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"""Utilities for handling Mewsli-X data and evaluation.
This module is adapted from the utilities distributed along with Mewsli-X, i.e.
https://github.com/google-research/google-research/blob/master/dense_representations_for_entity_retrieval/mel/mewsli_x/schema.py
"""
from __future__ import annotations
import collections
import copy
import dataclasses
import json
import pathlib
import re
from typing import Any, Dict, Iterable, Iterator, List, Mapping, Optional, Sequence, Tuple, Type, TypeVar, Union
# Constants related to text preprocessing.
#
# Symbols for marking up a mention span in a text passage.
_MARKER_L = "{"
_MARKER_R = "}"
# Regular expressions for escaping pre-existing instances of the marker symbols.
_REGEX = re.compile(rf"{re.escape(_MARKER_L)}(.*?){re.escape(_MARKER_R)}")
_REPLACEMENT = r"(\1)"
# Constants related to task definition.
#
# Mewsli-X eval languages.
MENTION_LANGUAGES = ("ar", "de", "en", "es", "fa", "ja", "pl", "ro", "ta", "tr",
"uk")
# The retrieval task for Mewsli-X in XTREME-R is capped at evaluating the top-K
# retrieved entities.
TOP_K = 20
JsonValue = Union[str, int, float, bool, None, Dict[str, Any], List[Any]]
JsonDict = Dict[str, JsonValue]
JsonList = List[JsonValue]
StrOrPurePath = Union[str, pathlib.PurePath]
def to_jsonl(obj: JsonDict) -> str:
return json.dumps(obj, ensure_ascii=False)
@dataclasses.dataclass(frozen=True)
class Span:
"""A [start:end]-span in some external string."""
start: int
end: int
def __post_init__(self):
if self.start < 0:
raise ValueError(f"start offset is out of bounds {self}")
if self.end < 0:
raise ValueError(f"end offset is out of bounds {self}")
if self.start >= self.end:
raise ValueError(f"start and end offsets are non-monotonic {self}")
@staticmethod
def from_json(json_dict: JsonDict) -> Span:
"""Creates a new Span instance from the given JSON-dictionary."""
return Span(start=json_dict["start"], end=json_dict["end"])
def to_json(self) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
return dict(start=self.start, end=self.end)
def validate_offsets_relative_to_context(self, context: str) -> None:
"""Validates the span's offsets relative to a context string."""
if self.start >= len(context):
raise ValueError(
f"start offset in {self} is out of bounds w.r.t. '{context}'")
if self.end > len(context):
raise ValueError(
f"end offset in {self} is out of bounds w.r.t. '{context}'")
def locate_in(self, spans: Iterable[Span]) -> Optional[int]:
"""Returns the index of the first span that fully contains `self`.
Args:
spans: The spans to search.
Returns:
First i such that spans[i].{start,end} covers `self.{start,end}`, or None
if there is no such span, indicating that `self` either is out of range
relative to spans or crosses span boundaries.
"""
for i, span in enumerate(spans):
# The starts may coincide and the ends may coincide.
if (span.start <= self.start and self.start < span.end and
span.start < self.end and self.end <= span.end):
return i
return None
@dataclasses.dataclass(frozen=True)
class TextSpan(Span):
"""A text span relative to an external string T, with text=T[start:end]."""
text: str
def validate_relative_to_context(self, context: str) -> None:
"""Validates that `self.text` matches the designated span in `context`."""
self.validate_offsets_relative_to_context(context)
ref_text = context[self.start:self.end]
if self.text != ref_text:
raise ValueError(f"{self} does not match against context '{context}': "
f"'{self.text}' != '{ref_text}'")
@staticmethod
def from_context(span: Span, context: str) -> TextSpan:
"""Creates a new TextSpan by extracting the given `span` from `context`."""
span.validate_offsets_relative_to_context(context)
return TextSpan(span.start, span.end, text=context[span.start:span.end])
@staticmethod
def from_elements(start: int, end: int, context: str) -> TextSpan:
"""Creates a new TextSpan by extracting [start:end] from `context`."""
return TextSpan.from_context(span=Span(start, end), context=context)
@staticmethod
def from_json(json_dict: JsonDict) -> TextSpan:
"""Creates a new TextSpan from the given JSON-dictionary."""
return TextSpan(
start=json_dict["start"], end=json_dict["end"], text=json_dict["text"])
def to_json(self) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
return dict(start=self.start, end=self.end, text=self.text)
@dataclasses.dataclass(frozen=True)
class Entity:
"""An entity and its textual representation.
Attributes:
entity_id: Unique identifier of the entity, e.g. WikiData QID.
title: A title phrase that names the entity.
description: A definitional description of the entity that serves as its
unique textual representation, e.g. taken from the beginning of the
entity's Wikipedia page.
sentence_spans: Sentence break annotations for the description, as
character-level Span objects that index into `description`
sentences: Sentences extracted from `description` according to
`sentence_spans`. These TextSpan objects include the actual sentence text
for added convenience. E.g., the string of the description's first
sentence is `sentences[0].text`.
description_language: Primary language code of the description and title,
matching the Wikipedia language edition from which they were extracted.
description_url: URL of the page where the description was extracted from.
"""
entity_id: str
title: str
description: str
sentence_spans: Tuple[Span, ...]
description_language: str
description_url: str
def __post_init__(self):
self.validate()
@property
def sentences(self) -> Iterator[TextSpan]:
for span in self.sentence_spans:
yield TextSpan.from_context(span, self.description)
def validate(self):
for sentence_span in self.sentence_spans:
sentence_span.validate_offsets_relative_to_context(self.description)
@staticmethod
def from_json(json_dict: JsonDict) -> Entity:
"""Creates a new Entity from the given JSON-dictionary."""
return Entity(
entity_id=json_dict["entity_id"],
title=json_dict["title"],
description=json_dict["description"],
description_language=json_dict["description_language"],
description_url=json_dict["description_url"],
sentence_spans=tuple(
Span.from_json(t) for t in json_dict["sentence_spans"]),
)
def to_json(self) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
return dict(
entity_id=self.entity_id,
title=self.title,
description=self.description,
description_language=self.description_language,
description_url=self.description_url,
sentence_spans=[t.to_json() for t in self.sentence_spans],
)
@dataclasses.dataclass(frozen=True)
class Mention:
"""A single mention of an entity, referring to some external context.
Attributes:
example_id: Unique identifier for the mention instance.
mention_span: A TextSpan denoting one mention, relative to external context.
entity_id: ID of the mentioned entity.
metadata: Optional dictionary of additional information about the instance.
"""
example_id: str
mention_span: TextSpan
entity_id: str
metadata: Optional[Dict[str, str]] = None
@staticmethod
def from_json(json_dict: JsonDict) -> Mention:
"""Creates a new Mention from the given JSON-dictionary."""
return Mention(
example_id=json_dict["example_id"],
mention_span=TextSpan.from_json(json_dict["mention_span"]),
entity_id=json_dict["entity_id"],
metadata=json_dict.get("metadata"),
)
def to_json(self) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
json_dict = dict(
example_id=self.example_id,
mention_span=self.mention_span.to_json(),
entity_id=self.entity_id,
)
if self.metadata is not None:
json_dict["metadata"] = self.metadata
return json_dict
@dataclasses.dataclass()
class Context:
"""A document text fragment and metadata.
Attributes:
document_title: Title of the document.
document_url: URL of the document.
document_id: An identifier for the document. For a Wikipedia page, this may
be the associated WikiData QID.
language: Primary language code of the document.
text: Original text from the document.
sentence_spans: Sentence break annotations for the text, as character-level
Span objects that index into `text`.
sentences: Sentences extracted from `text` according to `sentence_spans`.
These TextSpan objects include the actual sentence text for added
convenience. E.g., the first sentence's string is `sentences[0].text`.
section_title: Optional title of the section under which `text` appeared.
"""
document_title: str
document_url: str
document_id: str
language: str
text: str
sentence_spans: Tuple[Span, ...]
section_title: Optional[str] = None
def __post_init__(self):
self.validate()
@property
def sentences(self) -> Iterator[TextSpan]:
for span in self.sentence_spans:
yield TextSpan.from_context(span, self.text)
def validate(self):
for sentence_span in self.sentence_spans:
sentence_span.validate_offsets_relative_to_context(self.text)
@staticmethod
def from_json(json_dict: JsonDict) -> Context:
"""Creates a new Context from the given JSON-dictionary."""
return Context(
document_title=json_dict["document_title"],
section_title=json_dict.get("section_title"),
document_url=json_dict["document_url"],
document_id=json_dict["document_id"],
language=json_dict["language"],
text=json_dict["text"],
sentence_spans=tuple(
Span.from_json(t) for t in json_dict["sentence_spans"]),
)
def to_json(self, keep_text: bool = True) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
json_dict = dict(
document_title=self.document_title,
document_url=self.document_url,
document_id=self.document_id,
language=self.language,
text=self.text if keep_text else "",
sentence_spans=[t.to_json() for t in self.sentence_spans],
)
if self.section_title is not None:
json_dict["section_title"] = self.section_title
return json_dict
def truncate(self, focus: int, window_size: int) -> Tuple[int, Context]:
"""Truncates the Context to window_size sentences each side of focus.
This seeks to truncate the text and sentence_spans of `self` to
self.sentence_spans[focus - window_size:focus + window_size + 1].
When there are fewer than window_size sentences available before (after) the
focus, this attempts to retain additional context sentences after (before)
the focus.
Args:
focus: The index of the focus sentence in self.sentence_spans.
window_size: Number of sentences to retain on each side of the focus.
Returns:
- c, the number of characters removed from the start of the text, which is
useful for updating any Mention defined in relation to this Context.
- new_context, a copy of the Context that is updated to contain the
truncated text and sentence_spans.
Raises:
IndexError: if focus is not within the range of self.sentence_spans.
ValueError: if window_size is negative.
"""
if focus < 0 or focus >= len(self.sentence_spans):
raise IndexError(f"Index {focus} invalid for {self.sentence_spans}")
if window_size < 0:
raise ValueError(f"Expected a positive window, but got {window_size}")
snt_window = self._get_sentence_window(focus, window_size)
relevant_sentences = self.sentence_spans[snt_window.start:snt_window.end]
char_offset = relevant_sentences[0].start
char_end = relevant_sentences[-1].end
new_text = self.text[char_offset:char_end]
new_sentences = [
Span(old_sentence.start - char_offset, old_sentence.end - char_offset)
for old_sentence in relevant_sentences
]
new_context = dataclasses.replace(
self, text=new_text, sentence_spans=tuple(new_sentences))
return char_offset, new_context
def _get_sentence_window(self, focus: int, window_size: int) -> Span:
"""Gets Span of sentence indices to cover window around the focus index."""
# Add window to the left of focus. If there are fewer sentences before the
# focus sentence, carry over the remainder.
left_index = max(focus - window_size, 0)
remainder_left = window_size - (focus - left_index)
assert remainder_left >= 0, remainder_left
# Add window to the right of focus, including carryover. (Note, right_index
# is an inclusive index.) If there are fewer sentences after the focus
# sentence, carry back the remainder.
right_index = min(focus + window_size + remainder_left,
len(self.sentence_spans) - 1)
remainder_right = window_size - (right_index - focus)
if remainder_right > 0:
# Extend further leftward.
left_index = max(left_index - remainder_right, 0)
return Span(left_index, right_index + 1)
@dataclasses.dataclass()
class ContextualMentions:
"""Multiple entity mentions in a shared context."""
context: Context
mentions: List[Mention]
def __post_init__(self):
self.validate()
def validate(self):
self.context.validate()
for mention in self.mentions:
mention.mention_span.validate_relative_to_context(self.context.text)
@staticmethod
def from_json(json_dict: JsonDict) -> ContextualMentions:
"""Creates a new ContextualMentions from the given JSON-dictionary."""
return ContextualMentions(
context=Context.from_json(json_dict["context"]),
mentions=[Mention.from_json(m) for m in json_dict["mentions"]],
)
def to_json(self, keep_text: bool = True) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
json_dict = dict(
context=self.context.to_json(keep_text=keep_text),
mentions=[m.to_json() for m in self.mentions],
)
return json_dict
def unnest_to_single_mention_per_context(self) -> Iterator[ContextualMention]:
for mention in self.mentions:
yield ContextualMention(
context=copy.deepcopy(self.context), mention=copy.deepcopy(mention))
@staticmethod
def nest_mentions_by_shared_context(
contextual_mentions: Iterable[ContextualMention]
) -> Iterator[ContextualMentions]:
"""Inverse of unnest_to_single_mention_per_context."""
contexts = {}
groups = collections.defaultdict(list)
for cm in contextual_mentions:
context = cm.context
key = (context.document_id, context.section_title, context.text)
if key in contexts:
assert contexts[key] == context, key
else:
contexts[key] = context
groups[key].append(cm.mention)
for key, mentions in groups.items():
yield ContextualMentions(contexts[key], mentions)
@dataclasses.dataclass()
class ContextualMention:
"""A single entity mention in context."""
context: Context
mention: Mention
def __post_init__(self):
self.validate()
def validate(self):
self.context.validate()
self.mention.mention_span.validate_relative_to_context(self.context.text)
@staticmethod
def from_json(json_dict: JsonDict) -> ContextualMention:
"""Creates a new ContextualMention from the given JSON-dictionary."""
return ContextualMention(
context=Context.from_json(json_dict["context"]),
mention=Mention.from_json(json_dict["mention"]),
)
def to_json(self, keep_text: bool = True) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
json_dict = dict(
context=self.context.to_json(keep_text=keep_text),
mention=self.mention.to_json(),
)
return json_dict
def truncate(self, window_size: int) -> Optional[ContextualMention]:
"""Truncates the context to window_size sentences each side of the mention.
Args:
window_size: Number of sentences to retain on each side of the sentence
containing the mention. See Context.truncate for more detail.
Returns:
Returns None if no sentence spans were present or if the mention crosses
sentence boundaries. Otherwise, returns an update copy of the
ContextualMention where `.context` contains the truncated text and
sentences, and the character offsets in `.mention` updated accordingly.
"""
focus_snt = self.mention.mention_span.locate_in(self.context.sentence_spans)
if focus_snt is None:
# The context has no sentences or the mention crosses sentence boundaries.
return None
offset, new_context = self.context.truncate(
focus=focus_snt, window_size=window_size)
# Internal consistency check.
max_valid = window_size * 2 + 1
assert len(new_context.sentence_spans) <= max_valid, (
f"Got {len(new_context.sentence_spans)}>{max_valid} sentences for "
f"window_size={window_size} in truncated Context: {new_context}")
new_mention = dataclasses.replace(
self.mention,
mention_span=TextSpan(
start=self.mention.mention_span.start - offset,
end=self.mention.mention_span.end - offset,
text=self.mention.mention_span.text))
return ContextualMention(context=new_context, mention=new_mention)
@dataclasses.dataclass()
class MentionEntityPair:
"""A ContextualMention paired with the Entity it refers to."""
contextual_mention: ContextualMention
entity: Entity
def __post_init__(self):
self.validate()
def validate(self):
self.contextual_mention.validate()
self.entity.validate()
@staticmethod
def from_json(json_dict: JsonDict) -> MentionEntityPair:
"""Creates a new MentionEntityPair from the given JSON-dictionary."""
return MentionEntityPair(
contextual_mention=ContextualMention.from_json(
json_dict["contextual_mention"]),
entity=Entity.from_json(json_dict["entity"]),
)
def to_json(self) -> JsonDict:
"""Returns instance as JSON-compatible nested dictionary."""
json_dict = dict(
contextual_mention=self.contextual_mention.to_json(),
entity=self.entity.to_json(),
)
return json_dict
SchemaAnyT = TypeVar("SchemaAnyT", Entity, Context, ContextualMention,
ContextualMentions, MentionEntityPair)
SchemaAny = Union[ContextualMention, ContextualMentions, Entity,
MentionEntityPair]
def load_jsonl_as_dicts(path: StrOrPurePath) -> List[JsonDict]:
"""Returns dict-records from JSONL file (without parsing into dataclasses)."""
with open(path) as input_file:
return [json.loads(line) for line in input_file]
def load_jsonl(path: StrOrPurePath,
schema_cls: Type[SchemaAnyT]) -> List[SchemaAnyT]:
"""Loads the designated type of schema dataclass items from a JSONL file.
Args:
path: File path to load. Each line in the file is a JSON-serialized object.
schema_cls: The dataclass to parse into, e.g. `ContextualMention`, `Entity`,
etc.
Returns:
A list of validated instances of `schema_cls`, one per input line.
"""
result = []
for json_dict in load_jsonl_as_dicts(path):
result.append(schema_cls.from_json(json_dict))
return result
def write_jsonl(path: StrOrPurePath, items: Iterable[SchemaAny]) -> None:
"""Writes a list of any of the schema dataclass items to JSONL file.
Args:
path: Output file path that will store each item as a JSON-serialized line.
items: Items to output. Instances of a schema dataclass, e.g.
`ContextualMention`, `Entity`, etc.
"""
with open(path, "wt") as output_file:
for item in items:
print(to_jsonl(item.to_json()), file=output_file)
# Baseline preprocessing functions. Users are free to create other more nuanced
# approaches.
def preprocess_mention(contextual_mention: ContextualMention) -> str:
"""A baseline method for preprocessing a ContextualMention to string.
Args:
contextual_mention: The ContextualMention to preprocess for passing to a
tokenizer or model.
Returns:
A string representing the mention in context. This baseline implementation
uses one sentence of context, based on sentence annotations provided with
the Mewsli-X data. The mention span is accentuated by enclosing it in marker
symbols defined at the top of this module. As a simple scheme to prevent the
mention span from getting truncated due to a maximum model sequence length,
it is redundantly prepended. For example:
Smith: The verdict came back for { Smith }, who stepped down as AG of
Fictitious County in February, 2012.
"""
# Take 1 sentence of context text.
cm = contextual_mention.truncate(window_size=0)
assert cm is not None, contextual_mention
left = cm.context.text[:cm.mention.mention_span.start]
right = cm.context.text[cm.mention.mention_span.end:]
# Create a context markup that highlights the mention span, while escaping
# any existing instances of the markers.
replacements = 0
left, n = _REGEX.subn(_REPLACEMENT, left)
replacements += n
right, n = _REGEX.subn(_REPLACEMENT, right)
replacements += n
context_markup = (
f"{left} {_MARKER_L} {cm.mention.mention_span.text} {_MARKER_R} {right}")
# Also prepend the mention span to prevent truncation due to limited model
# sequence lengths.
query_string = f"{cm.mention.mention_span.text}: {context_markup}"
# Normalize away newlines and extra spaces.
query_string = " ".join(query_string.splitlines()).replace(" ", " ").strip()
if replacements > 0:
# Escaping does not occur in the WikiNews portion of Mewlis-X, but does
# occur a handful of times in the Wikipedia data.
print(f"Applied marker escaping for example_id {cm.mention.example_id}: "
f"{query_string}")
return query_string
def preprocess_entity_description(entity: Entity) -> str:
"""Returns a lightly normalized string from an Entity's description."""
sentences_text = " ".join(s.text for s in entity.sentences)
# Normalize away newlines and extra spaces.
return " ".join(sentences_text.splitlines()).replace(" ", " ").strip()
# Evaluation functions.
def mean_reciprocal_rank(golds: Sequence[str],
predictions: Sequence[str]) -> float:
"""Computes mean reciprocal rank.
Args:
golds: list of gold entity ids.
predictions: list of prediction lists
Returns:
mean reciprocal rank
"""
def _reciprocal_rank(labels):
for rank, label in enumerate(labels, start=1):
if label:
return 1.0 / rank
return 0.0
assert len(golds) == len(predictions)
reciprocal_ranks = []
for gold, prediction_list in zip(golds, predictions):
labels = [int(p == gold) for p in prediction_list]
reciprocal_ranks.append(_reciprocal_rank(labels))
if reciprocal_ranks:
return sum(reciprocal_ranks) / len(reciprocal_ranks)
return 0.0
def evaluate(
gold_data: Mapping[str, Sequence[str]],
predictions: Mapping[str, Sequence[str]],
k: int = TOP_K,
return_count_diff: bool = False) -> Union[float, Tuple[float, int, int]]:
"""Evaluates one set of entity linking predictions.
Args:
gold_data: dictionary that maps each unique example_id to a *singleton list*
containing its gold entity ID.
predictions: dictionary that maps each unique example_id to a list of
predicted entity IDs. Partial credit may be obtained even if some
instances are missing from this dictionary.
k: Number of top predictions to evaluate per evaluation instance.
return_count_diff: Whether to also return the number of missing and
unexpected example_ids in predictions.
Returns:
mean reciprocal rank in the interval [0, 1] by default, otherwise if
return_count_diff is True, returns the tuple
(mean reciprocal rank, num missing example_ids, num extra example_ids).
"""
# The dataset has a single gold label per instance, but the file provides
# it as a list.
gold_single_labels = {
ex_id: labels[0].strip() for ex_id, labels in gold_data.items()
}
# Convert to parallel lists, and truncate to top-k predictions.
gold_ids: List[str] = []
pred_ids: List[List[str]] = []
for example_id, gold in gold_single_labels.items():
top_k_preds = predictions.get(example_id, [])[:k]
gold_ids.append(gold)
pred_ids.append(top_k_preds)
assert len(gold_ids) == len(pred_ids), (len(gold_ids), len(pred_ids))
mrr = mean_reciprocal_rank(golds=gold_ids, predictions=pred_ids)
if return_count_diff:
unpredicted_count = len(set(gold_single_labels) - set(predictions))
unexpected_count = len(set(predictions) - set(gold_single_labels))
return mrr, unpredicted_count, unexpected_count
else:
return mrr
def evaluate_all(gold_file_pattern: str,
pred_file_pattern: str,
output_path: Optional[str] = None,
k: int = TOP_K) -> float:
"""Evaluates entity linking predictions from per-language files.
Args:
gold_file_pattern: file pattern for per-language gold labels, specified as
an f-string with argument "lang" for language, e.g. "gold-{lang}.json",
containing a single dictionary that maps each unique example id to a
*singleton list* with its gold entity ID. Assumes that files exist for all
languages in MENTION_LANGUAGES.
pred_file_pattern: file pattern for per-language predictions, specified as
an f-string with argument "lang" for language, e.g. "preds-{lang}.json",
containing a single dictionary that maps each unique example id to a list
of predicted entity IDs. Scoring proceeds even if some predictions are
missing, in which case an alert is printed.
output_path: Path to write results to. If None, results are printed to
standard output.
k: Number of top predictions to evaluate.
Returns:
mean reciprocal rank in interval [0, 1], macro-averaged over languages.
"""
outputs = []
columns = ["", f"MRR/MAP@{k}"]
outputs.append("\t".join(columns))
unpredicted_count = 0
unexpected_count = 0
mrr_sum = 0.0
for language in sorted(MENTION_LANGUAGES):
# Read the data for the language into dictionaries keyed on example_id,
# which allows evaluating incomplete predictions.
with open(gold_file_pattern.format(lang=language)) as f:
gold_data: Dict[str, List[str]] = json.load(f)
predictions: Dict[str, List[str]] = {}
pred_path = pathlib.Path(pred_file_pattern.format(lang=language))
if pred_path.exists():
with open(pred_path) as f:
predictions = json.load(f)
mrr, unpredicted, unexpected = evaluate(
gold_data=gold_data,
predictions=predictions,
k=k,
return_count_diff=True)
mrr_sum += mrr
columns = [language, f"{mrr * 100:.2f}"]
outputs.append("\t".join(columns))
unpredicted_count += unpredicted
unexpected_count += unexpected
macro_avg = mrr_sum / len(MENTION_LANGUAGES)
columns = ["MACRO_AVG", f"{macro_avg * 100:.2f}"]
outputs.append("\t".join(columns))
report_text = "\n".join(outputs)
if output_path is None:
print(report_text)
else:
with open(output_path, "w") as f:
f.write(report_text + "\n")
if unpredicted_count:
print(f"Gold examples without predictions: {unpredicted_count}")
if unexpected_count:
print(f"Predicted examples without gold: {unexpected_count}")
return macro_avg
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