Files
2026-07-13 12:37:18 +08:00

729 lines
26 KiB
Python

# -*- coding:utf-8 -*-
# Author: hankcs
# Date: 2020-06-12 20:34
import warnings
from typing import Dict, List, Tuple, Callable, Set, Optional
def generate_words_per_line(file_path):
with open(file_path, encoding='utf-8') as src:
for line in src:
cells = line.strip().split()
if not cells:
continue
yield cells
def words_to_bmes(words):
tags = []
for w in words:
if not w:
raise ValueError('{} contains None or zero-length word {}'.format(str(words), w))
if len(w) == 1:
tags.append('S')
else:
tags.extend(['B'] + ['M'] * (len(w) - 2) + ['E'])
return tags
def words_to_bi(words):
tags = []
for w in words:
if not w:
raise ValueError('{} contains None or zero-length word {}'.format(str(words), w))
tags.extend(['B'] + ['I'] * (len(w) - 1))
return tags
def bmes_to_words(chars, tags):
result = []
if len(chars) == 0:
return result
word = chars[0]
for c, t in zip(chars[1:], tags[1:]):
if t == 'B' or t == 'S':
result.append(word)
word = ''
word += c
if len(word) != 0:
result.append(word)
return result
def bmes_to_spans(tags):
result = []
offset = 0
pre_offset = 0
for t in tags[1:]:
offset += 1
if t == 'B' or t == 'S':
result.append((pre_offset, offset))
pre_offset = offset
if offset != len(tags):
result.append((pre_offset, len(tags)))
return result
def bmes_of(sentence, segmented):
if segmented:
chars = []
tags = []
words = sentence.split()
for w in words:
chars.extend(list(w))
if len(w) == 1:
tags.append('S')
else:
tags.extend(['B'] + ['M'] * (len(w) - 2) + ['E'])
else:
chars = list(sentence)
tags = ['S'] * len(chars)
return chars, tags
def iobes_to_bilou(src, dst):
with open(src) as src, open(dst, 'w') as out:
for line in src:
line = line.strip()
if not line:
out.write('\n')
continue
word, tag = line.split('\t')
if tag.startswith('E-'):
tag = 'L-' + tag[2:]
elif tag.startswith('S-'):
tag = 'U-' + tag[2:]
out.write(f'{word}\t{tag}\n')
def allowed_transitions(constraint_type: str, labels: Dict[int, str]) -> List[Tuple[int, int]]:
"""
Given labels and a constraint type, returns the allowed transitions. It will
additionally include transitions for the start and end states, which are used
by the conditional random field.
# Parameters
constraint_type : `str`, required
Indicates which constraint to apply. Current choices are
"BIO", "IOB1", "BIOUL", and "BMES".
labels : `Dict[int, str]`, required
A mapping {label_id -> label}. Most commonly this would be the value from
Vocabulary.get_index_to_token_vocabulary()
# Returns
`List[Tuple[int, int]]`
The allowed transitions (from_label_id, to_label_id).
"""
num_labels = len(labels)
start_tag = num_labels
end_tag = num_labels + 1
labels_with_boundaries = list(labels.items()) + [(start_tag, "START"), (end_tag, "END")]
allowed = []
for from_label_index, from_label in labels_with_boundaries:
if from_label in ("START", "END"):
from_tag = from_label
from_entity = ""
else:
from_tag = from_label[0]
from_entity = from_label[1:]
for to_label_index, to_label in labels_with_boundaries:
if to_label in ("START", "END"):
to_tag = to_label
to_entity = ""
else:
to_tag = to_label[0]
to_entity = to_label[1:]
if is_transition_allowed(constraint_type, from_tag, from_entity, to_tag, to_entity):
allowed.append((from_label_index, to_label_index))
return allowed
def is_transition_allowed(
constraint_type: str, from_tag: str, from_entity: str, to_tag: str, to_entity: str
):
"""
Given a constraint type and strings `from_tag` and `to_tag` that
represent the origin and destination of the transition, return whether
the transition is allowed under the given constraint type.
# Parameters
constraint_type : `str`, required
Indicates which constraint to apply. Current choices are
"BIO", "IOB1", "BIOUL", and "BMES".
from_tag : `str`, required
The tag that the transition originates from. For example, if the
label is `I-PER`, the `from_tag` is `I`.
from_entity : `str`, required
The entity corresponding to the `from_tag`. For example, if the
label is `I-PER`, the `from_entity` is `PER`.
to_tag : `str`, required
The tag that the transition leads to. For example, if the
label is `I-PER`, the `to_tag` is `I`.
to_entity : `str`, required
The entity corresponding to the `to_tag`. For example, if the
label is `I-PER`, the `to_entity` is `PER`.
# Returns
`bool`
Whether the transition is allowed under the given `constraint_type`.
"""
if to_tag == "START" or from_tag == "END":
# Cannot transition into START or from END
return False
if constraint_type == "BIOUL":
if from_tag == "START":
return to_tag in ("O", "B", "U")
if to_tag == "END":
return from_tag in ("O", "L", "U")
return any(
[
# O can transition to O, B-* or U-*
# L-x can transition to O, B-*, or U-*
# U-x can transition to O, B-*, or U-*
from_tag in ("O", "L", "U") and to_tag in ("O", "B", "U"),
# B-x can only transition to I-x or L-x
# I-x can only transition to I-x or L-x
from_tag in ("B", "I") and to_tag in ("I", "L") and from_entity == to_entity,
]
)
elif constraint_type == "BIO":
if from_tag == "START":
return to_tag in ("O", "B")
if to_tag == "END":
return from_tag in ("O", "B", "I")
return any(
[
# Can always transition to O or B-x
to_tag in ("O", "B"),
# Can only transition to I-x from B-x or I-x
to_tag == "I" and from_tag in ("B", "I") and from_entity == to_entity,
]
)
elif constraint_type == "IOB1":
if from_tag == "START":
return to_tag in ("O", "I")
if to_tag == "END":
return from_tag in ("O", "B", "I")
return any(
[
# Can always transition to O or I-x
to_tag in ("O", "I"),
# Can only transition to B-x from B-x or I-x, where
# x is the same tag.
to_tag == "B" and from_tag in ("B", "I") and from_entity == to_entity,
]
)
elif constraint_type == "BMES":
if from_tag == "START":
return to_tag in ("B", "S")
if to_tag == "END":
return from_tag in ("E", "S")
return any(
[
# Can only transition to B or S from E or S.
to_tag in ("B", "S") and from_tag in ("E", "S"),
# Can only transition to M-x from B-x, where
# x is the same tag.
to_tag == "M" and from_tag in ("B", "M") and from_entity == to_entity,
# Can only transition to E-x from B-x or M-x, where
# x is the same tag.
to_tag == "E" and from_tag in ("B", "M") and from_entity == to_entity,
]
)
else:
raise ValueError(f"Unknown constraint type: {constraint_type}")
TypedSpan = Tuple[int, Tuple[int, int]]
TypedStringSpan = Tuple[str, Tuple[int, int]]
class InvalidTagSequence(Exception):
def __init__(self, tag_sequence=None):
super().__init__()
self.tag_sequence = tag_sequence
def __str__(self):
return " ".join(self.tag_sequence)
T = str
def enumerate_spans(
sentence: List[T],
offset: int = 0,
max_span_width: int = None,
min_span_width: int = 1,
filter_function: Callable[[List[T]], bool] = None,
) -> List[Tuple[int, int]]:
"""
Given a sentence, return all token spans within the sentence. Spans are `inclusive`.
Additionally, you can provide a maximum and minimum span width, which will be used
to exclude spans outside of this range.
Finally, you can provide a function mapping `List[T] -> bool`, which will
be applied to every span to decide whether that span should be included. This
allows filtering by length, regex matches, pos tags or any Spacy `Token`
attributes, for example.
# Parameters
sentence : `List[T]`, required.
The sentence to generate spans for. The type is generic, as this function
can be used with strings, or Spacy `Tokens` or other sequences.
offset : `int`, optional (default = `0`)
A numeric offset to add to all span start and end indices. This is helpful
if the sentence is part of a larger structure, such as a document, which
the indices need to respect.
max_span_width : `int`, optional (default = `None`)
The maximum length of spans which should be included. Defaults to len(sentence).
min_span_width : `int`, optional (default = `1`)
The minimum length of spans which should be included. Defaults to 1.
filter_function : `Callable[[List[T]], bool]`, optional (default = `None`)
A function mapping sequences of the passed type T to a boolean value.
If `True`, the span is included in the returned spans from the
sentence, otherwise it is excluded..
"""
max_span_width = max_span_width or len(sentence)
filter_function = filter_function or (lambda x: True)
spans: List[Tuple[int, int]] = []
for start_index in range(len(sentence)):
last_end_index = min(start_index + max_span_width, len(sentence))
first_end_index = min(start_index + min_span_width - 1, len(sentence))
for end_index in range(first_end_index, last_end_index):
start = offset + start_index
end = offset + end_index
# add 1 to end index because span indices are inclusive.
if filter_function(sentence[slice(start_index, end_index + 1)]):
spans.append((start, end))
return spans
def bio_tags_to_spans(
tag_sequence: List[str], classes_to_ignore: List[str] = None
) -> List[TypedStringSpan]:
"""
Given a sequence corresponding to BIO tags, extracts spans.
Spans are inclusive and can be of zero length, representing a single word span.
Ill-formed spans are also included (i.e those which do not start with a "B-LABEL"),
as otherwise it is possible to get a perfect precision score whilst still predicting
ill-formed spans in addition to the correct spans. This function works properly when
the spans are unlabeled (i.e., your labels are simply "B", "I", and "O").
# Parameters
tag_sequence : `List[str]`, required.
The integer class labels for a sequence.
classes_to_ignore : `List[str]`, optional (default = `None`).
A list of string class labels `excluding` the bio tag
which should be ignored when extracting spans.
# Returns
spans : `List[TypedStringSpan]`
The typed, extracted spans from the sequence, in the format (label, (span_start, span_end)).
Note that the label `does not` contain any BIO tag prefixes.
"""
classes_to_ignore = classes_to_ignore or []
spans: Set[Tuple[str, Tuple[int, int]]] = set()
span_start = 0
span_end = 0
active_conll_tag = None
for index, string_tag in enumerate(tag_sequence):
# Actual BIO tag.
bio_tag = string_tag[0]
if bio_tag not in ["B", "I", "O"]:
raise InvalidTagSequence(tag_sequence)
conll_tag = string_tag[2:]
if bio_tag == "O" or conll_tag in classes_to_ignore:
# The span has ended.
if active_conll_tag is not None:
spans.add((active_conll_tag, (span_start, span_end)))
active_conll_tag = None
# We don't care about tags we are
# told to ignore, so we do nothing.
continue
elif bio_tag == "B":
# We are entering a new span; reset indices
# and active tag to new span.
if active_conll_tag is not None:
spans.add((active_conll_tag, (span_start, span_end)))
active_conll_tag = conll_tag
span_start = index
span_end = index
elif bio_tag == "I" and conll_tag == active_conll_tag:
# We're inside a span.
span_end += 1
else:
# This is the case the bio label is an "I", but either:
# 1) the span hasn't started - i.e. an ill formed span.
# 2) The span is an I tag for a different conll annotation.
# We'll process the previous span if it exists, but also
# include this span. This is important, because otherwise,
# a model may get a perfect F1 score whilst still including
# false positive ill-formed spans.
if active_conll_tag is not None:
spans.add((active_conll_tag, (span_start, span_end)))
active_conll_tag = conll_tag
span_start = index
span_end = index
# Last token might have been a part of a valid span.
if active_conll_tag is not None:
spans.add((active_conll_tag, (span_start, span_end)))
return list(spans)
def iob1_tags_to_spans(
tag_sequence: List[str], classes_to_ignore: List[str] = None
) -> List[TypedStringSpan]:
"""
Given a sequence corresponding to IOB1 tags, extracts spans.
Spans are inclusive and can be of zero length, representing a single word span.
Ill-formed spans are also included (i.e., those where "B-LABEL" is not preceded
by "I-LABEL" or "B-LABEL").
# Parameters
tag_sequence : `List[str]`, required.
The integer class labels for a sequence.
classes_to_ignore : `List[str]`, optional (default = `None`).
A list of string class labels `excluding` the bio tag
which should be ignored when extracting spans.
# Returns
spans : `List[TypedStringSpan]`
The typed, extracted spans from the sequence, in the format (label, (span_start, span_end)).
Note that the label `does not` contain any BIO tag prefixes.
"""
classes_to_ignore = classes_to_ignore or []
spans: Set[Tuple[str, Tuple[int, int]]] = set()
span_start = 0
span_end = 0
active_conll_tag = None
prev_bio_tag = None
prev_conll_tag = None
for index, string_tag in enumerate(tag_sequence):
curr_bio_tag = string_tag[0]
curr_conll_tag = string_tag[2:]
if curr_bio_tag not in ["B", "I", "O"]:
raise InvalidTagSequence(tag_sequence)
if curr_bio_tag == "O" or curr_conll_tag in classes_to_ignore:
# The span has ended.
if active_conll_tag is not None:
spans.add((active_conll_tag, (span_start, span_end)))
active_conll_tag = None
elif _iob1_start_of_chunk(prev_bio_tag, prev_conll_tag, curr_bio_tag, curr_conll_tag):
# We are entering a new span; reset indices
# and active tag to new span.
if active_conll_tag is not None:
spans.add((active_conll_tag, (span_start, span_end)))
active_conll_tag = curr_conll_tag
span_start = index
span_end = index
else:
# bio_tag == "I" and curr_conll_tag == active_conll_tag
# We're continuing a span.
span_end += 1
prev_bio_tag = string_tag[0]
prev_conll_tag = string_tag[2:]
# Last token might have been a part of a valid span.
if active_conll_tag is not None:
spans.add((active_conll_tag, (span_start, span_end)))
return list(spans)
def _iob1_start_of_chunk(
prev_bio_tag: Optional[str],
prev_conll_tag: Optional[str],
curr_bio_tag: str,
curr_conll_tag: str,
) -> bool:
if curr_bio_tag == "B":
return True
if curr_bio_tag == "I" and prev_bio_tag == "O":
return True
if curr_bio_tag != "O" and prev_conll_tag != curr_conll_tag:
return True
return False
def bioul_tags_to_spans(
tag_sequence: List[str], classes_to_ignore: List[str] = None
) -> List[TypedStringSpan]:
"""
Given a sequence corresponding to BIOUL tags, extracts spans.
Spans are inclusive and can be of zero length, representing a single word span.
Ill-formed spans are not allowed and will raise `InvalidTagSequence`.
This function works properly when the spans are unlabeled (i.e., your labels are
simply "B", "I", "O", "U", and "L").
# Parameters
tag_sequence : `List[str]`, required.
The tag sequence encoded in BIOUL, e.g. ["B-PER", "L-PER", "O"].
classes_to_ignore : `List[str]`, optional (default = `None`).
A list of string class labels `excluding` the bio tag
which should be ignored when extracting spans.
# Returns
spans : `List[TypedStringSpan]`
The typed, extracted spans from the sequence, in the format (label, (span_start, span_end)).
"""
spans = []
classes_to_ignore = classes_to_ignore or []
index = 0
while index < len(tag_sequence):
label = tag_sequence[index]
if label[0] == "U":
spans.append((label.partition("-")[2], (index, index)))
elif label[0] == "B":
start = index
while label[0] != "L":
index += 1
if index >= len(tag_sequence):
raise InvalidTagSequence(tag_sequence)
label = tag_sequence[index]
if not (label[0] == "I" or label[0] == "L"):
raise InvalidTagSequence(tag_sequence)
spans.append((label.partition("-")[2], (start, index)))
else:
if label != "O":
raise InvalidTagSequence(tag_sequence)
index += 1
return [span for span in spans if span[0] not in classes_to_ignore]
def iobes_tags_to_spans(
tag_sequence: List[str], classes_to_ignore: List[str] = None
) -> List[TypedStringSpan]:
"""
Given a sequence corresponding to BIOUL tags, extracts spans.
Spans are inclusive and can be of zero length, representing a single word span.
Ill-formed spans are not allowed and will raise `InvalidTagSequence`.
This function works properly when the spans are unlabeled (i.e., your labels are
simply "B", "I", "O", "U", and "L").
# Parameters
tag_sequence : `List[str]`, required.
The tag sequence encoded in BIOUL, e.g. ["B-PER", "L-PER", "O"].
classes_to_ignore : `List[str]`, optional (default = `None`).
A list of string class labels `excluding` the bio tag
which should be ignored when extracting spans.
# Returns
spans : `List[TypedStringSpan]`
The typed, extracted spans from the sequence, in the format (label, (span_start, span_end)).
"""
spans = []
classes_to_ignore = classes_to_ignore or []
index = 0
while index < len(tag_sequence):
label = tag_sequence[index]
if label[0] == "S":
spans.append((label.partition("-")[2], (index, index)))
elif label[0] == "B":
start = index
while label[0] != "E":
index += 1
if index >= len(tag_sequence):
raise InvalidTagSequence(tag_sequence)
label = tag_sequence[index]
if not (label[0] == "I" or label[0] == "E"):
raise InvalidTagSequence(tag_sequence)
spans.append((label.partition("-")[2], (start, index)))
else:
if label != "O":
raise InvalidTagSequence(tag_sequence)
index += 1
return [span for span in spans if span[0] not in classes_to_ignore]
def iob1_to_bioul(tag_sequence: List[str]) -> List[str]:
warnings.warn(
"iob1_to_bioul has been replaced with 'to_bioul' to allow more encoding options.",
FutureWarning,
)
return to_bioul(tag_sequence)
def to_bioul(tag_sequence: List[str], encoding: str = "IOB1") -> List[str]:
"""
Given a tag sequence encoded with IOB1 labels, recode to BIOUL.
In the IOB1 scheme, I is a token inside a span, O is a token outside
a span and B is the beginning of span immediately following another
span of the same type.
In the BIO scheme, I is a token inside a span, O is a token outside
a span and B is the beginning of a span.
# Parameters
tag_sequence : `List[str]`, required.
The tag sequence encoded in IOB1, e.g. ["I-PER", "I-PER", "O"].
encoding : `str`, optional, (default = `"IOB1"`).
The encoding type to convert from. Must be either "IOB1" or "BIO".
# Returns
bioul_sequence : `List[str]`
The tag sequence encoded in IOB1, e.g. ["B-PER", "L-PER", "O"].
"""
if encoding not in {"IOB1", "BIO"}:
raise ValueError(f"Invalid encoding {encoding} passed to 'to_bioul'.")
def replace_label(full_label, new_label):
# example: full_label = 'I-PER', new_label = 'U', returns 'U-PER'
parts = list(full_label.partition("-"))
parts[0] = new_label
return "".join(parts)
def pop_replace_append(in_stack, out_stack, new_label):
# pop the last element from in_stack, replace the label, append
# to out_stack
tag = in_stack.pop()
new_tag = replace_label(tag, new_label)
out_stack.append(new_tag)
def process_stack(stack, out_stack):
# process a stack of labels, add them to out_stack
if len(stack) == 1:
# just a U token
pop_replace_append(stack, out_stack, "U")
else:
# need to code as BIL
recoded_stack = []
pop_replace_append(stack, recoded_stack, "L")
while len(stack) >= 2:
pop_replace_append(stack, recoded_stack, "I")
pop_replace_append(stack, recoded_stack, "B")
recoded_stack.reverse()
out_stack.extend(recoded_stack)
# Process the tag_sequence one tag at a time, adding spans to a stack,
# then recode them.
bioul_sequence = []
stack: List[str] = []
for label in tag_sequence:
# need to make a dict like
# token = {'token': 'Matt', "labels": {'conll2003': "B-PER"}
# 'gold': 'I-PER'}
# where 'gold' is the raw value from the CoNLL data set
if label == "O" and len(stack) == 0:
bioul_sequence.append(label)
elif label == "O" and len(stack) > 0:
# need to process the entries on the stack plus this one
process_stack(stack, bioul_sequence)
bioul_sequence.append(label)
elif label[0] == "I":
# check if the previous type is the same as this one
# if it is then append to stack
# otherwise this start a new entity if the type
# is different
if len(stack) == 0:
if encoding == "BIO":
raise InvalidTagSequence(tag_sequence)
stack.append(label)
else:
# check if the previous type is the same as this one
this_type = label.partition("-")[2]
prev_type = stack[-1].partition("-")[2]
if this_type == prev_type:
stack.append(label)
else:
if encoding == "BIO":
raise InvalidTagSequence(tag_sequence)
# a new entity
process_stack(stack, bioul_sequence)
stack.append(label)
elif label[0] == "B":
if len(stack) > 0:
process_stack(stack, bioul_sequence)
stack.append(label)
else:
raise InvalidTagSequence(tag_sequence)
# process the stack
if len(stack) > 0:
process_stack(stack, bioul_sequence)
return bioul_sequence
def bmes_tags_to_spans(
tag_sequence: List[str], classes_to_ignore: List[str] = None
) -> List[TypedStringSpan]:
"""
Given a sequence corresponding to BMES tags, extracts spans.
Spans are inclusive and can be of zero length, representing a single word span.
Ill-formed spans are also included (i.e those which do not start with a "B-LABEL"),
as otherwise it is possible to get a perfect precision score whilst still predicting
ill-formed spans in addition to the correct spans.
This function works properly when the spans are unlabeled (i.e., your labels are
simply "B", "M", "E" and "S").
# Parameters
tag_sequence : `List[str]`, required.
The integer class labels for a sequence.
classes_to_ignore : `List[str]`, optional (default = `None`).
A list of string class labels `excluding` the bio tag
which should be ignored when extracting spans.
# Returns
spans : `List[TypedStringSpan]`
The typed, extracted spans from the sequence, in the format (label, (span_start, span_end)).
Note that the label `does not` contain any BIO tag prefixes.
"""
def extract_bmes_tag_label(text):
bmes_tag = text[0]
label = text[2:]
return bmes_tag, label
spans: List[Tuple[str, List[int]]] = []
prev_bmes_tag: Optional[str] = None
for index, tag in enumerate(tag_sequence):
bmes_tag, label = extract_bmes_tag_label(tag)
if bmes_tag in ("B", "S"):
# Regardless of tag, we start a new span when reaching B & S.
spans.append((label, [index, index]))
elif bmes_tag in ("M", "E") and prev_bmes_tag in ("B", "M") and spans[-1][0] == label:
# Only expand the span if
# 1. Valid transition: B/M -> M/E.
# 2. Matched label.
spans[-1][1][1] = index
else:
# Best effort split for invalid span.
spans.append((label, [index, index]))
# update previous BMES tag.
prev_bmes_tag = bmes_tag
classes_to_ignore = classes_to_ignore or []
return [
# to tuple.
(span[0], (span[1][0], span[1][1]))
for span in spans
if span[0] not in classes_to_ignore
]