):
# #extra = {"xtype":"edge","type":"i","t1":path[0],"t2":path[-1]}
# extra = {"xtype":"asym","type":"i","t1":path[0].get("id"),"t2":path[-1].get("id")}
# extra["deprev"] = False
# else:
# #extra = {"xtype":"edge","type":"i","t1":path[-1],"t2":path[0]}
# extra = {"xtype":"asym","type":"i","t1":path[-1].get("id"),"t2":path[0].get("id")}
# extra["deprev"] = True
extra = {
"xtype": "asym",
"type": "i",
"t1": token1.get("id"),
"t2": token2.get("id")
}
if entity1 != None:
#extra["e1"] = entity1
extra["e1"] = entity1.get("id")
if entity2 != None:
#extra["e2"] = entity2
extra["e2"] = entity2.get("id")
extra["categoryName"] = categoryName
sentenceOrigId = sentenceGraph.sentenceElement.get("origId")
if sentenceOrigId != None:
extra["SOID"] = sentenceOrigId
# make example
if "binary" in self.styles:
if categoryName != "neg":
category = 1
else:
category = -1
categoryName = "i"
else:
category = self.classSet.getId(categoryName)
return (sentenceGraph.getSentenceId() + ".x" + str(exampleIndex),
category, features, extra)
def __init__(self,
style=None,
length=None,
types=[],
featureSet=None,
classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert (classSet.getId("neg") == 1
or (len(classSet.Ids) == 2 and classSet.getId("neg") == -1))
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
self.styles = self.getParameters(style, [
"typed", "directed", "headsOnly", "graph_kernel", "noAnnType",
"noMasking", "maxFeatures", "genia_limits", "epi_limits",
"id_limits", "rel_limits", "bb_limits", "bi_limits", "co_limits",
"genia_task1", "ontology", "nodalida", "bacteria_renaming",
"trigger_features", "rel_features", "ddi_features", "evex",
"giuliano", "random", "themeOnly", "causeOnly", "no_path",
"entities", "skip_extra_triggers", "headsOnly", "graph_kernel",
"trigger_features", "no_task", "no_dependency",
"disable_entity_features", "disable_terminus_features",
"disable_single_element_features", "disable_ngram_features",
"disable_path_edge_features", "no_linear", "subset", "binary",
"pos_only", "entity_type"
])
if style == None: # no parameters given
style["typed"] = style["directed"] = style["headsOnly"] = True
# self.styles = style
# if "selftrain_group" in self.styles:
# self.selfTrainGroups = set()
# if "selftrain_group-1" in self.styles:
# self.selfTrainGroups.add("-1")
# if "selftrain_group0" in self.styles:
# self.selfTrainGroups.add("0")
# if "selftrain_group1" in self.styles:
# self.selfTrainGroups.add("1")
# if "selftrain_group2" in self.styles:
# self.selfTrainGroups.add("2")
# if "selftrain_group3" in self.styles:
# self.selfTrainGroups.add("3")
# print >> sys.stderr, "Self-train-groups:", self.selfTrainGroups
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
# NOTE Temporarily re-enabling predicted range
#self.multiEdgeFeatureBuilder.definePredictedValueRange([], None)
if self.styles["graph_kernel"]:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(
self.featureSet)
if self.styles["noAnnType"]:
self.multiEdgeFeatureBuilder.noAnnType = True
if self.styles["noMasking"]:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if self.styles["maxFeatures"]:
self.multiEdgeFeatureBuilder.maximum = True
if self.styles["genia_task1"]:
self.multiEdgeFeatureBuilder.filterAnnTypes.add("Entity")
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if self.styles["ontology"]:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(
self.featureSet)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(
self.featureSet)
if self.styles["bacteria_renaming"]:
self.bacteriaRenamingFeatureBuilder = BacteriaRenamingFeatureBuilder(
self.featureSet)
if self.styles["trigger_features"]:
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder.useNonNameEntities = True
if self.styles["genia_task1"]:
self.triggerFeatureBuilder.filterAnnTypes.add("Entity")
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
if self.styles["rel_features"]:
self.relFeatureBuilder = RELFeatureBuilder(featureSet)
if self.styles["ddi_features"]:
self.drugFeatureBuilder = DrugFeatureBuilder(featureSet)
if self.styles["evex"]:
self.evexFeatureBuilder = EVEXFeatureBuilder(featureSet)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder = GiulianoFeatureBuilder(featureSet)
self.pathLengths = length
assert (self.pathLengths == None)
self.types = types
if self.styles["random"]:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
class MultiEdgeExampleBuilder(ExampleBuilder):
"""
This example builder makes edge examples, i.e. examples describing
the event arguments.
"""
def __init__(self,
style=None,
length=None,
types=[],
featureSet=None,
classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert (classSet.getId("neg") == 1
or (len(classSet.Ids) == 2 and classSet.getId("neg") == -1))
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
self.styles = self.getParameters(style, [
"typed", "directed", "headsOnly", "graph_kernel", "noAnnType",
"noMasking", "maxFeatures", "genia_limits", "epi_limits",
"id_limits", "rel_limits", "bb_limits", "bi_limits", "co_limits",
"genia_task1", "ontology", "nodalida", "bacteria_renaming",
"trigger_features", "rel_features", "ddi_features", "evex",
"giuliano", "random", "themeOnly", "causeOnly", "no_path",
"entities", "skip_extra_triggers", "headsOnly", "graph_kernel",
"trigger_features", "no_task", "no_dependency",
"disable_entity_features", "disable_terminus_features",
"disable_single_element_features", "disable_ngram_features",
"disable_path_edge_features", "no_linear", "subset", "binary",
"pos_only", "entity_type"
])
if style == None: # no parameters given
style["typed"] = style["directed"] = style["headsOnly"] = True
# self.styles = style
# if "selftrain_group" in self.styles:
# self.selfTrainGroups = set()
# if "selftrain_group-1" in self.styles:
# self.selfTrainGroups.add("-1")
# if "selftrain_group0" in self.styles:
# self.selfTrainGroups.add("0")
# if "selftrain_group1" in self.styles:
# self.selfTrainGroups.add("1")
# if "selftrain_group2" in self.styles:
# self.selfTrainGroups.add("2")
# if "selftrain_group3" in self.styles:
# self.selfTrainGroups.add("3")
# print >> sys.stderr, "Self-train-groups:", self.selfTrainGroups
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
# NOTE Temporarily re-enabling predicted range
#self.multiEdgeFeatureBuilder.definePredictedValueRange([], None)
if self.styles["graph_kernel"]:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(
self.featureSet)
if self.styles["noAnnType"]:
self.multiEdgeFeatureBuilder.noAnnType = True
if self.styles["noMasking"]:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if self.styles["maxFeatures"]:
self.multiEdgeFeatureBuilder.maximum = True
if self.styles["genia_task1"]:
self.multiEdgeFeatureBuilder.filterAnnTypes.add("Entity")
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if self.styles["ontology"]:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(
self.featureSet)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(
self.featureSet)
if self.styles["bacteria_renaming"]:
self.bacteriaRenamingFeatureBuilder = BacteriaRenamingFeatureBuilder(
self.featureSet)
if self.styles["trigger_features"]:
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder.useNonNameEntities = True
if self.styles["genia_task1"]:
self.triggerFeatureBuilder.filterAnnTypes.add("Entity")
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
if self.styles["rel_features"]:
self.relFeatureBuilder = RELFeatureBuilder(featureSet)
if self.styles["ddi_features"]:
self.drugFeatureBuilder = DrugFeatureBuilder(featureSet)
if self.styles["evex"]:
self.evexFeatureBuilder = EVEXFeatureBuilder(featureSet)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder = GiulianoFeatureBuilder(featureSet)
self.pathLengths = length
assert (self.pathLengths == None)
self.types = types
if self.styles["random"]:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
def definePredictedValueRange(self, sentences, elementName):
self.multiEdgeFeatureBuilder.definePredictedValueRange(
sentences, elementName)
def getPredictedValueRange(self):
return self.multiEdgeFeatureBuilder.predictedRange
def filterEdgesByType(self, edges, typesToInclude):
if len(typesToInclude) == 0:
return edges
edgesToKeep = []
for edge in edges:
if edge.get("type") in typesToInclude:
edgesToKeep.append(edge)
return edgesToKeep
def getCategoryNameFromTokens(self, sentenceGraph, t1, t2, directed=True):
"""
Example class. Multiple overlapping edges create a merged type.
"""
types = set()
# if sentenceGraph.interactionGraph.has_edge(t1, t2):
# intEdges = sentenceGraph.interactionGraph.get_edge_data(t1, t2, default={})
# # NOTE: Only works if keys are ordered integers
# for i in range(len(intEdges)):
# types.add(intEdges[i]["element"].get("type"))
# if (not directed) and sentenceGraph.interactionGraph.has_edge(t2, t1):
# intEdges = sentenceGraph.interactionGraph.get_edge(t2, t1, default={})
# # NOTE: Only works if keys are ordered integers
# for i in range(len(intEdges)):
# types.add(intEdges[i]["element"].get("type"))
intEdges = sentenceGraph.interactionGraph.getEdges(t1, t2)
if (not directed):
intEdges = intEdges + sentenceGraph.interactionGraph.getEdges(
t2, t1)
for intEdge in intEdges:
types.add(intEdge[2].get("type"))
types = list(types)
types.sort()
categoryName = ""
for name in types:
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def getCategoryName(self,
sentenceGraph,
e1,
e2,
directed=True,
duplicateEntities=None):
"""
Example class. Multiple overlapping edges create a merged type.
"""
# interactions = []
# e1s = [e1]
# if duplicateEntities != None and e1 in duplicateEntities:
# e1s += duplicateEntities[e1]
# e2s = [e2]
# if duplicateEntities != None and e2 in duplicateEntities:
# e2s += duplicateEntities[e2]
# for entity1 in e1s:
# for entity2 in e2s:
# interactions = interactions + sentenceGraph.getInteractions(entity1, entity2)
# if not directed:
# interactions = interactions + sentenceGraph.getInteractions(entity2, entity1)
interactions = sentenceGraph.getInteractions(e1, e2, True)
#print interactions
types = set()
for interaction in interactions:
types.add(interaction[2].get("type"))
types = list(types)
types.sort()
categoryName = ""
for name in types:
if self.styles["causeOnly"] and name != "Cause":
continue
if self.styles["themeOnly"] and name != "Theme":
continue
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def isPotentialRELInteraction(self, e1, e2):
if e1.get("type") == "Protein" and e2.get("type") == "Entity":
return True
else:
return False
def isPotentialBBInteraction(self, e1, e2, sentenceGraph):
#if e1.get("type") == "Bacterium" and e2.get("type") in ["Host", "HostPart", "Geographical", "Environmental", "Food", "Medical", "Soil", "Water"]:
# Note: "Environment" type is misspelled as "Environmental" in the BB-task documentation
if e1.get("type") == "Bacterium" and e2.get("type") in [
"Host", "HostPart", "Geographical", "Environment", "Food",
"Medical", "Soil", "Water"
]:
return True
elif e1.get("type") == "Host" and e2.get("type") == "HostPart":
return True
else:
return False
def getBISuperType(self, eType):
if eType in [
"GeneProduct", "Protein", "ProteinFamily", "PolymeraseComplex"
]:
return "ProteinEntity"
elif eType in [
"Gene", "GeneFamily", "GeneComplex", "Regulon", "Site",
"Promoter"
]:
return "GeneEntity"
else:
return None
def isPotentialBIInteraction(self, e1, e2, sentenceGraph, stats):
e1Type = e1.get("type")
e1SuperType = self.getBISuperType(e1Type)
e2Type = e2.get("type")
e2SuperType = self.getBISuperType(e2Type)
tag = "(" + e1Type + "/" + e2Type + ")"
if e1Type == "Regulon":
if e2SuperType in ["GeneEntity", "ProteinEntity"]:
return True
if e1SuperType == "ProteinEntity":
if e2Type in ["Site", "Promoter", "Gene", "GeneComplex"]:
return True
if e1Type in ["Action", "Transcription", "Expression"]:
return True
if e1Type == "Site":
if e2SuperType == "GeneEntity":
return True
if e1Type == "Promoter":
if e2SuperType in ["GeneEntity", "ProteinEntity"]:
return True
if e1SuperType in ["GeneEntity", "ProteinEntity"]:
if e2SuperType in ["GeneEntity", "ProteinEntity"]:
return True
stats.filter("bi_limits") #+tag)
return False
def isPotentialEPIInteraction(self, e1, e2, sentenceGraph):
if e1.get("type") != "Catalysis":
if e1.get("type") in ["Protein", "Entity"]:
return False
elif e2.get("type") in ["Protein", "Entity"]:
return True
else:
return False
else: # Catalysis
if e2.get("type") != "Entity":
return True
else:
return False
assert False, (e1.get("type"), e2.get("type"))
def isPotentialIDInteraction(self, e1, e2, sentenceGraph):
e1Type = e1.get("type")
e2Type = e2.get("type")
e1IsCore = e1Type in [
"Protein", "Regulon-operon", "Two-component-system", "Chemical",
"Organism"
]
e2IsCore = e2Type in [
"Protein", "Regulon-operon", "Two-component-system", "Chemical",
"Organism"
]
if e1IsCore:
return False
elif e1Type in ["Gene_expression", "Transcription"]:
if e2Type in ["Protein", "Regulon-operon"]:
return True
else:
return False
elif e1Type in ["Protein_catabolism", "Phosphorylation"]:
if e2Type == "Protein":
return True
else:
return False
elif e1Type == "Localization":
if e2IsCore or e2Type == "Entity":
return True
else:
return False
elif e1Type in ["Binding", "Process"]:
if e2IsCore:
return True
else:
return False
elif "egulation" in e1Type:
if e2Type != "Entity":
return True
else:
return False
elif e1Type == "Entity":
if e2IsCore:
return True
else:
return False
assert False, (e1Type, e2Type)
def isPotentialCOInteraction(self, e1, e2, sentenceGraph):
if e1.get("type") == "Exp" and e2.get("type") == "Exp":
anaphoraTok = sentenceGraph.entityHeadTokenByEntity[e1]
antecedentTok = sentenceGraph.entityHeadTokenByEntity[e2]
antecedentTokenFound = False
for token in sentenceGraph.tokens:
if token == antecedentTok:
antecedentTokenFound = True
if token == anaphoraTok: # if, not elif, to take into accoutn cases where e1Tok == e2Tok
if antecedentTokenFound:
return True
else:
return False
assert False
elif e1.get("type") == "Exp" and e2.get("type") == "Protein":
return True
else:
return False
def isPotentialGeniaInteraction(self, e1, e2):
e1Type = e1.get("type")
e2Type = e2.get("type")
if e1Type == "Protein":
return False
elif e1Type in [
"Entity", "Gene_expression", "Transcription",
"Protein_catabolism", "Phosphorylation", "Binding"
]:
if e2Type == "Protein":
return True
else:
return False
elif e1Type == "Localization":
if e2Type in ["Protein", "Entity"]:
return True
else:
return False
elif "egulation" in e1Type:
if e2Type != "Entity":
return True
else:
return False
assert False, (e1Type, e2Type)
def getGoldCategoryName(self,
goldGraph,
entityToGold,
e1,
e2,
directed=True):
if len(entityToGold[e1]) > 0 and len(entityToGold[e2]) > 0:
return self.getCategoryName(goldGraph,
entityToGold[e1][0],
entityToGold[e2][0],
directed=directed)
else:
return "neg"
def buildExamplesFromGraph(self, sentenceGraph, outfile, goldGraph=None):
"""
Build examples for a single sentence. Returns a list of examples.
See Core/ExampleUtils for example format.
"""
#examples = []
exampleIndex = 0
if self.styles["trigger_features"]:
self.triggerFeatureBuilder.initSentence(sentenceGraph)
if self.styles["evex"]:
self.evexFeatureBuilder.initSentence(sentenceGraph)
# Filter entities, if needed
#mergedIds = None
#duplicateEntities = None
#entities = sentenceGraph.entities
#entities, mergedIds, duplicateEntities = self.mergeEntities(sentenceGraph, False) # "no_duplicates" in self.styles)
sentenceGraph.mergeInteractionGraph(True)
entities = sentenceGraph.mergedEntities
entityToDuplicates = sentenceGraph.mergedEntityToDuplicates
self.exampleStats.addValue("Duplicate entities skipped",
len(sentenceGraph.entities) - len(entities))
# Connect to optional gold graph
if goldGraph != None:
entityToGold = EvaluateInteractionXML.mapEntities(
entities, goldGraph.entities)
paths = None
if not self.styles["no_path"]:
##undirected = sentenceGraph.getUndirectedDependencyGraph()
#undirected = self.nxMultiDiGraphToUndirected(sentenceGraph.dependencyGraph)
###undirected = sentenceGraph.dependencyGraph.to_undirected()
####undirected = NX10.MultiGraph(sentenceGraph.dependencyGraph) This didn't work
undirected = sentenceGraph.dependencyGraph.toUndirected()
#paths = NX10.all_pairs_shortest_path(undirected, cutoff=999)
paths = undirected
#for edge in sentenceGraph.dependencyGraph.edges:
# assert edge[2] != None
#for edge in undirected.edges:
# assert edge[2] != None
#if sentenceGraph.sentenceElement.get("id") == "GENIA.d70.s5":
# print [(x[0].get("id"), x[1].get("id"), x[2].get("id")) for x in sentenceGraph.dependencyGraph.edges]
# Generate examples based on interactions between entities or interactions between tokens
if self.styles["entities"]:
loopRange = len(entities)
else:
loopRange = len(sentenceGraph.tokens)
for i in range(loopRange - 1):
for j in range(i + 1, loopRange):
eI = None
eJ = None
if self.styles["entities"]:
eI = entities[i]
eJ = entities[j]
tI = sentenceGraph.entityHeadTokenByEntity[eI]
tJ = sentenceGraph.entityHeadTokenByEntity[eJ]
#if "no_ne_interactions" in self.styles and eI.get("isName") == "True" and eJ.get("isName") == "True":
# continue
if eI.get("type") == "neg" or eJ.get("type") == "neg":
continue
if self.styles["skip_extra_triggers"]:
if eI.get("source") != None or eJ.get(
"source") != None:
continue
else:
tI = sentenceGraph.tokens[i]
tJ = sentenceGraph.tokens[j]
# only consider paths between entities (NOTE! entities, not only named entities)
if self.styles["headsOnly"]:
if (len(sentenceGraph.tokenIsEntityHead[tI]) == 0) or (len(
sentenceGraph.tokenIsEntityHead[tJ]) == 0):
continue
if self.styles["directed"]:
# define forward
if self.styles["entities"]:
categoryName = self.getCategoryName(
sentenceGraph, eI, eJ, True)
if goldGraph != None:
categoryName = self.getGoldCategoryName(
goldGraph, entityToGold, eI, eJ, True)
else:
categoryName = self.getCategoryNameFromTokens(
sentenceGraph, tI, tJ, True)
# make forward
self.exampleStats.beginExample(categoryName)
makeExample = True
if self.styles[
"genia_limits"] and not self.isPotentialGeniaInteraction(
eI, eJ):
makeExample = False
self.exampleStats.filter("genia_limits")
if self.styles["genia_task1"] and (
eI.get("type") == "Entity"
or eJ.get("type") == "Entity"):
makeExample = False
self.exampleStats.filter("genia_task1")
if self.styles[
"rel_limits"] and not self.isPotentialRELInteraction(
eI, eJ):
makeExample = False
self.exampleStats.filter("rel_limits")
if self.styles[
"co_limits"] and not self.isPotentialCOInteraction(
eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("co_limits")
if self.styles[
"bb_limits"] and not self.isPotentialBBInteraction(
eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("bb_limits")
if categoryName != "neg":
self.exampleStats.filter("bb_limits(" +
categoryName + ":" +
eI.get("type") + "/" +
eJ.get("type") + ")")
if self.styles[
"bi_limits"] and not self.isPotentialBIInteraction(
eI, eJ, sentenceGraph, self.exampleStats):
makeExample = False
#self.exampleStats.filter("bi_limits")
if self.styles[
"epi_limits"] and not self.isPotentialEPIInteraction(
eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("epi_limits")
if self.styles[
"id_limits"] and not self.isPotentialIDInteraction(
eI, eJ, sentenceGraph):
makeExample = False
self.exampleStats.filter("id_limits")
# if self.styles["selftrain_limits"] and (eI.get("selftrain") == "False" or eJ.get("selftrain") == "False"):
# makeExample = False
# self.exampleStats.filter("selftrain_limits")
# if self.styles["selftrain_group"] and (eI.get("selftraingroup") not in self.selfTrainGroups or eJ.get("selftraingroup") not in self.selfTrainGroups):
# makeExample = False
# self.exampleStats.filter("selftrain_group")
if self.styles["pos_only"] and categoryName == "neg":
makeExample = False
self.exampleStats.filter("pos_only")
if makeExample:
#examples.append( self.buildExample(tI, tJ, paths, sentenceGraph, categoryName, exampleIndex, eI, eJ) )
ExampleUtils.appendExamples([
self.buildExample(tI, tJ, paths, sentenceGraph,
categoryName, exampleIndex, eI,
eJ)
], outfile)
exampleIndex += 1
self.exampleStats.endExample()
# define reverse
if self.styles["entities"]:
categoryName = self.getCategoryName(
sentenceGraph, eJ, eI, True)
if goldGraph != None:
categoryName = self.getGoldCategoryName(
goldGraph, entityToGold, eJ, eI, True)
else:
categoryName = self.getCategoryNameFromTokens(
sentenceGraph, tJ, tI, True)
# make reverse
self.exampleStats.beginExample(categoryName)
makeExample = True
if self.styles[
"genia_limits"] and not self.isPotentialGeniaInteraction(
eJ, eI):
makeExample = False
self.exampleStats.filter("genia_limits")
if self.styles["genia_task1"] and (
eI.get("type") == "Entity"
or eJ.get("type") == "Entity"):
makeExample = False
self.exampleStats.filter("genia_task1")
if self.styles[
"rel_limits"] and not self.isPotentialRELInteraction(
eJ, eI):
makeExample = False
self.exampleStats.filter("rel_limits")
if self.styles[
"co_limits"] and not self.isPotentialCOInteraction(
eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("co_limits")
if self.styles[
"bb_limits"] and not self.isPotentialBBInteraction(
eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("bb_limits")
if categoryName != "neg":
self.exampleStats.filter("bb_limits(" +
categoryName + ":" +
eJ.get("type") + "/" +
eI.get("type") + ")")
if self.styles[
"bi_limits"] and not self.isPotentialBIInteraction(
eJ, eI, sentenceGraph, self.exampleStats):
makeExample = False
#self.exampleStats.filter("bi_limits")
if self.styles[
"epi_limits"] and not self.isPotentialEPIInteraction(
eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("epi_limits")
if self.styles[
"id_limits"] and not self.isPotentialIDInteraction(
eJ, eI, sentenceGraph):
makeExample = False
self.exampleStats.filter("id_limits")
# if self.styles["selftrain_limits"] and (eI.get("selftrain") == "False" or eJ.get("selftrain") == "False"):
# makeExample = False
# self.exampleStats.filter("selftrain_limits")
# if self.styles["selftrain_group"] and (eI.get("selftraingroup") not in self.selfTrainGroups or eJ.get("selftraingroup") not in self.selfTrainGroups):
# makeExample = False
# self.exampleStats.filter("selftrain_group")
if self.styles["pos_only"] and categoryName == "neg":
makeExample = False
self.exampleStats.filter("pos_only")
if makeExample:
#examples.append( self.buildExample(tJ, tI, paths, sentenceGraph, categoryName, exampleIndex, eJ, eI) )
ExampleUtils.appendExamples([
self.buildExample(tJ, tI, paths, sentenceGraph,
categoryName, exampleIndex, eJ,
eI)
], outfile)
exampleIndex += 1
self.exampleStats.endExample()
else:
if self.styles["entities"]:
categoryName = self.getCategoryName(
sentenceGraph, eI, eJ, False)
else:
categoryName = self.getCategoryNameFromTokens(
sentenceGraph, tI, tJ, False)
self.exampleStats.beginExample(categoryName)
forwardExample = self.buildExample(tI, tJ, paths,
sentenceGraph,
categoryName,
exampleIndex, eI, eJ)
if not self.styles["graph_kernel"]:
reverseExample = self.buildExample(
tJ, tI, paths, sentenceGraph, categoryName,
exampleIndex, eJ, eI)
forwardExample[2].update(reverseExample[2])
#examples.append(forwardExample)
ExampleUtils.appendExamples([forwardExample], outfile)
exampleIndex += 1
self.exampleStats.endExample()
#return examples
return exampleIndex
def buildExample(self,
token1,
token2,
paths,
sentenceGraph,
categoryName,
exampleIndex,
entity1=None,
entity2=None):
"""
Build a single directed example for the potential edge between token1 and token2
"""
# dummy return for speed testing
#return (sentenceGraph.getSentenceId()+".x"+str(exampleIndex),1,{},{})
# define features
features = {}
if True: #token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
#if token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
# path = paths[token1][token2]
#else:
# path = [token1, token2]
if not self.styles["no_path"]:
# directedPath reduces performance by 0.01 pp
#directedPath = sentenceGraph.dependencyGraph.getPaths(token1, token2)
#if len(directedPath) == 0:
# directedPath = sentenceGraph.dependencyGraph.getPaths(token2, token1)
# for dp in directedPath:
# dp.reverse()
#if len(directedPath) == 0:
# path = paths.getPaths(token1, token2)
#else:
# path = directedPath
path = paths.getPaths(token1, token2)
if len(path) > 0:
#if len(path) > 1:
# print len(path)
path = path[0]
pathExists = True
else:
path = [token1, token2]
pathExists = False
else:
path = [token1, token2]
pathExists = False
#print token1.get("id"), token2.get("id")
assert (self.pathLengths == None)
if self.pathLengths == None or len(path) - 1 in self.pathLengths:
# if not "no_ontology" in self.styles:
# self.ontologyFeatureBuilder.setFeatureVector(features)
# self.ontologyFeatureBuilder.buildOntologyFeaturesForPath(sentenceGraph, path)
# self.ontologyFeatureBuilder.setFeatureVector(None)
if self.styles["trigger_features"]: # F 85.52 -> 85.55
self.triggerFeatureBuilder.setFeatureVector(features)
self.triggerFeatureBuilder.tag = "trg1_"
self.triggerFeatureBuilder.buildFeatures(token1)
self.triggerFeatureBuilder.tag = "trg2_"
self.triggerFeatureBuilder.buildFeatures(token2)
self.triggerFeatureBuilder.setFeatureVector(None)
# REL features
if self.styles["rel_features"] and not self.styles["no_task"]:
self.relFeatureBuilder.setFeatureVector(features)
self.relFeatureBuilder.tag = "rel1_"
self.relFeatureBuilder.buildAllFeatures(
sentenceGraph.tokens,
sentenceGraph.tokens.index(token1))
self.relFeatureBuilder.tag = "rel2_"
self.relFeatureBuilder.buildAllFeatures(
sentenceGraph.tokens,
sentenceGraph.tokens.index(token2))
self.relFeatureBuilder.setFeatureVector(None)
if self.styles[
"bacteria_renaming"] and not self.styles["no_task"]:
self.bacteriaRenamingFeatureBuilder.setFeatureVector(
features)
self.bacteriaRenamingFeatureBuilder.buildPairFeatures(
entity1, entity2)
#self.bacteriaRenamingFeatureBuilder.buildSubstringFeatures(entity1, entity2) # decreases perf. 74.76 -> 72.41
self.bacteriaRenamingFeatureBuilder.setFeatureVector(None)
if self.styles["co_limits"] and not self.styles["no_task"]:
e1Offset = Range.charOffsetToSingleTuple(
entity1.get("charOffset"))
e2Offset = Range.charOffsetToSingleTuple(
entity2.get("charOffset"))
if Range.contains(e1Offset, e2Offset):
features[self.featureSet.getId("e1_contains_e2")] = 1
if entity2.get("isName") == "True":
features[self.featureSet.getId(
"e1_contains_e2name")] = 1
if Range.contains(e2Offset, e1Offset):
features[self.featureSet.getId("e2_contains_e1")] = 1
if entity1.get("isName") == "True":
features[self.featureSet.getId(
"e2_contains_e1name")] = 1
if self.styles["ddi_features"]:
self.drugFeatureBuilder.setFeatureVector(features)
self.drugFeatureBuilder.tag = "ddi_"
self.drugFeatureBuilder.buildPairFeatures(entity1, entity2)
if self.styles["ddi_mtmx"]:
self.drugFeatureBuilder.buildMTMXFeatures(
entity1, entity2)
self.drugFeatureBuilder.setFeatureVector(None)
#if "graph_kernel" in self.styles or not "no_dependency" in self.styles:
# #print "Getting edges"
# if token1 != token2 and pathExists:
# #print "g1"
# edges = self.multiEdgeFeatureBuilder.getEdges(sentenceGraph.dependencyGraph, path)
# #print "g2"
# else:
# edges = None
if self.styles["graph_kernel"]:
self.graphKernelFeatureBuilder.setFeatureVector(
features, entity1, entity2)
self.graphKernelFeatureBuilder.buildGraphKernelFeatures(
sentenceGraph, path)
self.graphKernelFeatureBuilder.setFeatureVector(None)
if self.styles["entity_type"]:
features[self.featureSet.getId("e1_" +
entity1.get("type"))] = 1
features[self.featureSet.getId("e2_" +
entity2.get("type"))] = 1
features[self.featureSet.getId("distance_" +
str(len(path)))] = 1
if not self.styles["no_dependency"]:
#print "Dep features"
self.multiEdgeFeatureBuilder.setFeatureVector(
features, entity1, entity2)
#self.multiEdgeFeatureBuilder.buildStructureFeatures(sentenceGraph, paths) # remove for fast
if not self.styles["disable_entity_features"]:
self.multiEdgeFeatureBuilder.buildEntityFeatures(
sentenceGraph)
self.multiEdgeFeatureBuilder.buildPathLengthFeatures(path)
if not self.styles["disable_terminus_features"]:
self.multiEdgeFeatureBuilder.buildTerminusTokenFeatures(
path, sentenceGraph) # remove for fast
if not self.styles["disable_single_element_features"]:
self.multiEdgeFeatureBuilder.buildSingleElementFeatures(
path, sentenceGraph)
if not self.styles["disable_ngram_features"]:
#print "NGrams"
self.multiEdgeFeatureBuilder.buildPathGrams(
2, path, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(
3, path, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(
4, path, sentenceGraph) # remove for fast
#self.buildEdgeCombinations(path, edges, sentenceGraph, features) # remove for fast
#if edges != None:
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[0], edges[0][1]+edges[1][0], "t1", sentenceGraph) # remove for fast
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[-1], edges[len(path)-1][len(path)-2]+edges[len(path)-2][len(path)-1], "t2", sentenceGraph) # remove for fast
if not self.styles["disable_path_edge_features"]:
self.multiEdgeFeatureBuilder.buildPathEdgeFeatures(
path, sentenceGraph)
self.multiEdgeFeatureBuilder.buildSentenceFeatures(
sentenceGraph)
self.multiEdgeFeatureBuilder.setFeatureVector(None)
if self.styles["nodalida"]:
self.nodalidaFeatureBuilder.setFeatureVector(
features, entity1, entity2)
shortestPaths = self.nodalidaFeatureBuilder.buildShortestPaths(
sentenceGraph.dependencyGraph, path)
print shortestPaths
if len(shortestPaths) > 0:
self.nodalidaFeatureBuilder.buildNGrams(
shortestPaths, sentenceGraph)
self.nodalidaFeatureBuilder.setFeatureVector(None)
if not self.styles["no_linear"]:
self.tokenFeatureBuilder.setFeatureVector(features)
for i in range(len(sentenceGraph.tokens)):
if sentenceGraph.tokens[i] == token1:
token1Index = i
if sentenceGraph.tokens[i] == token2:
token2Index = i
linearPreTag = "linfw_"
if token1Index > token2Index:
token1Index, token2Index = token2Index, token1Index
linearPreTag = "linrv_"
self.tokenFeatureBuilder.buildLinearOrderFeatures(
token1Index, sentenceGraph, 2, 2, preTag="linTok1")
self.tokenFeatureBuilder.buildLinearOrderFeatures(
token2Index, sentenceGraph, 2, 2, preTag="linTok2")
# Before, middle, after
# self.tokenFeatureBuilder.buildTokenGrams(0, token1Index-1, sentenceGraph, "bf")
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, "bw")
# self.tokenFeatureBuilder.buildTokenGrams(token2Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, "af")
# before-middle, middle, middle-after
# self.tokenFeatureBuilder.buildTokenGrams(0, token2Index-1, sentenceGraph, linearPreTag+"bf", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, linearPreTag+"bw", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, linearPreTag+"af", max=2)
self.tokenFeatureBuilder.setFeatureVector(None)
if self.styles["random"]:
self.randomFeatureBuilder.setFeatureVector(features)
self.randomFeatureBuilder.buildRandomFeatures(100, 0.01)
self.randomFeatureBuilder.setFeatureVector(None)
if self.styles["genia_limits"] and not self.styles["no_task"]:
e1Type = entity1.get("type")
e2Type = entity2.get("type")
assert (entity1.get("isName") == "False")
if entity2.get("isName") == "True":
features[self.featureSet.getId(
"GENIA_target_protein")] = 1
else:
features[self.featureSet.getId(
"GENIA_nested_event")] = 1
if e1Type.find(
"egulation"
) != -1: # leave r out to avoid problems with capitalization
if entity2.get("isName") == "True":
features[self.featureSet.getId(
"GENIA_regulation_of_protein")] = 1
else:
features[self.featureSet.getId(
"GENIA_regulation_of_event")] = 1
if self.styles["bi_limits"]:
# Make features based on entity types
e1Type = entity1.get("type")
e2Type = entity2.get("type")
e1SuperType = str(self.getBISuperType(e1Type))
e2SuperType = str(self.getBISuperType(e2Type))
features[self.featureSet.getId("BI_e1_" + e1Type)] = 1
features[self.featureSet.getId("BI_e2_" + e2Type)] = 1
features[self.featureSet.getId("BI_e1sup_" +
e1SuperType)] = 1
features[self.featureSet.getId("BI_e2sup_" +
e2SuperType)] = 1
features[self.featureSet.getId("BI_e1e2_" + e1Type + "_" +
e2Type)] = 1
features[self.featureSet.getId("BI_e1e2sup_" +
e1SuperType + "_" +
e2SuperType)] = 1
if self.styles["evex"]:
self.evexFeatureBuilder.setFeatureVector(
features, entity1, entity2)
self.evexFeatureBuilder.buildEdgeFeatures(
entity1, entity2, token1, token2, path, sentenceGraph)
self.evexFeatureBuilder.setFeatureVector(None)
if self.styles["giuliano"]:
self.giulianoFeatureBuilder.setFeatureVector(
features, entity1, entity2)
self.giulianoFeatureBuilder.buildEdgeFeatures(
entity1, entity2, token1, token2, path, sentenceGraph)
self.giulianoFeatureBuilder.setFeatureVector(None)
else:
features[self.featureSet.getId("always_negative")] = 1
if self.styles["subset"]:
features[self.featureSet.getId("out_of_scope")] = 1
else:
features[self.featureSet.getId("always_negative")] = 1
if self.styles["subset"]:
features[self.featureSet.getId("out_of_scope")] = 1
path = [token1, token2]
# define extra attributes
#if int(path[0].get("id").split("_")[-1]) < int(path[-1].get("id").split("_")[-1]):
if int(path[0].get("charOffset").split("-")[0]) < int(
path[-1].get("charOffset").split("-")[0]):
#extra = {"xtype":"edge","type":"i","t1":path[0],"t2":path[-1]}
extra = {
"xtype": "edge",
"type": "i",
"t1": path[0].get("id"),
"t2": path[-1].get("id")
}
extra["deprev"] = False
else:
#extra = {"xtype":"edge","type":"i","t1":path[-1],"t2":path[0]}
extra = {
"xtype": "edge",
"type": "i",
"t1": path[-1].get("id"),
"t2": path[0].get("id")
}
extra["deprev"] = True
if entity1 != None:
#extra["e1"] = entity1
extra["e1"] = entity1.get("id")
if sentenceGraph.mergedEntityToDuplicates != None:
#extra["e1GoldIds"] = mergedEntityIds[entity1]
extra["e1DuplicateIds"] = ",".join([
x.get("id")
for x in sentenceGraph.mergedEntityToDuplicates[entity1]
])
if entity2 != None:
#extra["e2"] = entity2
extra["e2"] = entity2.get("id")
if sentenceGraph.mergedEntityToDuplicates != None:
extra["e2DuplicateIds"] = ",".join([
x.get("id")
for x in sentenceGraph.mergedEntityToDuplicates[entity2]
])
#extra["e2GoldIds"] = mergedEntityIds[entity2]
extra["categoryName"] = categoryName
if self.styles["bacteria_renaming"]:
if entity1.get("text") != None and entity1.get("text") != "":
extra["e1t"] = entity1.get("text").replace(" ", "---").replace(
":", "-COL-")
if entity2.get("text") != None and entity2.get("text") != "":
extra["e2t"] = entity2.get("text").replace(" ", "---").replace(
":", "-COL-")
sentenceOrigId = sentenceGraph.sentenceElement.get("origId")
if sentenceOrigId != None:
extra["SOID"] = sentenceOrigId
# make example
if self.styles["binary"]:
if categoryName != "neg":
category = 1
else:
category = -1
categoryName = "i"
else:
category = self.classSet.getId(categoryName)
# NOTE: temporarily disable for replicating 110310 experiment
#features[self.featureSet.getId("extra_constant")] = 1
return (sentenceGraph.getSentenceId() + ".x" + str(exampleIndex),
category, features, extra)
class AsymmetricEventExampleBuilder(ExampleBuilder):
def __init__(self, style=["typed","directed"], length=None, types=[], featureSet=None, classSet=None):
if featureSet == None:
featureSet = IdSet()
if classSet == None:
classSet = IdSet(1)
else:
classSet = classSet
assert( classSet.getId("neg") == 1 )
ExampleBuilder.__init__(self, classSet=classSet, featureSet=featureSet)
if style.find(",") != -1:
style = style.split(",")
self.styles = style
self.negFrac = None
self.posPairGaz = POSPairGazetteer()
for s in style:
if s.find("negFrac") != -1:
self.negFrac = float(s.split("_")[-1])
print >> sys.stderr, "Downsampling negatives to", self.negFrac
self.negRand = random.Random(15)
elif s.find("posPairGaz") != -1:
self.posPairGaz = POSPairGazetteer(loadFrom=s.split("_", 1)[-1])
self.multiEdgeFeatureBuilder = MultiEdgeFeatureBuilder(self.featureSet)
self.triggerFeatureBuilder = TriggerFeatureBuilder(self.featureSet)
if "graph_kernel" in self.styles:
from FeatureBuilders.GraphKernelFeatureBuilder import GraphKernelFeatureBuilder
self.graphKernelFeatureBuilder = GraphKernelFeatureBuilder(self.featureSet)
if "noAnnType" in self.styles:
self.multiEdgeFeatureBuilder.noAnnType = True
if "noMasking" in self.styles:
self.multiEdgeFeatureBuilder.maskNamedEntities = False
if "maxFeatures" in self.styles:
self.multiEdgeFeatureBuilder.maximum = True
self.tokenFeatureBuilder = TokenFeatureBuilder(self.featureSet)
if "ontology" in self.styles:
self.multiEdgeFeatureBuilder.ontologyFeatureBuilder = BioInferOntologyFeatureBuilder(self.featureSet)
if "nodalida" in self.styles:
self.nodalidaFeatureBuilder = NodalidaFeatureBuilder(self.featureSet)
#IF LOCAL
if "bioinfer_limits" in self.styles:
self.bioinferOntologies = OntologyUtils.getBioInferTempOntology()
#self.bioinferOntologies = OntologyUtils.loadOntologies(OntologyUtils.g_bioInferFileName)
#ENDIF
self.pathLengths = length
assert(self.pathLengths == None)
self.types = types
if "random" in self.styles:
from FeatureBuilders.RandomFeatureBuilder import RandomFeatureBuilder
self.randomFeatureBuilder = RandomFeatureBuilder(self.featureSet)
#self.outFile = open("exampleTempFile.txt","wt")
@classmethod
def run(cls, input, output, parse, tokenization, style, idFileTag=None):
classSet, featureSet = cls.getIdSets(idFileTag)
if style != None:
e = cls(style=style, classSet=classSet, featureSet=featureSet)
else:
e = cls(classSet=classSet, featureSet=featureSet)
sentences = cls.getSentences(input, parse, tokenization)
e.buildExamplesForSentences(sentences, output, idFileTag)
if "printClassIds" in e.styles:
print >> sys.stderr, e.classSet.Ids
def definePredictedValueRange(self, sentences, elementName):
self.multiEdgeFeatureBuilder.definePredictedValueRange(sentences, elementName)
def getPredictedValueRange(self):
return self.multiEdgeFeatureBuilder.predictedRange
def filterEdgesByType(self, edges, typesToInclude):
if len(typesToInclude) == 0:
return edges
edgesToKeep = []
for edge in edges:
if edge.get("type") in typesToInclude:
edgesToKeep.append(edge)
return edgesToKeep
def getCategoryNameFromTokens(self, sentenceGraph, t1, t2, directed=True):
types = set()
themeE1Types = set()
intEdges = []
if sentenceGraph.interactionGraph.has_edge(t1, t2):
intEdges = sentenceGraph.interactionGraph.get_edge_data(t1, t2, default={})
# NOTE: Only works if keys are ordered integers
for i in range(len(intEdges)):
types.add(intEdges[i]["element"].get("type"))
# if (not directed) and sentenceGraph.interactionGraph.has_edge(t2, t1):
# intEdgesReverse = sentenceGraph.interactionGraph.get_edge(t2, t1, default={})
# # NOTE: Only works if keys are ordered integers
# for i in range(len(intEdgesReverse)):
# intElement = intEdgesReverse[i]["element"]
# intType = intElement.get("type")
# types.add(intType)
# intEdges.extend(intEdgesReverse)
for i in range(len(intEdges)):
intElement = intEdges[i]["element"]
intType = intElement.get("type")
if intType == "Theme":
e1Entity = sentenceGraph.entitiesById[intElement.get("e1")]
themeE1Types.add(e1Entity.get("type"))
#types.add(intType)
if len(themeE1Types) != 0:
themeE1Types = list(themeE1Types)
themeE1Types.sort()
categoryName = ""
for name in themeE1Types:
if categoryName != "":
categoryName += "---"
categoryName += name
return categoryName
else:
types = list(types)
types.sort()
categoryName = ""
for name in types:
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def getCategoryName(self, sentenceGraph, e1, e2, directed=True):
interactions = sentenceGraph.getInteractions(e1, e2)
if not directed:
interactions.extend(sentenceGraph.getInteractions(e2, e1))
types = set()
for interaction in interactions:
types.add(interaction.attrib["type"])
types = list(types)
types.sort()
categoryName = ""
for name in types:
if categoryName != "":
categoryName += "---"
categoryName += name
if categoryName != "":
return categoryName
else:
return "neg"
def preProcessExamples(self, allExamples):
# Duplicates cannot be removed here, as they should only be removed from the training set. This is done
# in the classifier.
# if "no_duplicates" in self.styles:
# count = len(allExamples)
# print >> sys.stderr, " Removing duplicates,",
# allExamples = ExampleUtils.removeDuplicates(allExamples)
# print >> sys.stderr, "removed", count - len(allExamples)
if "normalize" in self.styles:
print >> sys.stderr, " Normalizing feature vectors"
ExampleUtils.normalizeFeatureVectors(allExamples)
return allExamples
def isPotentialGeniaInteraction(self, e1, e2):
if e1.get("isName") == "True":
return False
else:
return True
#IF LOCAL
def getBioInferParentType(self, eType):
if eType == "Physical_entity" or OntologyUtils.hasParent(eType, "Physical_entity", self.bioinferOntologies):
return "Physical"
elif eType == "Property_entity" or OntologyUtils.hasParent(eType, "Property_entity", self.bioinferOntologies):
return "Property"
elif OntologyUtils.hasParent(eType, "Relationship", self.bioinferOntologies):
return "Process"
else:
assert False, eType
# if self.bioinferOntologies["Entity"].has_key(eType):
# if OntologyUtils.hasParent(eType, "Physical_entity", self.bioinferOntologies):
# assert not OntologyUtils.hasParent(eType, "Property_entity", self.bioinferOntologies), eType
# return "Physical"
# else:
# assert OntologyUtils.hasParent(eType, "Property_entity", self.bioinferOntologies), eType
# return "Property"
#
# else:
# assert self.bioinferOntologies.has_key(eType), eType
# #assert OntologyUtils.hasParent(eType, "Process_entity", self.bioinferOntologies["Relationship"]), eType
# return "Process"
def isPotentialBioInferInteraction(self, e1, e2, categoryName):
e1Type = self.getBioInferParentType(e1.get("type"))
e2Type = self.getBioInferParentType(e2.get("type"))
if e1Type == "Process" or e1Type == "Property":
return True
elif e1Type == "Physical" and e2Type == "Physical":
return True
elif e1Type == "Physical" and e2Type == "Process": # hack
return True
else:
assert(categoryName == "neg"), categoryName + " category for " + e1Type + " and " + e2Type
return False
#ENDIF
def nxMultiDiGraphToUndirected(self, graph):
undirected = NX10.MultiGraph(name=graph.name)
undirected.add_nodes_from(graph)
undirected.add_edges_from(graph.edges_iter())
return undirected
def buildExamples(self, sentenceGraph):
examples = []
exampleIndex = 0
clearGraph = sentenceGraph.getCleared()
#undirected = sentenceGraph.getUndirectedDependencyGraph()
undirected = self.nxMultiDiGraphToUndirected(sentenceGraph.dependencyGraph)
##undirected = sentenceGraph.dependencyGraph.to_undirected()
###undirected = NX10.MultiGraph(sentenceGraph.dependencyGraph) This didn't work
paths = NX10.all_pairs_shortest_path(undirected, cutoff=999)
self.triggerFeatureBuilder.initSentence(clearGraph)
# Generate examples based on interactions between entities or interactions between tokens
if "entities" in self.styles:
loopRange = len(sentenceGraph.entities)
else:
loopRange = len(sentenceGraph.tokens)
#for i in range(loopRange-1):
for i in range(loopRange): # allow self-interactions
#for j in range(i+1,loopRange):
for j in range(i,loopRange): # allow self-interactions
eI = None
eJ = None
if "entities" in self.styles:
eI = sentenceGraph.entities[i]
eJ = sentenceGraph.entities[j]
tI = sentenceGraph.entityHeadTokenByEntity[eI]
tJ = sentenceGraph.entityHeadTokenByEntity[eJ]
#if "no_ne_interactions" in self.styles and eI.get("isName") == "True" and eJ.get("isName") == "True":
# continue
if eI.get("type") == "neg" or eJ.get("type") == "neg":
continue
else:
tI = sentenceGraph.tokens[i]
tJ = sentenceGraph.tokens[j]
# # only consider paths between entities (NOTE! entities, not only named entities)
# if "headsOnly" in self.styles:
# if (len(sentenceGraph.tokenIsEntityHead[tI]) == 0) or (len(sentenceGraph.tokenIsEntityHead[tJ]) == 0):
# continue
if "directed" in self.styles:
# define forward
if "entities" in self.styles:
categoryName = self.getCategoryName(sentenceGraph, eI, eJ, True)
else:
categoryName = self.getCategoryNameFromTokens(sentenceGraph, tI, tJ, True)
self.exampleStats.beginExample(categoryName)
if self.negFrac == None or categoryName != "neg" or (categoryName == "neg" and self.negRand.random() < self.negFrac):
makeExample = True
if ("genia_limits" in self.styles) and not self.isPotentialGeniaInteraction(eI, eJ):
makeExample = False
self.exampleStats.filter("genia_limits")
if self.posPairGaz.getNegFrac((tI.get("POS"), tJ.get("POS"))) == 1.0:
makeExample = False
self.exampleStats.filter("pos_pair")
if makeExample:
if not sentenceGraph.tokenIsName[tI]:
examples.append( self.buildExample(tI, tJ, paths, clearGraph, categoryName, exampleIndex, eI, eJ) )
exampleIndex += 1
else:
self.exampleStats.filter("genia_token_limits")
else:
self.exampleStats.filter("neg_frac")
self.exampleStats.endExample()
# define reverse
if "entities" in self.styles:
categoryName = self.getCategoryName(sentenceGraph, eJ, eI, True)
else:
categoryName = self.getCategoryNameFromTokens(sentenceGraph, tJ, tI, True)
self.exampleStats.beginExample(categoryName)
if self.negFrac == None or categoryName != "neg" or (categoryName == "neg" and self.negRand.random() < self.negFrac):
makeExample = True
if ("genia_limits" in self.styles) and not self.isPotentialGeniaInteraction(eJ, eI):
makeExample = False
self.exampleStats.filter("genia_limits")
if ("bioinfer_limits" in self.styles) and not self.isPotentialBioInferInteraction(eJ, eI, categoryName):
makeExample = False
self.exampleStats.filter("bioinfer_limits")
if self.posPairGaz.getNegFrac((tJ.get("POS"), tI.get("POS"))) == 1.0:
makeExample = False
self.exampleStats.filter("pos_pair")
if makeExample:
if not sentenceGraph.tokenIsName[tJ]:
examples.append( self.buildExample(tJ, tI, paths, clearGraph, categoryName, exampleIndex, eJ, eI) )
exampleIndex += 1
else:
self.exampleStats.filter("genia_token_limits")
else:
self.exampleStats.filter("neg_frac")
self.exampleStats.endExample()
# else:
# if "entities" in self.styles:
# categoryName = self.getCategoryName(sentenceGraph, eI, eJ, False)
# else:
# categoryName = self.getCategoryNameFromTokens(sentenceGraph, tI, tJ, False)
# forwardExample = self.buildExample(tI, tJ, paths, clearGraph, categoryName, exampleIndex, eI, eJ)
# if not "graph_kernel" in self.styles:
# reverseExample = self.buildExample(tJ, tI, paths, clearGraph, categoryName, exampleIndex, eJ, eI)
# forwardExample[2].update(reverseExample[2])
# examples.append(forwardExample)
# exampleIndex += 1
return examples
def buildExample(self, token1, token2, paths, sentenceGraph, categoryName, exampleIndex, entity1=None, entity2=None):
# define features
features = {}
if True: #token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
if token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
path = paths[token1][token2]
else:
path = [token1, token2]
assert(self.pathLengths == None)
if self.pathLengths == None or len(path)-1 in self.pathLengths:
if not "no_trigger":
self.triggerFeatureBuilder.setFeatureVector(self.features)
self.triggerFeatureBuilder.tag = "trg_t1_"
self.triggerFeatureBuilder.buildFeatures(eventToken)
self.triggerFeatureBuilder.tag = "trg_t2_"
self.triggerFeatureBuilder.buildFeatures(eventToken)
# if not "no_ontology" in self.styles:
# self.ontologyFeatureBuilder.setFeatureVector(features)
# self.ontologyFeatureBuilder.buildOntologyFeaturesForPath(sentenceGraph, path)
# self.ontologyFeatureBuilder.setFeatureVector(None)
if "graph_kernel" in self.styles or not "no_dependency" in self.styles:
if token1 != token2 and paths.has_key(token1) and paths[token1].has_key(token2):
edges = self.multiEdgeFeatureBuilder.getEdges(sentenceGraph.dependencyGraph, path)
else:
edges = None
if "graph_kernel" in self.styles:
self.graphKernelFeatureBuilder.setFeatureVector(features, entity1, entity2)
self.graphKernelFeatureBuilder.buildGraphKernelFeatures(sentenceGraph, path, edges)
self.graphKernelFeatureBuilder.setFeatureVector(None)
if "entity_type" in self.styles:
features[self.featureSet.getId("e1_"+entity1.attrib["type"])] = 1
features[self.featureSet.getId("e2_"+entity2.attrib["type"])] = 1
features[self.featureSet.getId("distance_"+str(len(path)))] = 1
if not "no_dependency" in self.styles:
if token1 == token2:
features[self.featureSet.getId("tokenSelfLoop")] = 1
self.multiEdgeFeatureBuilder.setFeatureVector(features, entity1, entity2)
#self.multiEdgeFeatureBuilder.buildStructureFeatures(sentenceGraph, paths) # remove for fast
if not "disable_entity_features" in self.styles:
self.multiEdgeFeatureBuilder.buildEntityFeatures(sentenceGraph)
self.multiEdgeFeatureBuilder.buildPathLengthFeatures(path)
if not "disable_terminus_features" in self.styles:
self.multiEdgeFeatureBuilder.buildTerminusTokenFeatures(path, sentenceGraph) # remove for fast
if not "disable_single_element_features" in self.styles:
self.multiEdgeFeatureBuilder.buildSingleElementFeatures(path, edges, sentenceGraph)
if not "disable_ngram_features" in self.styles:
self.multiEdgeFeatureBuilder.buildPathGrams(2, path, edges, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(3, path, edges, sentenceGraph) # remove for fast
self.multiEdgeFeatureBuilder.buildPathGrams(4, path, edges, sentenceGraph) # remove for fast
#self.buildEdgeCombinations(path, edges, sentenceGraph, features) # remove for fast
#if edges != None:
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[0], edges[0][1]+edges[1][0], "t1", sentenceGraph) # remove for fast
# self.multiEdgeFeatureBuilder.buildTerminusFeatures(path[-1], edges[len(path)-1][len(path)-2]+edges[len(path)-2][len(path)-1], "t2", sentenceGraph) # remove for fast
if not "disable_path_edge_features" in self.styles:
self.multiEdgeFeatureBuilder.buildPathEdgeFeatures(path, edges, sentenceGraph)
self.multiEdgeFeatureBuilder.buildSentenceFeatures(sentenceGraph)
self.multiEdgeFeatureBuilder.setFeatureVector(None)
if "nodalida" in self.styles:
self.nodalidaFeatureBuilder.setFeatureVector(features, entity1, entity2)
shortestPaths = self.nodalidaFeatureBuilder.buildShortestPaths(sentenceGraph.dependencyGraph, path)
print shortestPaths
if len(shortestPaths) > 0:
self.nodalidaFeatureBuilder.buildNGrams(shortestPaths, sentenceGraph)
self.nodalidaFeatureBuilder.setFeatureVector(None)
if not "no_linear" in self.styles:
self.tokenFeatureBuilder.setFeatureVector(features)
for i in range(len(sentenceGraph.tokens)):
if sentenceGraph.tokens[i] == token1:
token1Index = i
if sentenceGraph.tokens[i] == token2:
token2Index = i
linearPreTag = "linfw_"
if token1Index > token2Index:
token1Index, token2Index = token2Index, token1Index
linearPreTag = "linrv_"
self.tokenFeatureBuilder.buildLinearOrderFeatures(token1Index, sentenceGraph, 2, 2, preTag="linTok1")
self.tokenFeatureBuilder.buildLinearOrderFeatures(token2Index, sentenceGraph, 2, 2, preTag="linTok2")
# Before, middle, after
# self.tokenFeatureBuilder.buildTokenGrams(0, token1Index-1, sentenceGraph, "bf")
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, "bw")
# self.tokenFeatureBuilder.buildTokenGrams(token2Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, "af")
# before-middle, middle, middle-after
# self.tokenFeatureBuilder.buildTokenGrams(0, token2Index-1, sentenceGraph, linearPreTag+"bf", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, token2Index-1, sentenceGraph, linearPreTag+"bw", max=2)
# self.tokenFeatureBuilder.buildTokenGrams(token1Index+1, len(sentenceGraph.tokens)-1, sentenceGraph, linearPreTag+"af", max=2)
self.tokenFeatureBuilder.setFeatureVector(None)
if "random" in self.styles:
self.randomFeatureBuilder.setFeatureVector(features)
self.randomFeatureBuilder.buildRandomFeatures(100, 0.01)
self.randomFeatureBuilder.setFeatureVector(None)
if "genia_limits" in self.styles:
e1Type = entity1.get("type")
e2Type = entity2.get("type")
assert(entity1.get("isName") == "False")
if entity2.get("isName") == "True":
features[self.featureSet.getId("GENIA_target_protein")] = 1
else:
features[self.featureSet.getId("GENIA_nested_event")] = 1
if e1Type.find("egulation") != -1: # leave r out to avoid problems with capitalization
if entity2.get("isName") == "True":
features[self.featureSet.getId("GENIA_regulation_of_protein")] = 1
else:
features[self.featureSet.getId("GENIA_regulation_of_event")] = 1
else:
features[self.featureSet.getId("always_negative")] = 1
if "subset" in self.styles:
features[self.featureSet.getId("out_of_scope")] = 1
else:
features[self.featureSet.getId("always_negative")] = 1
if "subset" in self.styles:
features[self.featureSet.getId("out_of_scope")] = 1
path = [token1, token2]
self.triggerFeatureBuilder.tag = ""
self.triggerFeatureBuilder.setFeatureVector(None)
# define extra attributes
# if int(path[0].attrib["id"].split("_")[-1]) < int(path[-1].attrib["id"].split("_")[-1]):
# #extra = {"xtype":"edge","type":"i","t1":path[0],"t2":path[-1]}
# extra = {"xtype":"asym","type":"i","t1":path[0].get("id"),"t2":path[-1].get("id")}
# extra["deprev"] = False
# else:
# #extra = {"xtype":"edge","type":"i","t1":path[-1],"t2":path[0]}
# extra = {"xtype":"asym","type":"i","t1":path[-1].get("id"),"t2":path[0].get("id")}
# extra["deprev"] = True
extra = {"xtype":"asym","type":"i","t1":token1.get("id"),"t2":token2.get("id")}
if entity1 != None:
#extra["e1"] = entity1
extra["e1"] = entity1.get("id")
if entity2 != None:
#extra["e2"] = entity2
extra["e2"] = entity2.get("id")
extra["categoryName"] = categoryName
sentenceOrigId = sentenceGraph.sentenceElement.get("origId")
if sentenceOrigId != None:
extra["SOID"] = sentenceOrigId
# make example
if "binary" in self.styles:
if categoryName != "neg":
category = 1
else:
category = -1
categoryName = "i"
else:
category = self.classSet.getId(categoryName)
return (sentenceGraph.getSentenceId()+".x"+str(exampleIndex),category,features,extra)