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SpEL / span_annotation.py
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SpEL files required to run the streamlit app copied from https://github.com/shavarani/SpEL
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"""
Data structure classes required and used for multiple levels of granularity in spans.
"""
from data_loader import dl_sa
from mosestokenizer import MosesDetokenizer
detokenize = MosesDetokenizer('en')
class PhraseAnnotation:
def __init__(self, initial_word):
self.words = [initial_word]
self._resolved_annotation = initial_word.resolved_annotation
self.ppr_for_ned_candidates = initial_word.ppr_for_ned_candidates
@property
def has_valid_bioes_labels(self):
# B = 0, I = 1, O = 2, E = 3, S = 4
return all([x.has_valid_bioes_labels and x.bioes_labels is not None for x in self.words])
def add(self, word):
self.words.append(word)
# There are some phrases that are annotated as O but have PPRforNED candidates, those will be ignored!
if self._resolved_annotation > 0 and self.ppr_for_ned_candidates != word.ppr_for_ned_candidates:
self.ppr_for_ned_candidates = list(set(self.ppr_for_ned_candidates) & set(word.ppr_for_ned_candidates))
def all_possible_annotations(self):
all_common_ids = set.intersection(*[set([y[0] for y in x.candidates]) for x in self.words])
all_common_ids_average_confidence = map(lambda x: sum(x)/len(x), [
[sum(y[1])/len(y[1]) for x in self.words for y in x.candidates if y[0] == k] for k in all_common_ids])
return sorted(zip(all_common_ids, all_common_ids_average_confidence), key=lambda x: x[1], reverse=True)
def set_alternative_as_resolved_annotation(self, alternative):
self._resolved_annotation = alternative
@property
def resolved_annotation(self):
return self._resolved_annotation
@property
def subword_annotations(self):
return [x for w in self.words for x in w.annotations]
@property
def word_string(self):
return detokenize([x.word_string.replace("\n", "\u010a").replace("£", "£").replace("âĦ¢", '™')
.replace('ü','ü').replace('é', 'é').replace('ÃŃ', 'í') for x in self.words])
@property
def begin_character(self):
return self.words[0].token_offsets[0][1][0]
@property
def end_character(self):
return self.words[-1].token_offsets[-1][1][-1]
@property
def average_annotation_confidence(self):
ac = [x.resolved_annotation_confidence for x in self.words]
return sum(ac) / len(ac)
def __str__(self):
return f"{self.word_string} ({self.begin_character}, {self.end_character}) | annotation: " \
f"{self.words[0].annotations[0].idx2tag[self.resolved_annotation]}"
class WordAnnotation:
def __init__(self, subword_annotations, token_offsets, ppr_for_ned_candidates=None):
if ppr_for_ned_candidates is None:
ppr_for_ned_candidates = []
self.annotations = subword_annotations
self.token_offsets = token_offsets
self.ppr_for_ned_candidates = ppr_for_ned_candidates
self.is_valid_annotation = False if not subword_annotations else True
self.word_string = ''.join([x[0].replace('\u0120', '') for x in token_offsets])
# even if self.is_valid_annotation is True we could still have the candidates to be empty
# since there could be no consensus among the subword predictions.
self.candidates = sorted([] if not self.is_valid_annotation else [
(cid, self._get_assigned_probabilities(cid)) for cid in set.intersection(*[set(y.top_k_i_list)
for y in self.annotations])],
key=lambda x: sum(x[1])/len(x[1]), reverse=True)
self.resolved_annotation = self._resolve_annotation()
rc = self._get_assigned_probabilities(self.resolved_annotation)
self.resolved_annotation_confidence = sum(rc) / len(rc)
if not self.candidates:
self.candidates = [(self.resolved_annotation, rc)]
assert self.resolved_annotation in [x[0] for x in self.candidates]
self.has_valid_bioes_labels = all([x.has_valid_bioes_label for x in self.annotations])
self.bioes_labels = None if not self.has_valid_bioes_labels else [x.bioes_label for x in self.annotations]
def _resolve_annotation(self):
if not self.is_valid_annotation:
return 0
r = [x.item() for x in self.annotations]
if r.count(r[0]) == len(r):
annotation = r[0]
elif self.candidates:
# here we return the annotation with the highest average probability prediction over all the subwords
annotation = self.candidates[0][0]
else:
# here we return the annotation which the model has predicted as highest probability for
# the majority of the subwords
most_frequent = max(set(r), key=r.count)
if r.count(most_frequent) == 1:
annotation = r[0]
else:
annotation = most_frequent
return annotation
def _get_assigned_probabilities(self, cid):
assigned_probabilities = []
for a in self.annotations:
found = False
for i, p in zip(a.top_k_i_list, a.top_k_p_list):
if i == cid:
assigned_probabilities.append(p)
found = True
break
if not found:
assigned_probabilities.append(0.0)
assert len(assigned_probabilities) == len(self.annotations)
return assigned_probabilities
def __str__(self):
ann = self.annotations[0].idx2tag[self.resolved_annotation]
cdns = ','.join([f'({self.annotations[0].idx2tag[x[0]]}: {sum(x[1])/len(x[1])})' for x in self.candidates])
return f"{self.word_string} | annotation: {ann} | candidates: [{cdns}]"
class SubwordAnnotation:
"""
The value of his class will be equal to the value of its "self.top_k_i_list[0]", the rest of the information will be
carried over for future decision-making and evaluation.
"""
def __init__(self, top_k_p_list, top_k_i_list, subword_string):
self.top_k_p_list = top_k_p_list
self.top_k_i_list = top_k_i_list
subword_string = "UNDEF_STR" if not subword_string else subword_string
self.subword_string = subword_string.replace('\u0120', '')
self.bioes_label = 2
self.has_valid_bioes_label = False
self.bioes_probabilities = None
def __eq__(self, other):
if isinstance(other, int):
return self.top_k_i_list[0] == other
elif isinstance(other, SubwordAnnotation):
return self.top_k_i_list[0] == other.top_k_i_list[0]
else:
raise ValueError
def __str__(self):
return f"({self.subword_string}, <<" \
f"{'>> <<'.join([f'{dl_sa.mentions_itos[i]}: {p:.3f}' for i, p in zip(self.top_k_i_list, self.top_k_p_list)])}>>)"
def item(self):
return self.top_k_i_list[0]
def item_probability(self):
return self.top_k_p_list[0]
def set_bioes_label(self, label: int, probs: list):
assert 0 <= label <= 5
assert len(probs) == 5
self.has_valid_bioes_label = True
self.bioes_label = label
self.bioes_probabilities = probs