def crossValidate(exampleBuilder, corpusElements, examples, options, timer):
parameterOptimizationSet = None
constantParameterOptimizationSet = None
if options.paramOptData != None:
print >> sys.stderr, "Separating parameter optimization set"
parameterOptimizationDivision = Example.makeCorpusDivision(corpusElements, float(options.paramOptData))
exampleSets = Example.divideExamples(examples, parameterOptimizationDivision)
constantParameterOptimizationSet = exampleSets[0]
parameterOptimizationSet = constantParameterOptimizationSet
optDocs = 0
for k,v in parameterOptimizationDivision.iteritems():
if v == 0:
del corpusElements.documentsById[k]
optDocs += 1
print >> sys.stderr, " Documents for parameter optimization:", optDocs
discardedParameterCombinations = []
print >> sys.stderr, "Dividing data into folds"
corpusFolds = Example.makeCorpusFolds(corpusElements, options.folds[0])
exampleSets = Example.divideExamples(examples, corpusFolds)
keys = exampleSets.keys()
keys.sort()
evaluations = []
for key in keys:
testSet = exampleSets[key]
for example in testSet:
example[3]["visualizationSet"] = key + 1
trainSet = []
for key2 in keys:
if key != key2:
trainSet.extend(exampleSets[key2])
print >> sys.stderr, "Fold", str(key + 1)
# Create classifier object
if options.output != None:
if not os.path.exists(options.output+"/fold"+str(key+1)):
os.mkdir(options.output+"/fold"+str(key+1))
# if not os.path.exists(options.output+"/fold"+str(key+1)+"/classifier"):
# os.mkdir(options.output+"/fold"+str(key+1)+"/classifier")
classifier = Classifier(workDir = options.output + "/fold"+str(key + 1))
else:
classifier = Classifier()
classifier.featureSet = exampleBuilder.featureSet
# Optimize ####################
# Check whether there is need for included param opt set
if parameterOptimizationSet == None and options.folds[1] == 0: # 8-1-1 folds
assert(len(keys) > 1)
if keys.index(key) == 0:
parameterOptimizationSetKey = keys[-1]
else:
parameterOptimizationSetKey = keys[keys.index(key)-1]
parameterOptimizationSet = exampleSets[parameterOptimizationSetKey]
trainSet = []
for key2 in keys:
if key2 != key and key2 != parameterOptimizationSetKey:
trainSet.extend(exampleSets[key2])
if parameterOptimizationSet != None: # constant external parameter optimization set
evaluationArgs = {"classSet":exampleBuilder.classSet}
if options.parameters != None:
paramDict = splitParameters(options.parameters)
bestResults = classifier.optimize([trainSet], [parameterOptimizationSet], paramDict, Evaluation, evaluationArgs, combinationsThatTimedOut=discardedParameterCombinations)
else:
bestResults = classifier.optimize([trainSet], [parameterOptimizationSet], evaluationClass=Evaluation, evaluationArgs=evaluationArgs, combinationsThatTimedOut=discardedParameterCombinations)
else: # nested x-fold parameter optimization
assert (options.folds[1] >= 2)
optimizationFolds = Example.makeExampleFolds(trainSet, options.folds[1])
optimizationSets = Example.divideExamples(trainSet, optimizationFolds)
optimizationSetList = []
optSetKeys = optimizationSets.keys()
optSetKeys.sort()
for optSetKey in optSetKeys:
optimizationSetList.append(optimizationSets[optSetKey])
evaluationArgs = {"classSet":exampleBuilder.classSet}
if options.parameters != None:
paramDict = splitParameters(options.parameters)
bestResults = classifier.optimize(optimizationSetList, optimizationSetList, paramDict, Evaluation, evaluationArgs, combinationsThatTimedOut=discardedParameterCombinations)
else:
bestResults = classifier.optimize(optimizationSetList, optimizationSetList, evaluationClass=Evaluation, evaluationArgs=evaluationArgs, combinationsThatTimedOut=discardedParameterCombinations)
# Classify
print >> sys.stderr, "Classifying test data"
bestParams = bestResults[2]
if bestParams.has_key("timeout"):
del bestParams["timeout"]
print >> sys.stderr, "Parameters:", bestParams
print >> sys.stderr, "Training",
startTime = time.time()
classifier.train(trainSet, bestParams)
print >> sys.stderr, "(Time spent:", time.time() - startTime, "s)"
print >> sys.stderr, "Testing",
startTime = time.time()
predictions = classifier.classify(testSet)
if options.output != None:
pdict = []
fieldnames = ["class","prediction","id","fold"]
for p in predictions:
if "typed" in exampleBuilder.styles:
pdict.append( {"class":exampleBuilder.classSet.getName(p[0][1]), "prediction":exampleBuilder.classSet.getName(p[1]), "id":p[0][0], "fold":key} )
else:
pdict.append( {"class":p[0][1], "prediction":p[1], "id":p[0][0], "fold":key} )
TableUtils.addToCSV(pdict, options.output +"/predictions.csv", fieldnames)
print >> sys.stderr, "(Time spent:", time.time() - startTime, "s)"
# Calculate statistics
evaluation = Evaluation(predictions, classSet=exampleBuilder.classSet)
print >> sys.stderr, evaluation.toStringConcise()
print >> sys.stderr, timer.toString()
evaluations.append(evaluation)
# Save example sets
if options.output != None:
print >> sys.stderr, "Saving example sets to", options.output
Example.writeExamples(exampleSets[0], options.output +"/fold"+str(key+1) + "/examplesTest.txt")
Example.writeExamples(exampleSets[1], options.output +"/fold"+str(key+1) + "/examplesTrain.txt")
if parameterOptimizationSet == None:
for k,v in optimizationSets.iteritems():
Example.writeExamples(v, options.output +"/fold"+str(key+1) + "/examplesOptimizationSet" + str(k) + ".txt")
else:
Example.writeExamples(parameterOptimizationSet, options.output +"/fold"+str(key+1) + "/examplesOptimizationSetPredefined.txt")
TableUtils.writeCSV(bestResults[2], options.output +"/fold"+str(key+1) + "/parameters.csv")
evaluation.saveCSV(options.output +"/fold"+str(key+1) + "/results.csv")
print >> sys.stderr, "Compressing folder"
zipTree(options.output, "fold"+str(key+1))
parameterOptimizationSet = constantParameterOptimizationSet
print >> sys.stderr, "Cross-validation Results"
for i in range(len(evaluations)):
print >> sys.stderr, evaluations[i].toStringConcise(" Fold "+str(i)+": ")
averageResult = Evaluation.average(evaluations)
print >> sys.stderr, averageResult.toStringConcise(" Avg: ")
pooledResult = Evaluation.pool(evaluations)
print >> sys.stderr, pooledResult.toStringConcise(" Pool: ")
if options.output != None:
for i in range(len(evaluations)):
evaluations[i].saveCSV(options.output+"/results.csv", i)
averageResult.saveCSV(options.output+"/results.csv", "Avg")
pooledResult.saveCSV(options.output+"/results.csv", "Pool")
averageResult.saveCSV(options.output+"/resultsAverage.csv")
pooledResult.saveCSV(options.output+"/resultsPooled.csv")
# Visualize
if options.visualization != None:
visualize(sentences, pooledResult.classifications, options, exampleBuilder)
# Save interactionXML
if options.resultsToXML != None:
classSet = None
if "typed" in exampleBuilder.styles:
classSet = exampleBuilder.classSet
Example.writeToInteractionXML(pooledResult.classifications, corpusElements, options.resultsToXML, classSet)
else:
options.folds = (int(options.folds),int(options.folds))
if options.output != None:
if os.path.exists(options.output):
print >> sys.stderr, "Output directory exists, removing", options.output
shutil.rmtree(options.output)
os.makedirs(options.output)
# if not os.path.exists(options.output+"/classifier"):
# os.mkdir(options.output+"/classifier")
print >> sys.stderr, "Importing modules"
exec "from ExampleBuilders." + options.exampleBuilder + " import " + options.exampleBuilder + " as ExampleBuilder"
exec "from Classifiers." + options.classifier + " import " + options.classifier + " as Classifier"
exec "from Evaluators." + options.evaluator + " import " + options.evaluator + " as Evaluation"
# Load corpus and make sentence graphs
corpusElements = loadCorpus(options.input, options.parse, options.tokenization)
sentences = []
for sentence in corpusElements.sentences:
sentences.append( [sentence.sentenceGraph,None,None] )
# Build examples
exampleBuilder = ExampleBuilder(**splitParameters(options.exampleBuilderParameters))
examples = buildExamples(exampleBuilder, sentences, options)
crossValidate(exampleBuilder, corpusElements, examples, options, timer)
print >> sys.stderr, timer.toString()
optparser.add_option("-y", "--parameters", default=None, dest="parameters", help="Parameters for the classifier")
optparser.add_option("-b", "--exampleBuilder", default="SimpleDependencyExampleBuilder", dest="exampleBuilder", help="Example Builder Class")
optparser.add_option("-e", "--evaluator", default="BinaryEvaluator", dest="evaluator", help="Prediction evaluator class")
optparser.add_option("-v", "--visualization", default=None, dest="visualization", help="Visualization output directory. NOTE: If the directory exists, it will be deleted!")
optparser.add_option("-m", "--resultsToXML", default=None, dest="resultsToXML", help="Results in analysis xml. NOTE: for edges, pairs, not interactions")
(options, args) = optparser.parse_args()
if options.output != None:
if os.path.exists(options.output):
print >> sys.stderr, "Output directory exists, removing", options.output
shutil.rmtree(options.output)
os.mkdir(options.output)
if not os.path.exists(options.output+"/classifier"):
os.mkdir(options.output+"/classifier")
classifierParamDict = splitParameters(options.parameters)
print >> sys.stderr, "Importing modules"
exec "from ExampleBuilders." + options.exampleBuilder + " import " + options.exampleBuilder + " as ExampleBuilder"
exec "from Classifiers." + options.classifier + " import " + options.classifier + " as Classifier"
exec "from Evaluators." + options.evaluator + " import " + options.evaluator + " as Evaluation"
trainExamples = []
exampleSets = [[],[]]
if not classifierParamDict.has_key("predefined"):
print >> sys.stderr, "No-predefined model"
exampleBuilder = ExampleBuilder(**splitParameters(options.exampleBuilderParameters))
# Load corpus and make sentence graphs
trainCorpusElements = loadCorpus(options.input, options.parse, options.tokenization)
sentences = []
for sentence in trainCorpusElements.sentences:
def crossValidate(exampleBuilder, corpusElements, examples, options, timer):
parameterOptimizationSet = None
constantParameterOptimizationSet = None
if options.paramOptData != None:
print >> sys.stderr, "Separating parameter optimization set"
parameterOptimizationDivision = Example.makeCorpusDivision(
corpusElements, float(options.paramOptData))
exampleSets = Example.divideExamples(examples,
parameterOptimizationDivision)
constantParameterOptimizationSet = exampleSets[0]
parameterOptimizationSet = constantParameterOptimizationSet
optDocs = 0
for k, v in parameterOptimizationDivision.iteritems():
if v == 0:
del corpusElements.documentsById[k]
optDocs += 1
print >> sys.stderr, " Documents for parameter optimization:", optDocs
discardedParameterCombinations = []
print >> sys.stderr, "Dividing data into folds"
corpusFolds = Example.makeCorpusFolds(corpusElements, options.folds[0])
exampleSets = Example.divideExamples(examples, corpusFolds)
keys = exampleSets.keys()
keys.sort()
evaluations = []
for key in keys:
testSet = exampleSets[key]
for example in testSet:
example[3]["visualizationSet"] = key + 1
trainSet = []
for key2 in keys:
if key != key2:
trainSet.extend(exampleSets[key2])
print >> sys.stderr, "Fold", str(key + 1)
# Create classifier object
if options.output != None:
if not os.path.exists(options.output + "/fold" + str(key + 1)):
os.mkdir(options.output + "/fold" + str(key + 1))
# if not os.path.exists(options.output+"/fold"+str(key+1)+"/classifier"):
# os.mkdir(options.output+"/fold"+str(key+1)+"/classifier")
classifier = Classifier(workDir=options.output + "/fold" +
str(key + 1))
else:
classifier = Classifier()
classifier.featureSet = exampleBuilder.featureSet
# Optimize ####################
# Check whether there is need for included param opt set
if parameterOptimizationSet == None and options.folds[
1] == 0: # 8-1-1 folds
assert (len(keys) > 1)
if keys.index(key) == 0:
parameterOptimizationSetKey = keys[-1]
else:
parameterOptimizationSetKey = keys[keys.index(key) - 1]
parameterOptimizationSet = exampleSets[parameterOptimizationSetKey]
trainSet = []
for key2 in keys:
if key2 != key and key2 != parameterOptimizationSetKey:
trainSet.extend(exampleSets[key2])
if parameterOptimizationSet != None: # constant external parameter optimization set
evaluationArgs = {"classSet": exampleBuilder.classSet}
if options.parameters != None:
paramDict = splitParameters(options.parameters)
bestResults = classifier.optimize(
[trainSet], [parameterOptimizationSet],
paramDict,
Evaluation,
evaluationArgs,
combinationsThatTimedOut=discardedParameterCombinations)
else:
bestResults = classifier.optimize(
[trainSet], [parameterOptimizationSet],
evaluationClass=Evaluation,
evaluationArgs=evaluationArgs,
combinationsThatTimedOut=discardedParameterCombinations)
else: # nested x-fold parameter optimization
assert (options.folds[1] >= 2)
optimizationFolds = Example.makeExampleFolds(
trainSet, options.folds[1])
optimizationSets = Example.divideExamples(trainSet,
optimizationFolds)
optimizationSetList = []
optSetKeys = optimizationSets.keys()
optSetKeys.sort()
for optSetKey in optSetKeys:
optimizationSetList.append(optimizationSets[optSetKey])
evaluationArgs = {"classSet": exampleBuilder.classSet}
if options.parameters != None:
paramDict = splitParameters(options.parameters)
bestResults = classifier.optimize(
optimizationSetList,
optimizationSetList,
paramDict,
Evaluation,
evaluationArgs,
combinationsThatTimedOut=discardedParameterCombinations)
else:
bestResults = classifier.optimize(
optimizationSetList,
optimizationSetList,
evaluationClass=Evaluation,
evaluationArgs=evaluationArgs,
combinationsThatTimedOut=discardedParameterCombinations)
# Classify
print >> sys.stderr, "Classifying test data"
bestParams = bestResults[2]
if bestParams.has_key("timeout"):
del bestParams["timeout"]
print >> sys.stderr, "Parameters:", bestParams
print >> sys.stderr, "Training",
startTime = time.time()
classifier.train(trainSet, bestParams)
print >> sys.stderr, "(Time spent:", time.time() - startTime, "s)"
print >> sys.stderr, "Testing",
startTime = time.time()
predictions = classifier.classify(testSet)
if options.output != None:
pdict = []
fieldnames = ["class", "prediction", "id", "fold"]
for p in predictions:
if "typed" in exampleBuilder.styles:
pdict.append({
"class":
exampleBuilder.classSet.getName(p[0][1]),
"prediction":
exampleBuilder.classSet.getName(p[1]),
"id":
p[0][0],
"fold":
key
})
else:
pdict.append({
"class": p[0][1],
"prediction": p[1],
"id": p[0][0],
"fold": key
})
TableUtils.addToCSV(pdict, options.output + "/predictions.csv",
fieldnames)
print >> sys.stderr, "(Time spent:", time.time() - startTime, "s)"
# Calculate statistics
evaluation = Evaluation(predictions, classSet=exampleBuilder.classSet)
print >> sys.stderr, evaluation.toStringConcise()
print >> sys.stderr, timer.toString()
evaluations.append(evaluation)
# Save example sets
if options.output != None:
print >> sys.stderr, "Saving example sets to", options.output
Example.writeExamples(
exampleSets[0],
options.output + "/fold" + str(key + 1) + "/examplesTest.txt")
Example.writeExamples(
exampleSets[1],
options.output + "/fold" + str(key + 1) + "/examplesTrain.txt")
if parameterOptimizationSet == None:
for k, v in optimizationSets.iteritems():
Example.writeExamples(
v, options.output + "/fold" + str(key + 1) +
"/examplesOptimizationSet" + str(k) + ".txt")
else:
Example.writeExamples(
parameterOptimizationSet, options.output + "/fold" +
str(key + 1) + "/examplesOptimizationSetPredefined.txt")
TableUtils.writeCSV(
bestResults[2],
options.output + "/fold" + str(key + 1) + "/parameters.csv")
evaluation.saveCSV(options.output + "/fold" + str(key + 1) +
"/results.csv")
print >> sys.stderr, "Compressing folder"
zipTree(options.output, "fold" + str(key + 1))
parameterOptimizationSet = constantParameterOptimizationSet
print >> sys.stderr, "Cross-validation Results"
for i in range(len(evaluations)):
print >> sys.stderr, evaluations[i].toStringConcise(" Fold " +
str(i) + ": ")
averageResult = Evaluation.average(evaluations)
print >> sys.stderr, averageResult.toStringConcise(" Avg: ")
pooledResult = Evaluation.pool(evaluations)
print >> sys.stderr, pooledResult.toStringConcise(" Pool: ")
if options.output != None:
for i in range(len(evaluations)):
evaluations[i].saveCSV(options.output + "/results.csv", i)
averageResult.saveCSV(options.output + "/results.csv", "Avg")
pooledResult.saveCSV(options.output + "/results.csv", "Pool")
averageResult.saveCSV(options.output + "/resultsAverage.csv")
pooledResult.saveCSV(options.output + "/resultsPooled.csv")
# Visualize
if options.visualization != None:
visualize(sentences, pooledResult.classifications, options,
exampleBuilder)
# Save interactionXML
if options.resultsToXML != None:
classSet = None
if "typed" in exampleBuilder.styles:
classSet = exampleBuilder.classSet
Example.writeToInteractionXML(pooledResult.classifications,
corpusElements, options.resultsToXML,
classSet)
else:
options.folds = (int(options.folds), int(options.folds))
if options.output != None:
if os.path.exists(options.output):
print >> sys.stderr, "Output directory exists, removing", options.output
shutil.rmtree(options.output)
os.makedirs(options.output)
# if not os.path.exists(options.output+"/classifier"):
# os.mkdir(options.output+"/classifier")
print >> sys.stderr, "Importing modules"
exec "from ExampleBuilders." + options.exampleBuilder + " import " + options.exampleBuilder + " as ExampleBuilder"
exec "from Classifiers." + options.classifier + " import " + options.classifier + " as Classifier"
exec "from Evaluators." + options.evaluator + " import " + options.evaluator + " as Evaluation"
# Load corpus and make sentence graphs
corpusElements = loadCorpus(options.input, options.parse,
options.tokenization)
sentences = []
for sentence in corpusElements.sentences:
sentences.append([sentence.sentenceGraph, None, None])
# Build examples
exampleBuilder = ExampleBuilder(
**splitParameters(options.exampleBuilderParameters))
examples = buildExamples(exampleBuilder, sentences, options)
crossValidate(exampleBuilder, corpusElements, examples, options, timer)
print >> sys.stderr, timer.toString()
help="Results in analysis xml. NOTE: for edges, pairs, not interactions"
)
(options, args) = optparser.parse_args()
mainTimer = Timer()
print >> sys.stderr, __file__ + " start, " + mainTimer.toString()
if options.output != None:
if os.path.exists(options.output):
print >> sys.stderr, "Output directory exists, removing", options.output
shutil.rmtree(options.output)
os.mkdir(options.output)
if not os.path.exists(options.output + "/classifier"):
os.mkdir(options.output + "/classifier")
classifierParamDict = splitParameters(options.parameters)
print >> sys.stderr, "Importing modules"
exec "from ExampleBuilders." + options.exampleBuilder + " import " + options.exampleBuilder + " as ExampleBuilder"
exec "from Classifiers." + options.classifier + " import " + options.classifier + " as Classifier"
exec "from Evaluators." + options.evaluator + " import " + options.evaluator + " as Evaluation"
testCorpusElements = None
exampleSets = [[], []]
if not classifierParamDict.has_key("predefined"):
print >> sys.stderr, "No-predefined model"
exampleBuilder = ExampleBuilder(
**splitParameters(options.exampleBuilderParameters))
# Load corpus and make sentence graphs
trainCorpusElements = loadCorpus(options.input, options.parse,
options.tokenization)
