def getEntityType(self, entityName):
types = self.getEntityTypes(entityName)
entityDetector = EntityDetector()
entityTypeResult = entityDetector.detect(types.get("type", []))
result = {"entity_detection": entityTypeResult, "types": types}
return result
def __init__(self):
Detector.__init__(self)
self.triggerDetector = EntityDetector()
self.edgeDetector = EdgeDetector()
self.unmergingDetector = UnmergingDetector()
self.doUnmergingSelfTraining = True #False
self.modifierDetector = ModifierDetector()
#self.stEvaluator = Evaluators.BioNLP11GeniaTools
#self.stWriteScores = False
self.STATE_COMPONENT_TRAIN = "COMPONENT_TRAIN"
self.tag = "event-"
def getEntityType(self, entityName):
types = self.getEntityTypes(entityName)
entityDetector = EntityDetector()
entityTypeResult = entityDetector.detect(types.get("type", []))
result = {
"entity_detection": entityTypeResult,
"types": types
}
return result
def __init__(self):
Detector.__init__(self)
self.triggerDetector = EntityDetector()
self.edgeDetector = EdgeDetector()
self.unmergingDetector = UnmergingDetector()
self.doUnmergingSelfTraining = True #False
self.modifierDetector = ModifierDetector()
#self.stEvaluator = Evaluators.BioNLP11GeniaTools
#self.stWriteScores = False
self.STATE_COMPONENT_TRAIN = "COMPONENT_TRAIN"
self.tag = "event-"
class EventDetector(Detector):
"""
A multi-stage detector used for the BioNLP Shared Task type events.
"""
def __init__(self):
Detector.__init__(self)
self.triggerDetector = EntityDetector()
self.edgeDetector = EdgeDetector()
self.unmergingDetector = UnmergingDetector()
self.doUnmergingSelfTraining = True #False
self.modifierDetector = ModifierDetector()
#self.stEvaluator = Evaluators.BioNLP11GeniaTools
#self.stWriteScores = False
self.STATE_COMPONENT_TRAIN = "COMPONENT_TRAIN"
self.tag = "event-"
def setConnection(self, connection):
self.triggerDetector.setConnection(connection)
self.edgeDetector.setConnection(connection)
self.unmergingDetector.setConnection(connection)
self.modifierDetector.setConnection(connection)
return connection
def setWorkDir(self, workDir):
Detector.setWorkDir(self, workDir) # for EventDetector
# setup components
for detector in [
self.triggerDetector, self.edgeDetector,
self.unmergingDetector, self.modifierDetector
]:
if detector != None:
detector.setWorkDir(workDir)
def train(self,
trainData=None,
optData=None,
model=None,
combinedModel=None,
triggerExampleStyle=None,
edgeExampleStyle=None,
unmergingExampleStyle=None,
modifierExampleStyle=None,
triggerClassifierParameters=None,
edgeClassifierParameters=None,
unmergingClassifierParameters=None,
modifierClassifierParameters=None,
recallAdjustParameters=None,
unmerging=None,
trainModifiers=None,
fullGrid=False,
task=None,
parse=None,
tokenization=None,
fromStep=None,
toStep=None,
workDir=None):
# Initialize the training process ##############################
self.initVariables(
trainData=trainData,
optData=optData,
model=model,
combinedModel=combinedModel,
triggerExampleStyle=triggerExampleStyle,
edgeExampleStyle=edgeExampleStyle,
unmergingExampleStyle=unmergingExampleStyle,
modifierExampleStyle=modifierExampleStyle,
triggerClassifierParameters=triggerClassifierParameters,
edgeClassifierParameters=edgeClassifierParameters,
unmergingClassifierParameters=unmergingClassifierParameters,
modifierClassifierParameters=modifierClassifierParameters,
recallAdjustParameters=recallAdjustParameters,
unmerging=unmerging,
trainModifiers=trainModifiers,
fullGrid=fullGrid,
task=task,
parse=parse,
tokenization=tokenization)
self.setWorkDir(workDir)
# Begin the training process ####################################
self.enterState(self.STATE_TRAIN, [
"ANALYZE", "EXAMPLES", "BEGIN-MODEL", "END-MODEL",
"BEGIN-COMBINED-MODEL", "SELF-TRAIN-EXAMPLES-FOR-UNMERGING",
"UNMERGING-EXAMPLES", "BEGIN-UNMERGING-MODEL",
"END-UNMERGING-MODEL", "GRID", "BEGIN-COMBINED-MODEL-FULLGRID",
"END-COMBINED-MODEL"
], fromStep, toStep)
self.triggerDetector.enterState(self.STATE_COMPONENT_TRAIN)
self.edgeDetector.enterState(self.STATE_COMPONENT_TRAIN)
self.unmergingDetector.enterState(self.STATE_COMPONENT_TRAIN)
self.modifierDetector.enterState(self.STATE_COMPONENT_TRAIN)
if self.checkStep("ANALYZE"):
# General training initialization done at the beginning of the first state
self.model = self.initModel(
self.model,
[("triggerExampleStyle",
self.triggerDetector.tag + "example-style"),
("triggerClassifierParameters",
self.triggerDetector.tag + "classifier-parameters-train"),
("edgeExampleStyle", self.edgeDetector.tag + "example-style"),
("edgeClassifierParameters",
self.edgeDetector.tag + "classifier-parameters-train"),
("unmergingExampleStyle",
self.unmergingDetector.tag + "example-style"),
("unmergingClassifierParameters",
self.unmergingDetector.tag + "classifier-parameters-train"),
("modifierExampleStyle",
self.modifierDetector.tag + "example-style"),
("modifierClassifierParameters",
self.modifierDetector.tag + "classifier-parameters-train")])
self.combinedModel = self.initModel(self.combinedModel)
tags = [
self.triggerDetector.tag, self.edgeDetector.tag,
self.unmergingDetector.tag, self.modifierDetector.tag
]
stringDict = {}
for tag in tags:
stringDict[tag + "parse"] = parse
stringDict[tag + "task"] = task
self.saveStrings(stringDict, self.model)
self.saveStrings(stringDict, self.combinedModel, False)
# Perform structure analysis
self.structureAnalyzer.analyze([optData, trainData], self.model)
print >> sys.stderr, self.structureAnalyzer.toString()
# (Re-)open models in case we start after the first ("ANALYZE") step
self.model = self.openModel(model, "a")
self.combinedModel = self.openModel(combinedModel, "a")
# Use structure analysis to define automatic parameters
if self.unmerging == None:
if not self.structureAnalyzer.isInitialized():
self.structureAnalyzer.load(self.model)
self.unmerging = self.structureAnalyzer.hasEvents()
if self.trainModifiers == None:
if not self.structureAnalyzer.isInitialized():
self.structureAnalyzer.load(self.model)
self.trainModifiers = self.structureAnalyzer.hasModifiers()
if self.checkStep("EXAMPLES"):
self.triggerDetector.buildExamples(self.model, [
optData.replace("-nodup", ""),
trainData.replace("-nodup", "")
], [
self.workDir + self.triggerDetector.tag + "opt-examples.gz",
self.workDir + self.triggerDetector.tag + "train-examples.gz"
],
saveIdsToModel=True)
self.edgeDetector.buildExamples(self.model, [
optData.replace("-nodup", ""),
trainData.replace("-nodup", "")
], [
self.workDir + self.edgeDetector.tag + "opt-examples.gz",
self.workDir + self.edgeDetector.tag + "train-examples.gz"
],
saveIdsToModel=True)
if self.trainModifiers:
self.modifierDetector.buildExamples(
self.model, [optData, trainData], [
self.workDir + self.modifierDetector.tag +
"opt-examples.gz", self.workDir +
self.modifierDetector.tag + "train-examples.gz"
],
saveIdsToModel=True)
if self.checkStep("BEGIN-MODEL"):
#for model in [self.model, self.combinedModel]:
# if model != None:
# model.addStr("BioNLPSTParams", Parameters.toString(self.bioNLPSTParams))
self.triggerDetector.bioNLPSTParams = self.bioNLPSTParams
self.triggerDetector.beginModel(
None, self.model, [
self.workDir + self.triggerDetector.tag +
"train-examples.gz"
], self.workDir + self.triggerDetector.tag + "opt-examples.gz")
self.edgeDetector.beginModel(
None, self.model,
[self.workDir + self.edgeDetector.tag + "train-examples.gz"],
self.workDir + self.edgeDetector.tag + "opt-examples.gz")
if self.trainModifiers:
self.modifierDetector.beginModel(
None, self.model, [
self.workDir + self.modifierDetector.tag +
"train-examples.gz"
], self.workDir + self.modifierDetector.tag +
"opt-examples.gz")
if self.checkStep("END-MODEL"):
self.triggerDetector.endModel(
None, self.model,
self.workDir + self.triggerDetector.tag + "opt-examples.gz")
self.edgeDetector.endModel(
None, self.model,
self.workDir + self.edgeDetector.tag + "opt-examples.gz")
if self.trainModifiers:
self.modifierDetector.endModel(
None, self.model, self.workDir +
self.modifierDetector.tag + "opt-examples.gz")
if self.checkStep("BEGIN-COMBINED-MODEL"):
if not self.fullGrid:
print >> sys.stderr, "Training combined model before grid search"
self.triggerDetector.beginModel(
None, self.combinedModel, [
self.workDir + self.triggerDetector.tag +
"train-examples.gz", self.workDir +
self.triggerDetector.tag + "opt-examples.gz"
], self.workDir + self.triggerDetector.tag +
"opt-examples.gz", self.model)
self.edgeDetector.beginModel(
None, self.combinedModel, [
self.workDir + self.edgeDetector.tag +
"train-examples.gz", self.workDir +
self.edgeDetector.tag + "opt-examples.gz"
],
self.workDir + self.edgeDetector.tag + "opt-examples.gz",
self.model)
else:
print >> sys.stderr, "Combined model will be trained after grid search"
if self.trainModifiers:
print >> sys.stderr, "Training combined model for modifier detection"
self.modifierDetector.beginModel(
None, self.combinedModel, [
self.workDir + self.modifierDetector.tag +
"train-examples.gz", self.workDir +
self.modifierDetector.tag + "opt-examples.gz"
], self.workDir + self.modifierDetector.tag +
"opt-examples.gz", self.model)
self.trainUnmergingDetector()
if self.checkStep("GRID"):
self.doGrid()
if self.checkStep("BEGIN-COMBINED-MODEL-FULLGRID"):
if self.fullGrid:
print >> sys.stderr, "Training combined model after grid search"
self.triggerDetector.beginModel(
None, self.combinedModel, [
self.workDir + self.triggerDetector.tag +
"train-examples.gz", self.workDir +
self.triggerDetector.tag + "opt-examples.gz"
], self.workDir + self.triggerDetector.tag +
"opt-examples.gz", self.model)
self.edgeDetector.beginModel(
None, self.combinedModel, [
self.workDir + self.edgeDetector.tag +
"train-examples.gz", self.workDir +
self.edgeDetector.tag + "opt-examples.gz"
],
self.workDir + self.edgeDetector.tag + "opt-examples.gz",
self.model)
if self.trainModifiers:
print >> sys.stderr, "Training combined model for modifier detection"
self.modifierDetector.beginModel(
None, self.combinedModel, [
self.workDir + self.modifierDetector.tag +
"train-examples.gz", self.workDir +
self.modifierDetector.tag + "opt-examples.gz"
], self.workDir + self.modifierDetector.tag +
"opt-examples.gz", self.model)
else:
print >> sys.stderr, "Combined model has been trained before grid search"
if self.checkStep("END-COMBINED-MODEL"):
self.triggerDetector.endModel(
None, self.combinedModel,
self.workDir + self.triggerDetector.tag + "opt-examples.gz")
self.edgeDetector.endModel(
None, self.combinedModel,
self.workDir + self.edgeDetector.tag + "opt-examples.gz")
if self.trainModifiers:
self.modifierDetector.endModel(
None, self.combinedModel, self.workDir +
self.modifierDetector.tag + "opt-examples.gz")
# End the training process ####################################
if workDir != None:
self.setWorkDir("")
self.exitState()
self.triggerDetector.exitState()
self.edgeDetector.exitState()
self.unmergingDetector.exitState()
self.modifierDetector.exitState()
def doGrid(self):
print >> sys.stderr, "--------- Parameter grid search ---------"
# Build trigger examples
self.triggerDetector.buildExamples(
self.model, [self.optData],
[self.workDir + "grid-trigger-examples"])
if self.fullGrid:
stepParams = {
"trigger":
Parameters.get(self.model.getStr(self.triggerDetector.tag +
"classifier-parameters-train",
defaultIfNotExist=""),
valueListKey="c"),
"booster":
[float(i) for i in self.recallAdjustParameters.split(",")],
"edge":
Parameters.get(self.model.getStr(self.edgeDetector.tag +
"classifier-parameters-train",
defaultIfNotExist=""),
valueListKey="c")
}
else:
stepParams = {
"trigger":
Parameters.get(self.model.getStr(self.triggerDetector.tag +
"classifier-parameter",
defaultIfNotExist=""),
valueListKey="c"),
"booster":
[float(i) for i in self.recallAdjustParameters.split(",")],
"edge":
Parameters.get(self.model.getStr(self.edgeDetector.tag +
"classifier-parameter",
defaultIfNotExist=""),
valueListKey="c")
}
for step in ["trigger", "edge"]:
stepParams[step] = Parameters.getCombinations(stepParams[step])
for i in range(len(stepParams[step])):
stepParams[step][i] = Parameters.toString(stepParams[step][i])
print >> sys.stderr, "Parameters", [
stepParams[x] for x in ["trigger", "booster", "edge"]
]
paramCombinations = combine(
*[stepParams[x] for x in ["trigger", "booster", "edge"]])
print >> sys.stderr, "Combinations", paramCombinations
for i in range(len(paramCombinations)):
paramCombinations[i] = {
"trigger": paramCombinations[i][0],
"booster": paramCombinations[i][1],
"edge": paramCombinations[i][2]
}
#paramCombinations = Parameters.getCombinations(ALL_PARAMS, ["trigger", "booster", "edge"])
prevParams = None
EDGE_MODEL_STEM = os.path.join(
self.edgeDetector.workDir,
os.path.normpath(self.model.path) + "-edge-models/model")
TRIGGER_MODEL_STEM = os.path.join(
self.triggerDetector.workDir,
os.path.normpath(self.model.path) + "-trigger-models/model")
self.structureAnalyzer.load(self.model)
bestResults = None
for i in range(len(paramCombinations)):
params = paramCombinations[i]
print >> sys.stderr, "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
print >> sys.stderr, "Processing params", str(i + 1) + "/" + str(
len(paramCombinations)), params
print >> sys.stderr, "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
# Triggers and Boost (the trigger predictions are recalculated only when the relevant parameters change)
if (prevParams == None) or (
prevParams["trigger"] != params["trigger"]) or (
prevParams["booster"] != params["booster"]):
print >> sys.stderr, "Classifying trigger examples for parameters", "trigger:" + str(
params["trigger"]), "booster:" + str(params["booster"])
xml = self.triggerDetector.classifyToXML(
self.optData,
self.model,
self.workDir + "grid-trigger-examples",
self.workDir + "grid-",
classifierModel=TRIGGER_MODEL_STEM +
Parameters.toId(params["trigger"]),
recallAdjust=params["booster"],
useExistingExamples=True)
prevParams = params
## Build edge examples
#self.edgeDetector.buildExamples(self.model, [xml], [self.workDir+"grid-edge-examples"], [self.optData])
# Classify with pre-defined model
edgeClassifierModel = EDGE_MODEL_STEM + Parameters.toId(
params["edge"])
xml = self.edgeDetector.classifyToXML(
xml,
self.model,
self.workDir + "grid-edge-examples",
self.workDir + "grid-",
classifierModel=edgeClassifierModel,
goldData=self.optData)
bestResults = self.evaluateGrid(xml, params, bestResults)
# Remove remaining intermediate grid files
for tag1 in ["edge", "trigger", "unmerging"]:
for tag2 in ["examples", "pred.xml.gz"]:
if os.path.exists(self.workDir + "grid-" + tag1 + "-" + tag2):
os.remove(self.workDir + "grid-" + tag1 + "-" + tag2)
print >> sys.stderr, "Parameter grid search complete"
print >> sys.stderr, "Tested", len(paramCombinations), "combinations"
print >> sys.stderr, "Best parameters:", bestResults[0]
print >> sys.stderr, "Best result:", bestResults[2] # f-score
# Save grid model
self.saveStr("recallAdjustParameter", str(bestResults[0]["booster"]),
self.model)
self.saveStr("recallAdjustParameter", str(bestResults[0]["booster"]),
self.combinedModel, False)
if self.fullGrid: # define best models
self.triggerDetector.addClassifierModel(
self.model,
TRIGGER_MODEL_STEM + str(bestResults[0]["trigger"]),
bestResults[0]["trigger"])
self.edgeDetector.addClassifierModel(
self.model, EDGE_MODEL_STEM + str(bestResults[0]["edge"]),
bestResults[0]["edge"])
# Remove work files
for stepTag in [
self.workDir + "grid-trigger", self.workDir + "grid-edge",
self.workDir + "grid-unmerging"
]:
for fileStem in [
"-classifications", "-classifications.log", "examples.gz",
"pred.xml.gz"
]:
if os.path.exists(stepTag + fileStem):
os.remove(stepTag + fileStem)
def evaluateGrid(self, xml, params, bestResults):
if xml != None:
# TODO: Where should the EvaluateInteractionXML evaluator come from?
EIXMLResult = EvaluateInteractionXML.run(
self.edgeDetector.evaluator, xml, self.optData, self.parse)
# Convert to ST-format
if self.unmerging:
xml = self.unmergingDetector.classifyToXML(
xml,
self.model,
None,
self.workDir + "grid-",
goldData=self.optData)
#self.structureAnalyzer.validate(xml)
if self.bioNLPSTParams["evaluate"]:
Utils.STFormat.ConvertXML.toSTFormat(
xml, self.workDir + "grid-unmerging-geniaformat", "a2")
stFormatDir = self.workDir + "grid-unmerging-geniaformat"
elif self.bioNLPSTParams["evaluate"]:
#self.structureAnalyzer.validate(xml)
Utils.STFormat.ConvertXML.toSTFormat(
xml, self.workDir + "grid-flat-geniaformat",
"a2") #getA2FileTag(options.task, subTask))
stFormatDir = self.workDir + "grid-flat-geniaformat"
# Evaluation
# Attempt shared task evaluation
stEvaluation = None
if self.bioNLPSTParams["evaluate"]:
stEvaluation = self.stEvaluator.evaluate(
stFormatDir, self.task)
if stEvaluation != None:
if bestResults == None or stEvaluation[0] > bestResults[1][0]:
bestResults = (params, stEvaluation, stEvaluation[0])
else: # If shared task evaluation was not done (failed or not requested) fall back to internal evaluation
if bestResults == None or EIXMLResult.getData(
).fscore > bestResults[1].getData().fscore:
bestResults = (params, EIXMLResult,
EIXMLResult.getData().fscore)
# Remove ST-format files
if os.path.exists(self.workDir + "grid-flat-geniaformat"):
shutil.rmtree(self.workDir + "grid-flat-geniaformat")
if os.path.exists(self.workDir + "grid-unmerging-geniaformat"):
shutil.rmtree(self.workDir + "grid-unmerging-geniaformat")
else:
print >> sys.stderr, "No predicted edges"
return bestResults
def trainUnmergingDetector(self):
xml = None
if not self.unmerging:
print >> sys.stderr, "No unmerging"
if self.checkStep("SELF-TRAIN-EXAMPLES-FOR-UNMERGING",
self.unmerging) and self.unmerging:
# Self-classified train data for unmerging
if self.doUnmergingSelfTraining:
# This allows limiting to a subcorpus
triggerStyle = copy.copy(
Parameters.get(self.triggerExampleStyle))
edgeStyle = copy.copy(Parameters.get(self.edgeExampleStyle))
unmergingStyle = Parameters.get(self.unmergingExampleStyle)
if "sentenceLimit" in unmergingStyle and unmergingStyle[
"sentenceLimit"]:
triggerStyle["sentenceLimit"] = unmergingStyle[
"sentenceLimit"]
edgeStyle["sentenceLimit"] = unmergingStyle[
"sentenceLimit"]
# Build the examples
xml = self.triggerDetector.classifyToXML(
self.trainData,
self.model,
None,
self.workDir + "unmerging-extra-",
exampleStyle=triggerStyle) #, recallAdjust=0.5)
xml = self.edgeDetector.classifyToXML(
xml,
self.model,
None,
self.workDir + "unmerging-extra-",
exampleStyle=edgeStyle) #, recallAdjust=0.5)
assert xml != None
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml,
self.trainData, self.parse)
else:
print >> sys.stderr, "No self-training for unmerging"
if self.checkStep("UNMERGING-EXAMPLES",
self.unmerging) and self.unmerging:
# Unmerging example generation
GOLD_TEST_FILE = self.optData.replace("-nodup", "")
GOLD_TRAIN_FILE = self.trainData.replace("-nodup", "")
if self.doUnmergingSelfTraining:
if xml == None:
xml = self.workDir + "unmerging-extra-edge-pred.xml.gz"
self.unmergingDetector.buildExamples(
self.model, [
self.optData.replace("-nodup", ""),
[self.trainData.replace("-nodup", ""), xml]
], [
self.workDir + "unmerging-opt-examples.gz",
self.workDir + "unmerging-train-examples.gz"
], [GOLD_TEST_FILE, [GOLD_TRAIN_FILE, GOLD_TRAIN_FILE]],
exampleStyle=self.unmergingExampleStyle,
saveIdsToModel=True)
xml = None
else:
self.unmergingDetector.buildExamples(
self.model, [
self.optData.replace("-nodup", ""),
self.trainData.replace("-nodup", "")
], [
self.workDir + "unmerging-opt-examples.gz",
self.workDir + "unmerging-train-examples.gz"
], [GOLD_TEST_FILE, GOLD_TRAIN_FILE],
exampleStyle=self.unmergingExampleStyle,
saveIdsToModel=True)
xml = None
#UnmergingExampleBuilder.run("/home/jari/biotext/EventExtension/TrainSelfClassify/test-predicted-edges.xml", GOLD_TRAIN_FILE, UNMERGING_TRAIN_EXAMPLE_FILE, PARSE, TOK, UNMERGING_FEATURE_PARAMS, UNMERGING_IDS, append=True)
if self.checkStep("BEGIN-UNMERGING-MODEL",
self.unmerging) and self.unmerging:
self.unmergingDetector.beginModel(
None, self.model, self.workDir + "unmerging-train-examples.gz",
self.workDir + "unmerging-opt-examples.gz")
if self.checkStep("END-UNMERGING-MODEL",
self.unmerging) and self.unmerging:
self.unmergingDetector.endModel(
None, self.model, self.workDir + "unmerging-opt-examples.gz")
print >> sys.stderr, "Adding unmerging classifier model to test-set event model"
if self.combinedModel != None:
self.combinedModel.addStr(
"unmerging-example-style",
self.model.getStr("unmerging-example-style"))
self.combinedModel.insert(
self.model.get("unmerging-ids.classes"),
"unmerging-ids.classes")
self.combinedModel.insert(
self.model.get("unmerging-ids.features"),
"unmerging-ids.features")
self.unmergingDetector.addClassifierModel(
self.combinedModel,
self.model.get("unmerging-classifier-model", True),
self.model.getStr("unmerging-classifier-parameter"))
self.combinedModel.save()
def classify(self,
data,
model,
output,
parse=None,
task=None,
goldData=None,
fromStep=None,
toStep=None,
omitSteps=None,
workDir=None):
#BINARY_RECALL_MODE = False # TODO: make a parameter
xml = None
model = self.openModel(model, "r")
self.initVariables(classifyData=data,
model=model,
xml=None,
task=task,
parse=parse)
self.enterState(
self.STATE_CLASSIFY,
["TRIGGERS", "EDGES", "UNMERGING", "MODIFIERS", "ST-CONVERT"],
fromStep, toStep, omitSteps)
#self.enterState(self.STATE_CLASSIFY, ["TRIGGERS", "RECALL-ADJUST", "EDGES", "UNMERGING", "MODIFIERS", "ST-CONVERT"], fromStep, toStep)
self.setWorkDir(workDir)
if workDir == None:
self.setTempWorkDir()
workOutputTag = os.path.join(self.workDir,
os.path.basename(output) + "-")
self.model = self.openModel(self.model, "r")
stParams = self.getBioNLPSharedTaskParams(self.bioNLPSTParams, model)
if self.checkStep("TRIGGERS"):
xml = self.triggerDetector.classifyToXML(
self.classifyData,
self.model,
None,
workOutputTag,
goldData=goldData,
parse=self.parse,
recallAdjust=float(
self.getStr("recallAdjustParameter", self.model)))
if self.checkStep("EDGES"):
xml = self.getWorkFile(xml, workOutputTag + "trigger-pred.xml.gz")
xml = self.edgeDetector.classifyToXML(xml,
self.model,
None,
workOutputTag,
goldData=goldData,
parse=self.parse)
assert xml != None
if self.parse == None:
edgeParse = self.getStr(self.edgeDetector.tag + "parse",
self.model)
else:
edgeParse = self.parse
#EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, self.classifyData, edgeParse)
if goldData != None:
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml,
goldData, edgeParse)
else:
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml,
self.classifyData, edgeParse)
if self.checkStep("UNMERGING"):
if self.model.getStr(
"unmerging-classifier-parameter", None
) != None: #self.model.hasMember("unmerging-classifier-model"):
#xml = self.getWorkFile(xml, output + "-edge-pred.xml.gz")
# To avoid running out of memory, always use file on disk
xml = self.getWorkFile(None,
workOutputTag + "edge-pred.xml.gz")
#goldData = None
#if type(self.classifyData) in types.StringTypes:
# if os.path.exists(self.classifyData.replace("-nodup", "")):
# goldData = self.classifyData.replace("-nodup", "")
xml = self.unmergingDetector.classifyToXML(xml,
self.model,
None,
workOutputTag,
goldData=goldData,
parse=self.parse)
# Evaluate after unmerging
if self.parse == None:
edgeParse = self.getStr(self.edgeDetector.tag + "parse",
self.model)
else:
edgeParse = self.parse
if goldData != None:
EvaluateInteractionXML.run(self.edgeDetector.evaluator,
xml, goldData, edgeParse)
else:
EvaluateInteractionXML.run(self.edgeDetector.evaluator,
xml, self.classifyData,
edgeParse)
else:
print >> sys.stderr, "No model for unmerging"
if self.checkStep("MODIFIERS"):
if self.model.hasMember("modifier-classifier-model"):
xml = self.getWorkFile(xml, [
workOutputTag + "unmerging-pred.xml.gz",
workOutputTag + "edge-pred.xml.gz"
])
xml = self.modifierDetector.classifyToXML(xml,
self.model,
None,
workOutputTag,
goldData=goldData,
parse=self.parse)
else:
print >> sys.stderr, "No model for modifier detection"
# if self.checkStep("VALIDATE"):
# xml = self.getWorkFile(xml, [workOutputTag + "modifier-pred.xml.gz", workOutputTag + "unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"])
# self.structureAnalyzer.load(model)
# self.structureAnalyzer.validate(xml)
# ETUtils.write(xml, workOutputTag + "validate-pred.xml.gz")
if self.checkStep("ST-CONVERT"):
if stParams["convert"]:
#xml = self.getWorkFile(xml, [workOutputTag + "validate-pred.xml.gz", workOutputTag + "modifier-pred.xml.gz", workOutputTag + "unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"])
xml = self.getWorkFile(xml, [
workOutputTag + "modifier-pred.xml.gz", workOutputTag +
"unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"
])
Utils.STFormat.ConvertXML.toSTFormat(
xml,
output + "-events.tar.gz",
outputTag=stParams["a2Tag"],
writeExtra=(stParams["scores"] == True))
if stParams["evaluate"]: #self.stEvaluator != None:
task = self.task
if task == None:
task = self.getStr(self.edgeDetector.tag + "task",
self.model)
self.stEvaluator.evaluate(output + "-events.tar.gz", task)
else:
print >> sys.stderr, "No BioNLP shared task format conversion"
finalXMLFile = self.getWorkFile(None, [
workOutputTag + "modifier-pred.xml.gz", workOutputTag +
"unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"
])
if finalXMLFile != None:
shutil.copy2(finalXMLFile, output + "-pred.xml.gz")
self.deleteTempWorkDir()
self.exitState()
def getWorkFile(self, fileObject, serializedPath=None):
"""
Returns fileObject if it is not None, otherwise tries all paths in serializedPath
and returns the first one that exists. Use this to get an intermediate file in a
stepwise process.
"""
if fileObject != None:
return fileObject
elif type(serializedPath
) not in types.StringTypes: # multiple files to try
for sPath in serializedPath:
if os.path.exists(sPath):
return sPath
assert False
else:
assert os.path.exists(serializedPath)
return serializedPath
class EventDetector(Detector):
"""
A multi-stage detector used for the BioNLP Shared Task type events.
"""
def __init__(self):
Detector.__init__(self)
self.triggerDetector = EntityDetector()
self.edgeDetector = EdgeDetector()
self.unmergingDetector = UnmergingDetector()
self.doUnmergingSelfTraining = True #False
self.modifierDetector = ModifierDetector()
#self.stEvaluator = Evaluators.BioNLP11GeniaTools
#self.stWriteScores = False
self.STATE_COMPONENT_TRAIN = "COMPONENT_TRAIN"
self.tag = "event-"
def setConnection(self, connection):
self.triggerDetector.setConnection(connection)
self.edgeDetector.setConnection(connection)
self.unmergingDetector.setConnection(connection)
self.modifierDetector.setConnection(connection)
return connection
def setWorkDir(self, workDir):
Detector.setWorkDir(self, workDir) # for EventDetector
# setup components
for detector in [self.triggerDetector, self.edgeDetector, self.unmergingDetector, self.modifierDetector]:
if detector != None:
detector.setWorkDir(workDir)
def train(self, trainData=None, optData=None,
model=None, combinedModel=None,
triggerExampleStyle=None, edgeExampleStyle=None, unmergingExampleStyle=None, modifierExampleStyle=None,
triggerClassifierParameters=None, edgeClassifierParameters=None,
unmergingClassifierParameters=None, modifierClassifierParameters=None,
recallAdjustParameters=None, unmerging=None, trainModifiers=None,
fullGrid=False, task=None,
parse=None, tokenization=None,
fromStep=None, toStep=None,
workDir=None):
# Initialize the training process ##############################
self.initVariables(trainData=trainData, optData=optData, model=model, combinedModel=combinedModel,
triggerExampleStyle=triggerExampleStyle, edgeExampleStyle=edgeExampleStyle,
unmergingExampleStyle=unmergingExampleStyle, modifierExampleStyle=modifierExampleStyle,
triggerClassifierParameters=triggerClassifierParameters,
edgeClassifierParameters=edgeClassifierParameters,
unmergingClassifierParameters=unmergingClassifierParameters,
modifierClassifierParameters=modifierClassifierParameters,
recallAdjustParameters=recallAdjustParameters, unmerging=unmerging, trainModifiers=trainModifiers,
fullGrid=fullGrid, task=task, parse=parse, tokenization=tokenization)
self.setWorkDir(workDir)
# Begin the training process ####################################
self.enterState(self.STATE_TRAIN, ["ANALYZE", "EXAMPLES", "BEGIN-MODEL", "END-MODEL", "BEGIN-COMBINED-MODEL",
"SELF-TRAIN-EXAMPLES-FOR-UNMERGING", "UNMERGING-EXAMPLES", "BEGIN-UNMERGING-MODEL", "END-UNMERGING-MODEL",
"GRID", "BEGIN-COMBINED-MODEL-FULLGRID", "END-COMBINED-MODEL"], fromStep, toStep)
self.triggerDetector.enterState(self.STATE_COMPONENT_TRAIN)
self.edgeDetector.enterState(self.STATE_COMPONENT_TRAIN)
self.unmergingDetector.enterState(self.STATE_COMPONENT_TRAIN)
self.modifierDetector.enterState(self.STATE_COMPONENT_TRAIN)
if self.checkStep("ANALYZE"):
# General training initialization done at the beginning of the first state
self.model = self.initModel(self.model,
[("triggerExampleStyle", self.triggerDetector.tag+"example-style"),
("triggerClassifierParameters", self.triggerDetector.tag+"classifier-parameters-train"),
("edgeExampleStyle", self.edgeDetector.tag+"example-style"),
("edgeClassifierParameters", self.edgeDetector.tag+"classifier-parameters-train"),
("unmergingExampleStyle", self.unmergingDetector.tag+"example-style"),
("unmergingClassifierParameters", self.unmergingDetector.tag+"classifier-parameters-train"),
("modifierExampleStyle", self.modifierDetector.tag+"example-style"),
("modifierClassifierParameters", self.modifierDetector.tag+"classifier-parameters-train")])
self.combinedModel = self.initModel(self.combinedModel)
tags = [self.triggerDetector.tag, self.edgeDetector.tag, self.unmergingDetector.tag, self.modifierDetector.tag]
stringDict = {}
for tag in tags:
stringDict[tag+"parse"] = parse
stringDict[tag+"task"] = task
self.saveStrings(stringDict, self.model)
self.saveStrings(stringDict, self.combinedModel, False)
# Perform structure analysis
self.structureAnalyzer.analyze([optData, trainData], self.model)
print >> sys.stderr, self.structureAnalyzer.toString()
# (Re-)open models in case we start after the first ("ANALYZE") step
self.model = self.openModel(model, "a")
self.combinedModel = self.openModel(combinedModel, "a")
# Use structure analysis to define automatic parameters
if self.unmerging == None:
if not self.structureAnalyzer.isInitialized():
self.structureAnalyzer.load(self.model)
self.unmerging = self.structureAnalyzer.hasEvents()
if self.trainModifiers == None:
if not self.structureAnalyzer.isInitialized():
self.structureAnalyzer.load(self.model)
self.trainModifiers = self.structureAnalyzer.hasModifiers()
if self.checkStep("EXAMPLES"):
self.triggerDetector.buildExamples(self.model, [optData.replace("-nodup", ""), trainData.replace("-nodup", "")], [self.workDir+self.triggerDetector.tag+"opt-examples.gz", self.workDir+self.triggerDetector.tag+"train-examples.gz"], saveIdsToModel=True)
self.edgeDetector.buildExamples(self.model, [optData.replace("-nodup", ""), trainData.replace("-nodup", "")], [self.workDir+self.edgeDetector.tag+"opt-examples.gz", self.workDir+self.edgeDetector.tag+"train-examples.gz"], saveIdsToModel=True)
if self.trainModifiers:
self.modifierDetector.buildExamples(self.model, [optData, trainData], [self.workDir+self.modifierDetector.tag+"opt-examples.gz", self.workDir+self.modifierDetector.tag+"train-examples.gz"], saveIdsToModel=True)
if self.checkStep("BEGIN-MODEL"):
#for model in [self.model, self.combinedModel]:
# if model != None:
# model.addStr("BioNLPSTParams", Parameters.toString(self.bioNLPSTParams))
self.triggerDetector.bioNLPSTParams = self.bioNLPSTParams
self.triggerDetector.beginModel(None, self.model, [self.workDir+self.triggerDetector.tag+"train-examples.gz"], self.workDir+self.triggerDetector.tag+"opt-examples.gz")
self.edgeDetector.beginModel(None, self.model, [self.workDir+self.edgeDetector.tag+"train-examples.gz"], self.workDir+self.edgeDetector.tag+"opt-examples.gz")
if self.trainModifiers:
self.modifierDetector.beginModel(None, self.model, [self.workDir+self.modifierDetector.tag+"train-examples.gz"], self.workDir+self.modifierDetector.tag+"opt-examples.gz")
if self.checkStep("END-MODEL"):
self.triggerDetector.endModel(None, self.model, self.workDir+self.triggerDetector.tag+"opt-examples.gz")
self.edgeDetector.endModel(None, self.model, self.workDir+self.edgeDetector.tag+"opt-examples.gz")
if self.trainModifiers:
self.modifierDetector.endModel(None, self.model, self.workDir+self.modifierDetector.tag+"opt-examples.gz")
if self.checkStep("BEGIN-COMBINED-MODEL"):
if not self.fullGrid:
print >> sys.stderr, "Training combined model before grid search"
self.triggerDetector.beginModel(None, self.combinedModel, [self.workDir+self.triggerDetector.tag+"train-examples.gz", self.workDir+self.triggerDetector.tag+"opt-examples.gz"], self.workDir+self.triggerDetector.tag+"opt-examples.gz", self.model)
self.edgeDetector.beginModel(None, self.combinedModel, [self.workDir+self.edgeDetector.tag+"train-examples.gz", self.workDir+self.edgeDetector.tag+"opt-examples.gz"], self.workDir+self.edgeDetector.tag+"opt-examples.gz", self.model)
else:
print >> sys.stderr, "Combined model will be trained after grid search"
if self.trainModifiers:
print >> sys.stderr, "Training combined model for modifier detection"
self.modifierDetector.beginModel(None, self.combinedModel, [self.workDir+self.modifierDetector.tag+"train-examples.gz", self.workDir+self.modifierDetector.tag+"opt-examples.gz"], self.workDir+self.modifierDetector.tag+"opt-examples.gz", self.model)
self.trainUnmergingDetector()
if self.checkStep("GRID"):
self.doGrid()
if self.checkStep("BEGIN-COMBINED-MODEL-FULLGRID"):
if self.fullGrid:
print >> sys.stderr, "Training combined model after grid search"
self.triggerDetector.beginModel(None, self.combinedModel, [self.workDir+self.triggerDetector.tag+"train-examples.gz", self.workDir+self.triggerDetector.tag+"opt-examples.gz"], self.workDir+self.triggerDetector.tag+"opt-examples.gz", self.model)
self.edgeDetector.beginModel(None, self.combinedModel, [self.workDir+self.edgeDetector.tag+"train-examples.gz", self.workDir+self.edgeDetector.tag+"opt-examples.gz"], self.workDir+self.edgeDetector.tag+"opt-examples.gz", self.model)
if self.trainModifiers:
print >> sys.stderr, "Training combined model for modifier detection"
self.modifierDetector.beginModel(None, self.combinedModel, [self.workDir+self.modifierDetector.tag+"train-examples.gz", self.workDir+self.modifierDetector.tag+"opt-examples.gz"], self.workDir+self.modifierDetector.tag+"opt-examples.gz", self.model)
else:
print >> sys.stderr, "Combined model has been trained before grid search"
if self.checkStep("END-COMBINED-MODEL"):
self.triggerDetector.endModel(None, self.combinedModel, self.workDir+self.triggerDetector.tag+"opt-examples.gz")
self.edgeDetector.endModel(None, self.combinedModel, self.workDir+self.edgeDetector.tag+"opt-examples.gz")
if self.trainModifiers:
self.modifierDetector.endModel(None, self.combinedModel, self.workDir+self.modifierDetector.tag+"opt-examples.gz")
# End the training process ####################################
if workDir != None:
self.setWorkDir("")
self.exitState()
self.triggerDetector.exitState()
self.edgeDetector.exitState()
self.unmergingDetector.exitState()
self.modifierDetector.exitState()
def doGrid(self):
print >> sys.stderr, "--------- Parameter grid search ---------"
# Build trigger examples
self.triggerDetector.buildExamples(self.model, [self.optData], [self.workDir+"grid-trigger-examples.gz"])
if self.fullGrid:
stepParams = {
"trigger":Parameters.get(self.model.getStr(self.triggerDetector.tag+"classifier-parameters-train", defaultIfNotExist=""), valueListKey="c"),
"booster":[float(i) for i in self.recallAdjustParameters.split(",")],
"edge":Parameters.get(self.model.getStr(self.edgeDetector.tag+"classifier-parameters-train", defaultIfNotExist=""), valueListKey="c")}
else:
stepParams = {
"trigger":Parameters.get(self.model.getStr(self.triggerDetector.tag+"classifier-parameter", defaultIfNotExist=""), valueListKey="c"),
"booster":[float(i) for i in self.recallAdjustParameters.split(",")],
"edge":Parameters.get(self.model.getStr(self.edgeDetector.tag+"classifier-parameter", defaultIfNotExist=""), valueListKey="c")}
for step in ["trigger", "edge"]:
stepParams[step] = Parameters.getCombinations(stepParams[step])
for i in range(len(stepParams[step])):
stepParams[step][i] = Parameters.toString(stepParams[step][i])
print >> sys.stderr, [stepParams[x] for x in ["trigger", "booster", "edge"]]
paramCombinations = combine(*[stepParams[x] for x in ["trigger", "booster", "edge"]])
print >> sys.stderr, paramCombinations
for i in range(len(paramCombinations)):
paramCombinations[i] = {"trigger":paramCombinations[i][0], "booster":paramCombinations[i][1], "edge":paramCombinations[i][2]}
#paramCombinations = Parameters.getCombinations(ALL_PARAMS, ["trigger", "booster", "edge"])
prevParams = None
EDGE_MODEL_STEM = os.path.join(self.edgeDetector.workDir, os.path.normpath(self.model.path)+"-edge-models/model")
TRIGGER_MODEL_STEM = os.path.join(self.triggerDetector.workDir, os.path.normpath(self.model.path)+"-trigger-models/model")
self.structureAnalyzer.load(self.model)
bestResults = None
for i in range(len(paramCombinations)):
params = paramCombinations[i]
print >> sys.stderr, "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
print >> sys.stderr, "Processing params", str(i+1) + "/" + str(len(paramCombinations)), params
print >> sys.stderr, "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
# Triggers and Boost
if prevParams == None or prevParams["trigger"] != params["trigger"] or prevParams["trigger"] != params["trigger"]:
print >> sys.stderr, "Classifying trigger examples for parameters", "trigger:" + str(params["trigger"]), "booster:" + str(params["booster"])
xml = self.triggerDetector.classifyToXML(self.optData, self.model, self.workDir+"grid-trigger-examples", self.workDir+"grid-", classifierModel=TRIGGER_MODEL_STEM + Parameters.toId(params["trigger"]), recallAdjust=params["booster"])
prevParams = params
## Build edge examples
#self.edgeDetector.buildExamples(self.model, [xml], [self.workDir+"grid-edge-examples"], [self.optData])
# Classify with pre-defined model
edgeClassifierModel = EDGE_MODEL_STEM + Parameters.toId(params["edge"])
xml = self.edgeDetector.classifyToXML(xml, self.model, self.workDir+"grid-edge-examples", self.workDir+"grid-", classifierModel=edgeClassifierModel, goldData=self.optData)
bestResults = self.evaluateGrid(xml, params, bestResults)
# Remove remaining intermediate grid files
for tag1 in ["edge", "trigger", "unmerging"]:
for tag2 in ["examples", "pred.xml.gz"]:
if os.path.exists(self.workDir+"grid-"+tag1+"-"+tag2):
os.remove(self.workDir+"grid-"+tag1+"-"+tag2)
print >> sys.stderr, "Parameter grid search complete"
print >> sys.stderr, "Tested", len(paramCombinations), "combinations"
print >> sys.stderr, "Best parameters:", bestResults[0]
print >> sys.stderr, "Best result:", bestResults[2] # f-score
# Save grid model
self.saveStr("recallAdjustParameter", str(bestResults[0]["booster"]), self.model)
self.saveStr("recallAdjustParameter", str(bestResults[0]["booster"]), self.combinedModel, False)
if self.fullGrid: # define best models
self.triggerDetector.addClassifierModel(self.model, TRIGGER_MODEL_STEM+str(bestResults[0]["trigger"]), bestResults[0]["trigger"])
self.edgeDetector.addClassifierModel(self.model, EDGE_MODEL_STEM+str(bestResults[0]["edge"]), bestResults[0]["edge"])
# Remove work files
for stepTag in [self.workDir+"grid-trigger", self.workDir+"grid-edge", self.workDir+"grid-unmerging"]:
for fileStem in ["-classifications", "-classifications.log", "examples.gz", "pred.xml.gz"]:
if os.path.exists(stepTag+fileStem):
os.remove(stepTag+fileStem)
def evaluateGrid(self, xml, params, bestResults):
if xml != None:
# TODO: Where should the EvaluateInteractionXML evaluator come from?
EIXMLResult = EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, self.optData, self.parse)
# Convert to ST-format
if self.unmerging:
xml = self.unmergingDetector.classifyToXML(xml, self.model, None, self.workDir+"grid-", goldData=self.optData)
#self.structureAnalyzer.validate(xml)
if self.bioNLPSTParams["evaluate"]:
Utils.STFormat.ConvertXML.toSTFormat(xml, self.workDir+"grid-unmerging-geniaformat", "a2")
stFormatDir = self.workDir+"grid-unmerging-geniaformat"
elif self.bioNLPSTParams["evaluate"]:
#self.structureAnalyzer.validate(xml)
Utils.STFormat.ConvertXML.toSTFormat(xml, self.workDir+"grid-flat-geniaformat", "a2") #getA2FileTag(options.task, subTask))
stFormatDir = self.workDir+"grid-flat-geniaformat"
# Evaluation
# Attempt shared task evaluation
stEvaluation = None
if self.bioNLPSTParams["evaluate"]:
stEvaluation = self.stEvaluator.evaluate(stFormatDir, self.task)
if stEvaluation != None:
if bestResults == None or stEvaluation[0] > bestResults[1][0]:
bestResults = (params, stEvaluation, stEvaluation[0])
else: # If shared task evaluation was not done (failed or not requested) fall back to internal evaluation
if bestResults == None or EIXMLResult.getData().fscore > bestResults[1].getData().fscore:
bestResults = (params, EIXMLResult, EIXMLResult.getData().fscore)
# Remove ST-format files
if os.path.exists(self.workDir+"grid-flat-geniaformat"):
shutil.rmtree(self.workDir+"grid-flat-geniaformat")
if os.path.exists(self.workDir+"grid-unmerging-geniaformat"):
shutil.rmtree(self.workDir+"grid-unmerging-geniaformat")
else:
print >> sys.stderr, "No predicted edges"
return bestResults
def trainUnmergingDetector(self):
xml = None
if not self.unmerging:
print >> sys.stderr, "No unmerging"
if self.checkStep("SELF-TRAIN-EXAMPLES-FOR-UNMERGING", self.unmerging) and self.unmerging:
# Self-classified train data for unmerging
if self.doUnmergingSelfTraining:
# This allows limiting to a subcorpus
triggerStyle = copy.copy(Parameters.get(self.triggerExampleStyle))
edgeStyle = copy.copy(Parameters.get(self.edgeExampleStyle))
unmergingStyle = Parameters.get(self.unmergingExampleStyle)
if "sentenceLimit" in unmergingStyle and unmergingStyle["sentenceLimit"]:
triggerStyle["sentenceLimit"] = unmergingStyle["sentenceLimit"]
edgeStyle["sentenceLimit"] = unmergingStyle["sentenceLimit"]
# Build the examples
xml = self.triggerDetector.classifyToXML(self.trainData, self.model, None, self.workDir+"unmerging-extra-", exampleStyle=triggerStyle)#, recallAdjust=0.5)
xml = self.edgeDetector.classifyToXML(xml, self.model, None, self.workDir+"unmerging-extra-", exampleStyle=edgeStyle)#, recallAdjust=0.5)
assert xml != None
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, self.trainData, self.parse)
else:
print >> sys.stderr, "No self-training for unmerging"
if self.checkStep("UNMERGING-EXAMPLES", self.unmerging) and self.unmerging:
# Unmerging example generation
GOLD_TEST_FILE = self.optData.replace("-nodup", "")
GOLD_TRAIN_FILE = self.trainData.replace("-nodup", "")
if self.doUnmergingSelfTraining:
if xml == None:
xml = self.workDir+"unmerging-extra-edge-pred.xml.gz"
self.unmergingDetector.buildExamples(self.model, [self.optData.replace("-nodup", ""), [self.trainData.replace("-nodup", ""), xml]],
[self.workDir+"unmerging-opt-examples.gz", self.workDir+"unmerging-train-examples.gz"],
[GOLD_TEST_FILE, [GOLD_TRAIN_FILE, GOLD_TRAIN_FILE]],
exampleStyle=self.unmergingExampleStyle, saveIdsToModel=True)
xml = None
else:
self.unmergingDetector.buildExamples(self.model, [self.optData.replace("-nodup", ""), self.trainData.replace("-nodup", "")],
[self.workDir+"unmerging-opt-examples.gz", self.workDir+"unmerging-train-examples.gz"],
[GOLD_TEST_FILE, GOLD_TRAIN_FILE],
exampleStyle=self.unmergingExampleStyle, saveIdsToModel=True)
xml = None
#UnmergingExampleBuilder.run("/home/jari/biotext/EventExtension/TrainSelfClassify/test-predicted-edges.xml", GOLD_TRAIN_FILE, UNMERGING_TRAIN_EXAMPLE_FILE, PARSE, TOK, UNMERGING_FEATURE_PARAMS, UNMERGING_IDS, append=True)
if self.checkStep("BEGIN-UNMERGING-MODEL", self.unmerging) and self.unmerging:
self.unmergingDetector.beginModel(None, self.model, self.workDir+"unmerging-train-examples.gz", self.workDir+"unmerging-opt-examples.gz")
if self.checkStep("END-UNMERGING-MODEL", self.unmerging) and self.unmerging:
self.unmergingDetector.endModel(None, self.model, self.workDir+"unmerging-opt-examples.gz")
print >> sys.stderr, "Adding unmerging classifier model to test-set event model"
if self.combinedModel != None:
self.combinedModel.addStr("unmerging-example-style", self.model.getStr("unmerging-example-style"))
self.combinedModel.insert(self.model.get("unmerging-ids.classes"), "unmerging-ids.classes")
self.combinedModel.insert(self.model.get("unmerging-ids.features"), "unmerging-ids.features")
self.unmergingDetector.addClassifierModel(self.combinedModel, self.model.get("unmerging-classifier-model", True),
self.model.getStr("unmerging-classifier-parameter"))
self.combinedModel.save()
def classify(self, data, model, output, parse=None, task=None, goldData=None, fromStep=None, toStep=None, omitSteps=None, workDir=None):
#BINARY_RECALL_MODE = False # TODO: make a parameter
xml = None
model = self.openModel(model, "r")
self.initVariables(classifyData=data, model=model, xml=None, task=task, parse=parse)
self.enterState(self.STATE_CLASSIFY, ["TRIGGERS", "EDGES", "UNMERGING", "MODIFIERS", "ST-CONVERT"], fromStep, toStep, omitSteps)
#self.enterState(self.STATE_CLASSIFY, ["TRIGGERS", "RECALL-ADJUST", "EDGES", "UNMERGING", "MODIFIERS", "ST-CONVERT"], fromStep, toStep)
self.setWorkDir(workDir)
if workDir == None:
self.setTempWorkDir()
workOutputTag = os.path.join(self.workDir, os.path.basename(output) + "-")
self.model = self.openModel(self.model, "r")
stParams = self.getBioNLPSharedTaskParams(self.bioNLPSTParams, model)
if self.checkStep("TRIGGERS"):
xml = self.triggerDetector.classifyToXML(self.classifyData, self.model, None, workOutputTag, goldData=goldData, parse=self.parse, recallAdjust=float(self.getStr("recallAdjustParameter", self.model)))
if self.checkStep("EDGES"):
xml = self.getWorkFile(xml, workOutputTag + "trigger-pred.xml.gz")
xml = self.edgeDetector.classifyToXML(xml, self.model, None, workOutputTag, goldData=goldData, parse=self.parse)
assert xml != None
if self.parse == None:
edgeParse = self.getStr(self.edgeDetector.tag+"parse", self.model)
else:
edgeParse = self.parse
#EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, self.classifyData, edgeParse)
if goldData != None:
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, goldData, edgeParse)
else:
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, self.classifyData, edgeParse)
if self.checkStep("UNMERGING"):
if self.model.getStr("unmerging-classifier-parameter", None) != None: #self.model.hasMember("unmerging-classifier-model"):
#xml = self.getWorkFile(xml, output + "-edge-pred.xml.gz")
# To avoid running out of memory, always use file on disk
xml = self.getWorkFile(None, workOutputTag + "edge-pred.xml.gz")
#goldData = None
#if type(self.classifyData) in types.StringTypes:
# if os.path.exists(self.classifyData.replace("-nodup", "")):
# goldData = self.classifyData.replace("-nodup", "")
xml = self.unmergingDetector.classifyToXML(xml, self.model, None, workOutputTag, goldData=goldData, parse=self.parse)
# Evaluate after unmerging
if self.parse == None:
edgeParse = self.getStr(self.edgeDetector.tag+"parse", self.model)
else:
edgeParse = self.parse
if goldData != None:
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, goldData, edgeParse)
else:
EvaluateInteractionXML.run(self.edgeDetector.evaluator, xml, self.classifyData, edgeParse)
else:
print >> sys.stderr, "No model for unmerging"
if self.checkStep("MODIFIERS"):
if self.model.hasMember("modifier-classifier-model"):
xml = self.getWorkFile(xml, [workOutputTag + "unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"])
xml = self.modifierDetector.classifyToXML(xml, self.model, None, workOutputTag, goldData=goldData, parse=self.parse)
else:
print >> sys.stderr, "No model for modifier detection"
# if self.checkStep("VALIDATE"):
# xml = self.getWorkFile(xml, [workOutputTag + "modifier-pred.xml.gz", workOutputTag + "unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"])
# self.structureAnalyzer.load(model)
# self.structureAnalyzer.validate(xml)
# ETUtils.write(xml, workOutputTag + "validate-pred.xml.gz")
if self.checkStep("ST-CONVERT"):
if stParams["convert"]:
#xml = self.getWorkFile(xml, [workOutputTag + "validate-pred.xml.gz", workOutputTag + "modifier-pred.xml.gz", workOutputTag + "unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"])
xml = self.getWorkFile(xml, [workOutputTag + "modifier-pred.xml.gz", workOutputTag + "unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"])
Utils.STFormat.ConvertXML.toSTFormat(xml, output+"-events.tar.gz", outputTag=stParams["a2Tag"], writeExtra=(stParams["scores"] == True))
if stParams["evaluate"]: #self.stEvaluator != None:
task = self.task
if task == None:
task = self.getStr(self.edgeDetector.tag+"task", self.model)
self.stEvaluator.evaluate(output + "-events.tar.gz", task)
else:
print >> sys.stderr, "No BioNLP shared task format conversion"
finalXMLFile = self.getWorkFile(None, [workOutputTag + "modifier-pred.xml.gz", workOutputTag + "unmerging-pred.xml.gz", workOutputTag + "edge-pred.xml.gz"])
if finalXMLFile != None:
shutil.copy2(finalXMLFile, output+"-pred.xml.gz")
self.deleteTempWorkDir()
self.exitState()
def getWorkFile(self, fileObject, serializedPath=None):
"""
Returns fileObject if it is not None, otherwise tries all paths in serializedPath
and returns the first one that exists. Use this to get an intermediate file in a
stepwise process.
"""
if fileObject != None:
return fileObject
elif type(serializedPath) not in types.StringTypes: # multiple files to try
for sPath in serializedPath:
if os.path.exists(sPath):
return sPath
assert False
else:
assert os.path.exists(serializedPath)
return serializedPath