mirror of
https://github.com/explosion/spaCy.git
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Add beta parameter to Scorer and PRFScore.
This commit is contained in:
Raphael Mitsch
parent
51863cd267
commit
ea9737a664
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@ -7,6 +7,8 @@ from typing import Optional, Tuple, Any, Dict, List
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import numpy
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import wasabi.tables
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from ..pipeline import TrainablePipe, Pipe
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from ..errors import Errors
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from ..training import Corpus
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from ._util import app, Arg, Opt, import_code, setup_gpu
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from .. import util
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@ -47,7 +49,7 @@ def find_threshold_cli(
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threshold_key (str): Key of threshold attribute in component's configuration.
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scores_key (str): Name of score to metric to optimize.
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n_trials (int): Number of trials to determine optimal thresholds
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beta (float): Beta for F1 calculation.
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beta (float): Beta for F-score calculation.
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code_path (Optional[Path]): Path to Python file with additional code (registered functions) to be imported.
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use_gpu (int): GPU ID or -1 for CPU.
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gold_preproc (bool): Whether to use gold preprocessing. Gold preprocessing helps the annotations align to the
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@ -79,10 +81,10 @@ def find_threshold(
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threshold_key: str,
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scores_key: str,
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*,
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n_trials: int = _DEFAULTS["n_trials"],
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beta: float = _DEFAULTS["beta"],
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use_gpu: int = _DEFAULTS["use_gpu"],
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gold_preproc: bool = _DEFAULTS["gold_preproc"],
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n_trials: int = _DEFAULTS["n_trials"], # type: ignore
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beta: float = _DEFAULTS["beta"], # type: ignore
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use_gpu: int = _DEFAULTS["use_gpu"], # type: ignore
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gold_preproc: bool = _DEFAULTS["gold_preproc"], # type: ignore
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silent: bool = True,
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) -> Tuple[float, float]:
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"""
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@ -93,7 +95,7 @@ def find_threshold(
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threshold_key (str): Key of threshold attribute in component's configuration.
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scores_key (str): Name of score to metric to optimize.
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n_trials (int): Number of trials to determine optimal thresholds.
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beta (float): Beta for F1 calculation.
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beta (float): Beta for F-score calculation.
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use_gpu (int): GPU ID or -1 for CPU.
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gold_preproc (bool): Whether to use gold preprocessing. Gold preprocessing helps the annotations align to the
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tokenization, and may result in sequences of more consistent length. However, it may reduce runtime accuracy due
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@ -108,10 +110,13 @@ def find_threshold(
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wasabi.msg.fail("Evaluation data not found", data_path, exits=1)
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nlp = util.load_model(model)
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pipe: Optional[Pipe] = None
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try:
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pipe = nlp.get_pipe(pipe_name)
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except KeyError as err:
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wasabi.msg.fail(title=str(err), exits=1)
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if not isinstance(pipe, TrainablePipe):
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raise TypeError(Errors.E1044)
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if not silent:
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wasabi.msg.info(
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@ -140,7 +145,9 @@ def find_threshold(
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scores: Dict[float, float] = {}
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for threshold in numpy.linspace(0, 1, n_trials):
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pipe.cfg = set_nested_item(pipe.cfg, config_keys, threshold)
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scores[threshold] = nlp.evaluate(dev_dataset)[scores_key]
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scores[threshold] = nlp.evaluate(dev_dataset, scorer_cfg={"beta": beta})[
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scores_key
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]
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if not (
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isinstance(scores[threshold], float) or isinstance(scores[threshold], int)
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):
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@ -939,6 +939,7 @@ class Errors(metaclass=ErrorsWithCodes):
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"`{arg2}`={arg2_values} but these arguments are conflicting.")
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E1043 = ("Expected None or a value in range [{range_start}, {range_end}] for entity linker threshold, but got "
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"{value}.")
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E1044 = ("Only components of type `TrainablePipe` are supported by `find_threshold()`.")
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# Deprecated model shortcuts, only used in errors and warnings
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@ -22,15 +22,12 @@ class PRFScore:
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"""A precision / recall / F score."""
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def __init__(
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self,
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*,
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tp: int = 0,
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fp: int = 0,
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fn: int = 0,
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self, *, tp: int = 0, fp: int = 0, fn: int = 0, beta: float = 1
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) -> None:
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self.tp = tp
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self.fp = fp
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self.fn = fn
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self.beta = beta
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def __len__(self) -> int:
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return self.tp + self.fp + self.fn
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@ -42,8 +39,12 @@ class PRFScore:
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return self
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def __add__(self, other):
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assert self.beta == other.beta
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return PRFScore(
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tp=self.tp + other.tp, fp=self.fp + other.fp, fn=self.fn + other.fn
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tp=self.tp + other.tp,
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fp=self.fp + other.fp,
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fn=self.fn + other.fn,
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beta=self.beta,
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)
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def score_set(self, cand: set, gold: set) -> None:
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@ -63,7 +64,7 @@ class PRFScore:
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def fscore(self) -> float:
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p = self.precision
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r = self.recall
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return 2 * ((p * r) / (p + r + 1e-100))
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return (1 + self.beta**2) * ((p * r) / ((self.beta**2 * p) + r + 1e-100))
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def to_dict(self) -> Dict[str, float]:
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return {"p": self.precision, "r": self.recall, "f": self.fscore}
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@ -101,6 +102,8 @@ class ROCAUCScore:
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class Scorer:
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"""Compute evaluation scores."""
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BETA = 1
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def __init__(
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self,
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nlp: Optional["Language"] = None,
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@ -149,8 +152,9 @@ class Scorer:
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DOCS: https://spacy.io/api/scorer#score_tokenization
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"""
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acc_score = PRFScore()
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prf_score = PRFScore()
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beta = cfg.get("beta", Scorer.BETA)
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acc_score = PRFScore(beta=beta)
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prf_score = PRFScore(beta=beta)
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for example in examples:
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gold_doc = example.reference
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pred_doc = example.predicted
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@ -210,7 +214,7 @@ class Scorer:
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DOCS: https://spacy.io/api/scorer#score_token_attr
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"""
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tag_score = PRFScore()
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tag_score = PRFScore(beta=cfg.get("beta", Scorer.BETA))
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for example in examples:
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gold_doc = example.reference
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pred_doc = example.predicted
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@ -261,7 +265,8 @@ class Scorer:
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key attr_micro_p/r/f and the per-feat PRF scores under
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attr_per_feat.
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"""
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micro_score = PRFScore()
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beta = cfg.get("beta", Scorer.BETA)
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micro_score = PRFScore(beta=beta)
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per_feat = {}
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for example in examples:
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pred_doc = example.predicted
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@ -276,7 +281,7 @@ class Scorer:
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for feat in morph.split(Morphology.FEATURE_SEP):
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field, values = feat.split(Morphology.FIELD_SEP)
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if field not in per_feat:
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per_feat[field] = PRFScore()
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per_feat[field] = PRFScore(beta=beta)
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if field not in gold_per_feat:
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gold_per_feat[field] = set()
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gold_per_feat[field].add((gold_i, feat))
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@ -298,7 +303,7 @@ class Scorer:
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for feat in morph.split(Morphology.FEATURE_SEP):
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field, values = feat.split(Morphology.FIELD_SEP)
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if field not in per_feat:
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per_feat[field] = PRFScore()
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per_feat[field] = PRFScore(beta=beta)
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if field not in pred_per_feat:
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pred_per_feat[field] = set()
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pred_per_feat[field].add((gold_i, feat))
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@ -353,7 +358,8 @@ class Scorer:
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DOCS: https://spacy.io/api/scorer#score_spans
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"""
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score = PRFScore()
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beta = cfg.get("beta", Scorer.BETA)
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score = PRFScore(beta=beta)
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score_per_type = dict()
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for example in examples:
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pred_doc = example.predicted
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@ -372,7 +378,7 @@ class Scorer:
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gold_per_type: Dict[str, Set] = {label: set() for label in labels}
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for label in labels:
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if label not in score_per_type:
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score_per_type[label] = PRFScore()
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score_per_type[label] = PRFScore(beta=beta)
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# Find all predidate labels, for all and per type
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gold_spans = set()
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pred_spans = set()
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@ -469,9 +475,10 @@ class Scorer:
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DOCS: https://spacy.io/api/scorer#score_cats
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"""
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beta = cfg.get("beta", Scorer.BETA)
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if threshold is None:
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threshold = 0.5 if multi_label else 0.0
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f_per_type = {label: PRFScore() for label in labels}
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f_per_type = {label: PRFScore(beta=beta) for label in labels}
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auc_per_type = {label: ROCAUCScore() for label in labels}
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labels = set(labels)
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if labels:
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@ -519,7 +526,7 @@ class Scorer:
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pred_label, pred_score = max(pred_cats.items(), key=lambda it: it[1])
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if pred_score >= threshold:
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f_per_type[pred_label].fp += 1
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micro_prf = PRFScore()
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micro_prf = PRFScore(beta=beta)
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for label_prf in f_per_type.values():
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micro_prf.tp += label_prf.tp
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micro_prf.fn += label_prf.fn
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@ -576,6 +583,7 @@ class Scorer:
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DOCS: https://spacy.io/api/scorer#score_links
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"""
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beta = cfg.get("beta", Scorer.BETA)
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f_per_type = {}
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for example in examples:
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gold_ent_by_offset = {}
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@ -589,7 +597,7 @@ class Scorer:
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if gold_span is not None:
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label = gold_span.label_
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if label not in f_per_type:
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f_per_type[label] = PRFScore()
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f_per_type[label] = PRFScore(beta=beta)
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gold = gold_span.kb_id_
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# only evaluating entities that overlap between gold and pred,
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# to disentangle the performance of the NEL from the NER
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@ -608,7 +616,7 @@ class Scorer:
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# a wrong prediction (e.g. Q42 != Q3) counts as both a FP as well as a FN
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f_per_type[label].fp += 1
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f_per_type[label].fn += 1
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micro_prf = PRFScore()
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micro_prf = PRFScore(beta=beta)
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for label_prf in f_per_type.values():
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micro_prf.tp += label_prf.tp
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micro_prf.fn += label_prf.fn
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@ -663,8 +671,9 @@ class Scorer:
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DOCS: https://spacy.io/api/scorer#score_deps
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"""
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unlabelled = PRFScore()
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labelled = PRFScore()
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beta = cfg.get("beta", Scorer.BETA)
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unlabelled = PRFScore(beta=beta)
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labelled = PRFScore(beta=beta)
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labelled_per_dep = dict()
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missing_indices = set()
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for example in examples:
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@ -680,7 +689,7 @@ class Scorer:
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if dep not in ignore_labels:
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gold_deps.add((gold_i, head.i, dep))
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if dep not in labelled_per_dep:
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labelled_per_dep[dep] = PRFScore()
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labelled_per_dep[dep] = PRFScore(beta=beta)
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if dep not in gold_deps_per_dep:
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gold_deps_per_dep[dep] = set()
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gold_deps_per_dep[dep].add((gold_i, head.i, dep))
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@ -711,7 +720,7 @@ class Scorer:
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else:
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pred_deps.add((gold_i, gold_head, dep))
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if dep not in labelled_per_dep:
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labelled_per_dep[dep] = PRFScore()
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labelled_per_dep[dep] = PRFScore(beta=beta)
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if dep not in pred_deps_per_dep:
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pred_deps_per_dep[dep] = set()
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pred_deps_per_dep[dep].add((gold_i, gold_head, dep))
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@ -742,6 +751,7 @@ class Scorer:
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def get_ner_prf(examples: Iterable[Example], **kwargs) -> Dict[str, Any]:
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"""Compute micro-PRF and per-entity PRF scores for a sequence of examples."""
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score_per_type = defaultdict(PRFScore)
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beta = kwargs.get("beta", Scorer.BETA)
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for eg in examples:
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if not eg.y.has_annotation("ENT_IOB"):
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continue
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@ -749,7 +759,7 @@ def get_ner_prf(examples: Iterable[Example], **kwargs) -> Dict[str, Any]:
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align_x2y = eg.alignment.x2y
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for pred_ent in eg.x.ents:
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if pred_ent.label_ not in score_per_type:
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score_per_type[pred_ent.label_] = PRFScore()
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score_per_type[pred_ent.label_] = PRFScore(beta=beta)
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indices = align_x2y[pred_ent.start : pred_ent.end]
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if len(indices):
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g_span = eg.y[indices[0] : indices[-1] + 1]
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@ -765,7 +775,7 @@ def get_ner_prf(examples: Iterable[Example], **kwargs) -> Dict[str, Any]:
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score_per_type[pred_ent.label_].fp += 1
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for label, start, end in golds:
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score_per_type[label].fn += 1
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totals = PRFScore()
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totals = PRFScore(beta=beta)
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for prf in score_per_type.values():
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totals += prf
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if len(totals) > 0:
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