def pipeline(collection, metamap, splitter, parser, ptb2dep, neg_detector, cuis, extra_args): """ Args: collection(BioCCollection): metamap(MetaMap): MetaMap instance splitter (NegBioSSplitter): parser (NegBioParser) ptb2dep (NegBioPtb2DepConverter) neg_detector (Detector): Returns: BioCCollection """ for document in collection.documents: splitter.split_doc(document) dner_mm.run_metamap_col(collection, metamap, cuis, extra_args) for document in collection.documents: document = parser.parse_doc(document) document = ptb2dep.convert_doc(document) document = negdetect.detect(document, neg_detector) # remove sentence for passage in document.passages: del passage.sentences[:] return collection
def classify(self, collection): """Classify each mention into one of negative, uncertain, or positive.""" documents = collection.documents if self.verbose: print("Classifying mentions...") documents = tqdm(documents) for document in documents: # Parse the impression text in place. parse.parse(document, self.parser) # Add the universal dependency graph in place. ptb2ud.convert(document, self.ptb2dep, self.lemmatizer) # Detect the negation and uncertainty rules in place. negdetect.detect(document, self.detector) # To reduce memory consumption, remove sentences text. del document.passages[0].sentences[:]
def pipeline(document, splitter, parser, ptb2dep, lemmatizer, neg_detector): document = ssplit.ssplit(document, splitter) document = parse.parse(document, parser) document = ptb2ud.convert(document, ptb2dep, lemmatizer) document = negdetect.detect(document, neg_detector) # remove sentence for passage in document.passages: del passage.sentences[:] return document
def pipeline(collection, metamap, splitter, parser, ptb2dep, lemmatizer, neg_detector, cuis): for document in collection.documents: ssplit.ssplit(document, splitter) dner_mm.run_metamap_col(collection, metamap, cuis) for document in collection.documents: document = parse.parse(document, parser) document = ptb2ud.convert(document, ptb2dep, lemmatizer) document = negdetect.detect(document, neg_detector) # remove sentence for passage in document.passages: del passage.sentences[:] return collection
def process_collection(collection, metamap, splitter, parser, ptb2dep, lemmatizer, neg_detector, cuis, sec_title_patterns): for document in collection.documents: normalize_mimiccxr.normalize(document) section_split.split_document(document, sec_title_patterns) ssplit.ssplit(document, splitter) dner_mm.run_metamap_col(collection, metamap, cuis) for document in collection.documents: document = parse.parse(document, parser) document = ptb2ud.convert(document, ptb2dep, lemmatizer) document = negdetect.detect(document, neg_detector) cleanup.clean_sentences(document) return collection
def pipeline(collection, loader, ssplitter, extractor, parser, ptb2dep, neg_detector, aggregator, verbose=False): """ Args: loader (NegBioLoader) ssplitter (NegBioSSplitter) parser (NegBioParser) extractor (NegBioExtractor) ptb2dep (NegBioPtb2DepConverter) neg_detector (ModifiedDetector) aggregator (NegBioAggregator) """ # for document in collection.documents: # # for passage in document.passages: # passage.text = clean(passage.text) # ssplitter.split_doc(document) for document in tqdm.tqdm(collection.documents, disable=not verbose): document = loader.clean_doc(document) document = ssplitter.split_doc(document) document = extractor.extract_doc(document) document = parser.parse_doc(document) document = ptb2dep.convert_doc(document) document = negdetect.detect(document, neg_detector) document = aggregator.aggregate_doc(document) # remove sentence for passage in document.passages: del passage.sentences[:] return collection