spaCy/spacy/scorer.py
2019-11-20 13:15:24 +01:00

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# coding: utf8
from __future__ import division, print_function, unicode_literals
import numpy as np
from .gold import tags_to_entities, GoldParse
from .errors import Errors
class PRFScore(object):
"""
A precision / recall / F score
"""
def __init__(self):
self.tp = 0
self.fp = 0
self.fn = 0
def score_set(self, cand, gold):
self.tp += len(cand.intersection(gold))
self.fp += len(cand - gold)
self.fn += len(gold - cand)
@property
def precision(self):
return self.tp / (self.tp + self.fp + 1e-100)
@property
def recall(self):
return self.tp / (self.tp + self.fn + 1e-100)
@property
def fscore(self):
p = self.precision
r = self.recall
return 2 * ((p * r) / (p + r + 1e-100))
class ROCAUCScore(object):
"""
An AUC ROC score.
"""
def __init__(self):
self.golds = []
self.cands = []
self.saved_score = 0.0
self.saved_score_at_len = 0
def score_set(self, cand, gold):
self.cands.append(cand)
self.golds.append(gold)
@property
def score(self):
if len(self.golds) == self.saved_score_at_len:
return self.saved_score
try:
self.saved_score = _roc_auc_score(self.golds, self.cands)
# catch ValueError: Only one class present in y_true.
# ROC AUC score is not defined in that case.
except ValueError:
self.saved_score = -float("inf")
self.saved_score_at_len = len(self.golds)
return self.saved_score
class Scorer(object):
"""Compute evaluation scores."""
def __init__(self, eval_punct=False, pipeline=None):
"""Initialize the Scorer.
eval_punct (bool): Evaluate the dependency attachments to and from
punctuation.
RETURNS (Scorer): The newly created object.
DOCS: https://spacy.io/api/scorer#init
"""
self.tokens = PRFScore()
self.sbd = PRFScore()
self.unlabelled = PRFScore()
self.labelled = PRFScore()
self.labelled_per_dep = dict()
self.tags = PRFScore()
self.ner = PRFScore()
self.ner_per_ents = dict()
self.eval_punct = eval_punct
self.textcat = None
self.textcat_per_cat = dict()
self.textcat_positive_label = None
self.textcat_multilabel = False
if pipeline:
for name, model in pipeline:
if name == "textcat":
self.textcat_positive_label = model.cfg.get("positive_label", None)
if self.textcat_positive_label:
self.textcat = PRFScore()
if not model.cfg.get("exclusive_classes", False):
self.textcat_multilabel = True
for label in model.cfg.get("labels", []):
self.textcat_per_cat[label] = ROCAUCScore()
else:
for label in model.cfg.get("labels", []):
self.textcat_per_cat[label] = PRFScore()
@property
def tags_acc(self):
"""RETURNS (float): Part-of-speech tag accuracy (fine grained tags,
i.e. `Token.tag`).
"""
return self.tags.fscore * 100
@property
def token_acc(self):
"""RETURNS (float): Tokenization accuracy."""
return self.tokens.precision * 100
@property
def uas(self):
"""RETURNS (float): Unlabelled dependency score."""
return self.unlabelled.fscore * 100
@property
def las(self):
"""RETURNS (float): Labelled dependency score."""
return self.labelled.fscore * 100
@property
def las_per_type(self):
"""RETURNS (dict): Scores per dependency label.
"""
return {
k: {"p": v.precision * 100, "r": v.recall * 100, "f": v.fscore * 100}
for k, v in self.labelled_per_dep.items()
}
@property
def ents_p(self):
"""RETURNS (float): Named entity accuracy (precision)."""
return self.ner.precision * 100
@property
def ents_r(self):
"""RETURNS (float): Named entity accuracy (recall)."""
return self.ner.recall * 100
@property
def ents_f(self):
"""RETURNS (float): Named entity accuracy (F-score)."""
return self.ner.fscore * 100
@property
def ents_per_type(self):
"""RETURNS (dict): Scores per entity label.
"""
return {
k: {"p": v.precision * 100, "r": v.recall * 100, "f": v.fscore * 100}
for k, v in self.ner_per_ents.items()
}
@property
def textcat_score(self):
"""RETURNS (float): f-score on positive label for binary exclusive,
macro-averaged f-score for 3+ exclusive,
macro-averaged AUC ROC score for multilabel (-1 if undefined)
"""
if not self.textcat_multilabel:
# binary multiclass
if self.textcat_positive_label:
return self.textcat.fscore * 100
# other multiclass
return (
sum([score.fscore for label, score in self.textcat_per_cat.items()])
/ (len(self.textcat_per_cat) + 1e-100)
* 100
)
# multilabel
return max(
sum([score.score for label, score in self.textcat_per_cat.items()])
/ (len(self.textcat_per_cat) + 1e-100),
-1,
)
@property
def textcats_per_cat(self):
"""RETURNS (dict): Scores per textcat label.
"""
if not self.textcat_multilabel:
return {
k: {"p": v.precision * 100, "r": v.recall * 100, "f": v.fscore * 100}
for k, v in self.textcat_per_cat.items()
}
return {
k: {"roc_auc_score": max(v.score, -1)}
for k, v in self.textcat_per_cat.items()
}
@property
def scores(self):
"""RETURNS (dict): All scores with keys `uas`, `las`, `ents_p`,
`ents_r`, `ents_f`, `tags_acc`, `token_acc`, and `textcat_score`.
"""
return {
"uas": self.uas,
"las": self.las,
"las_per_type": self.las_per_type,
"ents_p": self.ents_p,
"ents_r": self.ents_r,
"ents_f": self.ents_f,
"ents_per_type": self.ents_per_type,
"tags_acc": self.tags_acc,
"token_acc": self.token_acc,
"textcat_score": self.textcat_score,
"textcats_per_cat": self.textcats_per_cat,
}
def score(self, doc, gold, verbose=False, punct_labels=("p", "punct")):
"""Update the evaluation scores from a single Doc / GoldParse pair.
doc (Doc): The predicted annotations.
gold (GoldParse): The correct annotations.
verbose (bool): Print debugging information.
punct_labels (tuple): Dependency labels for punctuation. Used to
evaluate dependency attachments to punctuation if `eval_punct` is
`True`.
DOCS: https://spacy.io/api/scorer#score
"""
if len(doc) != len(gold):
gold = GoldParse.from_annot_tuples(
doc, tuple(zip(*gold.orig_annot)) + (gold.cats,)
)
gold_deps = set()
gold_deps_per_dep = {}
gold_tags = set()
gold_ents = set(tags_to_entities([annot[-1] for annot in gold.orig_annot]))
for id_, word, tag, head, dep, ner in gold.orig_annot:
gold_tags.add((id_, tag))
if dep not in (None, "") and dep.lower() not in punct_labels:
gold_deps.add((id_, head, dep.lower()))
if dep.lower() not in self.labelled_per_dep:
self.labelled_per_dep[dep.lower()] = PRFScore()
if dep.lower() not in gold_deps_per_dep:
gold_deps_per_dep[dep.lower()] = set()
gold_deps_per_dep[dep.lower()].add((id_, head, dep.lower()))
cand_deps = set()
cand_deps_per_dep = {}
cand_tags = set()
for token in doc:
if token.orth_.isspace():
continue
gold_i = gold.cand_to_gold[token.i]
if gold_i is None:
self.tokens.fp += 1
else:
self.tokens.tp += 1
cand_tags.add((gold_i, token.tag_))
if token.dep_.lower() not in punct_labels and token.orth_.strip():
gold_head = gold.cand_to_gold[token.head.i]
# None is indistinct, so we can't just add it to the set
# Multiple (None, None) deps are possible
if gold_i is None or gold_head is None:
self.unlabelled.fp += 1
self.labelled.fp += 1
else:
cand_deps.add((gold_i, gold_head, token.dep_.lower()))
if token.dep_.lower() not in self.labelled_per_dep:
self.labelled_per_dep[token.dep_.lower()] = PRFScore()
if token.dep_.lower() not in cand_deps_per_dep:
cand_deps_per_dep[token.dep_.lower()] = set()
cand_deps_per_dep[token.dep_.lower()].add(
(gold_i, gold_head, token.dep_.lower())
)
if "-" not in [token[-1] for token in gold.orig_annot]:
# Find all NER labels in gold and doc
ent_labels = set([x[0] for x in gold_ents] + [k.label_ for k in doc.ents])
# Set up all labels for per type scoring and prepare gold per type
gold_per_ents = {ent_label: set() for ent_label in ent_labels}
for ent_label in ent_labels:
if ent_label not in self.ner_per_ents:
self.ner_per_ents[ent_label] = PRFScore()
gold_per_ents[ent_label].update(
[x for x in gold_ents if x[0] == ent_label]
)
# Find all candidate labels, for all and per type
cand_ents = set()
cand_per_ents = {ent_label: set() for ent_label in ent_labels}
for ent in doc.ents:
first = gold.cand_to_gold[ent.start]
last = gold.cand_to_gold[ent.end - 1]
if first is None or last is None:
self.ner.fp += 1
self.ner_per_ents[ent.label_].fp += 1
else:
cand_ents.add((ent.label_, first, last))
cand_per_ents[ent.label_].add((ent.label_, first, last))
# Scores per ent
for k, v in self.ner_per_ents.items():
if k in cand_per_ents:
v.score_set(cand_per_ents[k], gold_per_ents[k])
# Score for all ents
self.ner.score_set(cand_ents, gold_ents)
self.tags.score_set(cand_tags, gold_tags)
self.labelled.score_set(cand_deps, gold_deps)
for dep in self.labelled_per_dep:
self.labelled_per_dep[dep].score_set(
cand_deps_per_dep.get(dep, set()), gold_deps_per_dep.get(dep, set())
)
self.unlabelled.score_set(
set(item[:2] for item in cand_deps), set(item[:2] for item in gold_deps)
)
if (
len(gold.cats) > 0
and set(self.textcat_per_cat) == set(gold.cats)
and set(gold.cats) == set(doc.cats)
):
goldcat = max(gold.cats, key=gold.cats.get)
candcat = max(doc.cats, key=doc.cats.get)
if self.textcat_positive_label:
self.textcat.score_set(
set([self.textcat_positive_label]) & set([candcat]),
set([self.textcat_positive_label]) & set([goldcat]),
)
for label in self.textcat_per_cat:
if self.textcat_multilabel:
self.textcat_per_cat[label].score_set(
doc.cats[label], gold.cats[label]
)
else:
self.textcat_per_cat[label].score_set(
set([label]) & set([candcat]), set([label]) & set([goldcat])
)
elif len(self.textcat_per_cat) > 0:
model_labels = set(self.textcat_per_cat)
eval_labels = set(gold.cats)
raise ValueError(
Errors.E162.format(model_labels=model_labels, eval_labels=eval_labels)
)
if verbose:
gold_words = [item[1] for item in gold.orig_annot]
for w_id, h_id, dep in cand_deps - gold_deps:
print("F", gold_words[w_id], dep, gold_words[h_id])
for w_id, h_id, dep in gold_deps - cand_deps:
print("M", gold_words[w_id], dep, gold_words[h_id])
#############################################################################
#
# The following implementation of roc_auc_score() is adapted from
# scikit-learn, which is distributed under the following license:
#
# New BSD License
#
# Copyright (c) 20072019 The scikit-learn developers.
# All rights reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# a. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# b. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# c. Neither the name of the Scikit-learn Developers nor the names of
# its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
# DAMAGE.
def _roc_auc_score(y_true, y_score):
"""Compute Area Under the Receiver Operating Characteristic Curve (ROC AUC)
from prediction scores.
Note: this implementation is restricted to the binary classification task
Parameters
----------
y_true : array, shape = [n_samples] or [n_samples, n_classes]
True binary labels or binary label indicators.
The multiclass case expects shape = [n_samples] and labels
with values in ``range(n_classes)``.
y_score : array, shape = [n_samples] or [n_samples, n_classes]
Target scores, can either be probability estimates of the positive
class, confidence values, or non-thresholded measure of decisions
(as returned by "decision_function" on some classifiers). For binary
y_true, y_score is supposed to be the score of the class with greater
label. The multiclass case expects shape = [n_samples, n_classes]
where the scores correspond to probability estimates.
Returns
-------
auc : float
References
----------
.. [1] `Wikipedia entry for the Receiver operating characteristic
<https://en.wikipedia.org/wiki/Receiver_operating_characteristic>`_
.. [2] Fawcett T. An introduction to ROC analysis[J]. Pattern Recognition
Letters, 2006, 27(8):861-874.
.. [3] `Analyzing a portion of the ROC curve. McClish, 1989
<https://www.ncbi.nlm.nih.gov/pubmed/2668680>`_
"""
if len(np.unique(y_true)) != 2:
raise ValueError(Errors.E165)
fpr, tpr, _ = _roc_curve(y_true, y_score)
return _auc(fpr, tpr)
def _roc_curve(y_true, y_score):
"""Compute Receiver operating characteristic (ROC)
Note: this implementation is restricted to the binary classification task.
Parameters
----------
y_true : array, shape = [n_samples]
True binary labels. If labels are not either {-1, 1} or {0, 1}, then
pos_label should be explicitly given.
y_score : array, shape = [n_samples]
Target scores, can either be probability estimates of the positive
class, confidence values, or non-thresholded measure of decisions
(as returned by "decision_function" on some classifiers).
Returns
-------
fpr : array, shape = [>2]
Increasing false positive rates such that element i is the false
positive rate of predictions with score >= thresholds[i].
tpr : array, shape = [>2]
Increasing true positive rates such that element i is the true
positive rate of predictions with score >= thresholds[i].
thresholds : array, shape = [n_thresholds]
Decreasing thresholds on the decision function used to compute
fpr and tpr. `thresholds[0]` represents no instances being predicted
and is arbitrarily set to `max(y_score) + 1`.
Notes
-----
Since the thresholds are sorted from low to high values, they
are reversed upon returning them to ensure they correspond to both ``fpr``
and ``tpr``, which are sorted in reversed order during their calculation.
References
----------
.. [1] `Wikipedia entry for the Receiver operating characteristic
<https://en.wikipedia.org/wiki/Receiver_operating_characteristic>`_
.. [2] Fawcett T. An introduction to ROC analysis[J]. Pattern Recognition
Letters, 2006, 27(8):861-874.
"""
fps, tps, thresholds = _binary_clf_curve(y_true, y_score)
# Add an extra threshold position
# to make sure that the curve starts at (0, 0)
tps = np.r_[0, tps]
fps = np.r_[0, fps]
thresholds = np.r_[thresholds[0] + 1, thresholds]
if fps[-1] <= 0:
fpr = np.repeat(np.nan, fps.shape)
else:
fpr = fps / fps[-1]
if tps[-1] <= 0:
tpr = np.repeat(np.nan, tps.shape)
else:
tpr = tps / tps[-1]
return fpr, tpr, thresholds
def _binary_clf_curve(y_true, y_score):
"""Calculate true and false positives per binary classification threshold.
Parameters
----------
y_true : array, shape = [n_samples]
True targets of binary classification
y_score : array, shape = [n_samples]
Estimated probabilities or decision function
Returns
-------
fps : array, shape = [n_thresholds]
A count of false positives, at index i being the number of negative
samples assigned a score >= thresholds[i]. The total number of
negative samples is equal to fps[-1] (thus true negatives are given by
fps[-1] - fps).
tps : array, shape = [n_thresholds <= len(np.unique(y_score))]
An increasing count of true positives, at index i being the number
of positive samples assigned a score >= thresholds[i]. The total
number of positive samples is equal to tps[-1] (thus false negatives
are given by tps[-1] - tps).
thresholds : array, shape = [n_thresholds]
Decreasing score values.
"""
pos_label = 1.0
y_true = np.ravel(y_true)
y_score = np.ravel(y_score)
# make y_true a boolean vector
y_true = y_true == pos_label
# sort scores and corresponding truth values
desc_score_indices = np.argsort(y_score, kind="mergesort")[::-1]
y_score = y_score[desc_score_indices]
y_true = y_true[desc_score_indices]
weight = 1.0
# y_score typically has many tied values. Here we extract
# the indices associated with the distinct values. We also
# concatenate a value for the end of the curve.
distinct_value_indices = np.where(np.diff(y_score))[0]
threshold_idxs = np.r_[distinct_value_indices, y_true.size - 1]
# accumulate the true positives with decreasing threshold
tps = _stable_cumsum(y_true * weight)[threshold_idxs]
fps = 1 + threshold_idxs - tps
return fps, tps, y_score[threshold_idxs]
def _stable_cumsum(arr, axis=None, rtol=1e-05, atol=1e-08):
"""Use high precision for cumsum and check that final value matches sum
Parameters
----------
arr : array-like
To be cumulatively summed as flat
axis : int, optional
Axis along which the cumulative sum is computed.
The default (None) is to compute the cumsum over the flattened array.
rtol : float
Relative tolerance, see ``np.allclose``
atol : float
Absolute tolerance, see ``np.allclose``
"""
out = np.cumsum(arr, axis=axis, dtype=np.float64)
expected = np.sum(arr, axis=axis, dtype=np.float64)
if not np.all(
np.isclose(
out.take(-1, axis=axis), expected, rtol=rtol, atol=atol, equal_nan=True
)
):
raise ValueError(Errors.E163)
return out
def _auc(x, y):
"""Compute Area Under the Curve (AUC) using the trapezoidal rule
This is a general function, given points on a curve. For computing the
area under the ROC-curve, see :func:`roc_auc_score`.
Parameters
----------
x : array, shape = [n]
x coordinates. These must be either monotonic increasing or monotonic
decreasing.
y : array, shape = [n]
y coordinates.
Returns
-------
auc : float
"""
x = np.ravel(x)
y = np.ravel(y)
direction = 1
dx = np.diff(x)
if np.any(dx < 0):
if np.all(dx <= 0):
direction = -1
else:
raise ValueError(Errors.E164.format(x))
area = direction * np.trapz(y, x)
if isinstance(area, np.memmap):
# Reductions such as .sum used internally in np.trapz do not return a
# scalar by default for numpy.memmap instances contrary to
# regular numpy.ndarray instances.
area = area.dtype.type(area)
return area