def predict(self, cas: Cas, layer: str, feature: str, project_id: str, document_id: str, user_id: str):
for sentence in cas.select(SENTENCE_TYPE):
cas_tokens = list(cas.select_covered(TOKEN_TYPE, sentence))
tokens = [t.get_covered_text() for t in cas_tokens]
grouped_bert_tokens = self._tokenize_bert(tokens)
predictions = self._predict(grouped_bert_tokens)
grouped_predictions = self._align_tokens(tokens, grouped_bert_tokens, predictions)
for token, grouped_prediction in zip(cas_tokens, grouped_predictions):
begin = token.begin
end = token.end
label = Counter([self._label_map[pred] for pred in grouped_prediction]).most_common(1)[0][0]
prediction = self.create_prediction(cas, layer, feature, begin, end, label)
cas.add_annotation(prediction)
def featurize_cas(fg: FeatureGenerator, cas: Cas) -> List:
features = get_features()
results = []
for qid, entity in enumerate(cas.select("webanno.custom.EntityLinking")):
candidates = list(
cas.select_covered("inception.internal.KbHandle", entity))
if len(candidates) == 0:
continue
for i, candidate in enumerate(candidates):
if entity.iri == candidate.iri:
gold_idx = i
break
else:
continue
sentences = list(
cas.select_covering(
"de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence",
entity))
assert len(sentences) == 1
sentence = sentences[0]
mention = entity.get_covered_text().lower()
context = sentence.get_covered_text().lower()
l = len(context)
# context = context[int(l * 0.25):int(l * 0.75)]
for cid, candidate in enumerate(candidates):
score = float(entity.iri == candidate.iri)
query = candidate.query
label = candidate.label.lower()
result = fg.featurize_candidate(qid, cid, "inception_rank", score,
mention, context, label or "",
candidate.description or "",
entity.iri, gold_idx,
candidate.iri, features)
result.update(fg.featurize_query(mention, query, label))
results.append(result)
return results
def predict(self, cas: Cas, layer: str, feature: str, project_id: str,
document_id: str, user_id: str):
model: Optional[sklearn_crfsuite.CRF] = self._load_model(user_id)
if model is None:
logger.debug("No trained model ready yet!")
return
all_tokens = []
featurized_sentences = []
for sentence in cas.select(SENTENCE_TYPE):
tokens = list(cas.select_covered(TOKEN_TYPE, sentence))
words = [token.get_covered_text() for token in tokens]
all_tokens.append(tokens)
featurized_sentences.append(self._sent2features(words))
all_predictions = model.predict(featurized_sentences)
assert len(all_predictions) == len(all_tokens)
for predictions, tokens in zip(all_predictions, all_tokens):
assert len(predictions) == len(tokens)
begin = None
end = None
prev_tag = "O"
for tag, token in zip(predictions, tokens):
if begin is not None and end is not None:
if tag == "O" or (tag.startswith("B")
and prev_tag.startswith("I")):
prediction = create_prediction(cas, layer, feature,
begin, end, "X")
cas.add_annotation(prediction)
if tag.startswith("B"):
begin = token.begin
end = token.end
elif tag.startswith("I"):
end = token.end
else:
begin = None
end = None
prev_tag = tag
def predict(self, cas: Cas, layer: str, feature: str, project_id: str,
document_id: str, user_id: str):
sentences = cas.select(SENTENCE_TYPE)
src_tokens = cas.select_covered("webanno.custom.Base", sentences[0])
trg_tokens = cas.select_covered("webanno.custom.Base", sentences[1])
src_sentence = [e.get_covered_text() for e in src_tokens]
trg_sentence = [e.get_covered_text() for e in trg_tokens]
print(src_sentence)
print(trg_sentence)
alignments = self._aligner.get_word_aligns(src_sentence, trg_sentence)
Relation = cas.typesystem.get_type(layer)
print(list(Relation.all_features))
for matching_method in alignments:
for source_idx, target_idx in alignments[matching_method]:
src = src_tokens[source_idx]
target = trg_tokens[target_idx]
prediction = Relation(
Governor=src,
Dependent=target,
begin=target.begin,
end=target.end,
inception_internal_predicted=True,
)
# setattr(prediction, feature, f"{src.get_covered_text()} -> {target.get_covered_text()}")
setattr(prediction, feature, "")
print(source_idx, target_idx, prediction)
cas.add_annotation(prediction)
break
def get_mappable_ann(self, cas: Cas, t: Type):
return next(cas.select_covered(FeatureExtractor.MAPPABLE_TYPE, t))