From d77e9801adfe549ef6057d8f0c2240377934c51c Mon Sep 17 00:00:00 2001
From: Blanche Miret <bmiret@teklia.com>
Date: Wed, 2 Jun 2021 07:33:54 +0000
Subject: [PATCH] Handle all beginning labels
---
nerval/evaluate.py | 47 ++++++++++----
tests/bioues.bio | 10 +++
tests/test_parse_bio.py | 141 +++++++++++++++++++++++++++-------------
3 files changed, 143 insertions(+), 55 deletions(-)
create mode 100644 tests/bioues.bio
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index 8b23527..3621865 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -12,6 +12,7 @@ import termtables as tt
NOT_ENTITY_TAG = "O"
THRESHOLD = 0.30
+BEGINNING_POS = ["B", "S", "U"]
def get_type_label(label: str) -> str:
@@ -31,6 +32,23 @@ def get_type_label(label: str) -> str:
return tag
+def get_position_label(label: str) -> str:
+ """Return the position of a label
+
+ Input format: "[BIELUS]-type"
+ """
+ try:
+ pos = (
+ NOT_ENTITY_TAG
+ if label == NOT_ENTITY_TAG
+ else re.match(r"([BIELUS])-.{3,4}", label)[1]
+ )
+ except TypeError:
+ raise (Exception(f"The label {label} is not valid in BIOES/BILOU format."))
+
+ return pos
+
+
def parse_bio(path: str) -> dict:
"""Parse a BIO file to get text content, character-level NE labels and entity types count.
@@ -75,13 +93,17 @@ def parse_bio(path: str) -> dict:
if index != 0:
# If new word has same tag as previous, not new entity and in entity, continue entity
- if last_tag == tag and "B" not in label and tag != NOT_ENTITY_TAG:
+ if (
+ last_tag == tag
+ and get_position_label(label) not in BEGINNING_POS
+ and tag != NOT_ENTITY_TAG
+ ):
labels.append(f"I-{last_tag}")
# If new word begins a new entity of different type, check for nested entity to correctly tag the space
elif (
last_tag != tag
- and "B" in label
+ and get_position_label(label) in BEGINNING_POS
and tag != NOT_ENTITY_TAG
and last_tag != NOT_ENTITY_TAG
):
@@ -99,7 +121,7 @@ def parse_bio(path: str) -> dict:
# Check for continuation of the original entity
if (
index < len(lines)
- and "B" not in future_label
+ and get_position_label(future_label) not in BEGINNING_POS
and get_type_label(future_label) == last_tag
):
labels.append(f"I-{last_tag}")
@@ -117,13 +139,13 @@ def parse_bio(path: str) -> dict:
in_nested_entity = False
# Add a tag for each letter in the word
- if "B" in label:
+ if get_position_label(label) in BEGINNING_POS:
labels += [f"B-{tag}"] + [f"I-{tag}"] * (len(word) - 1)
else:
labels += [label] * len(word)
# Count nb entity for each type
- if "B" in label:
+ if get_position_label(label) in BEGINNING_POS:
entity_count[tag] = entity_count.get(tag, 0) + 1
entity_count["All"] += 1
@@ -171,7 +193,7 @@ def look_for_further_entity_part(index, tag, characters, labels):
index += 1
while (
index < len(characters)
- and "B" not in labels[index]
+ and get_position_label(labels[index]) not in BEGINNING_POS
and get_type_label(labels[index]) == tag
):
visited.append(index)
@@ -254,7 +276,7 @@ def compute_matches(
else:
# If beginning new entity
- if "B" in label_ref:
+ if get_position_label(label_ref) in BEGINNING_POS:
current_ref, current_compar = [], []
last_tag = tag_ref
found_aligned_beginning = False
@@ -269,18 +291,21 @@ def compute_matches(
continue
# If just beginning new entity, backtrack tags on prediction string
- if len(current_ref) == 1 and "B" not in labels_predict[i]:
+ if (
+ len(current_ref) == 1
+ and get_position_label(labels_predict[i]) not in BEGINNING_POS
+ ):
j = i - 1
while (
j >= 0
and get_type_label(labels_predict[j]) == tag_ref
- and "B" not in labels_predict[j]
+ and get_position_label(labels_predict[j]) not in BEGINNING_POS
and j not in visited_predict
):
j -= 1
if (
- "B" in labels_predict[j]
+ get_position_label(labels_predict[j]) in BEGINNING_POS
and get_type_label(labels_predict[j]) == tag_ref
and j not in visited_predict
):
@@ -372,7 +397,7 @@ def get_labels_aligned(original: str, aligned: str, labels_original: list) -> li
elif not char == original[index_original]:
new_label = (
last_label
- if "B" not in last_label
+ if get_position_label(last_label) not in BEGINNING_POS
else f"I-{get_type_label(last_label)}"
)
diff --git a/tests/bioues.bio b/tests/bioues.bio
new file mode 100644
index 0000000..6faa87d
--- /dev/null
+++ b/tests/bioues.bio
@@ -0,0 +1,10 @@
+Gérard B-PER
+de I-PER
+Nerval I-PER
+was O
+born O
+in O
+Paris U-LOC
+in O
+1808 S-DAT
+. O
diff --git a/tests/test_parse_bio.py b/tests/test_parse_bio.py
index 2572dc8..7084c5e 100644
--- a/tests/test_parse_bio.py
+++ b/tests/test_parse_bio.py
@@ -8,58 +8,110 @@ EMPTY_BIO = "tests/test_empty.bio"
BAD_BIO = "tests/test_bad.bio"
FAKE_ANNOT_BIO = "tests/test_annot.bio"
FAKE_PREDICT_BIO = "tests/test_predict.bio"
+BIOUES_BIO = "tests/bioues.bio"
+
-# fmt: off
expected_parsed_annot = {
- 'entity_count': {'All': 3, 'DAT': 1, 'LOC': 1, 'PER': 1},
- 'labels': [
- 'B-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER',
- 'I-PER',
- 'I-PER', 'I-PER',
- 'I-PER',
- 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER',
- 'O',
- 'O', 'O', 'O',
- 'O',
- 'O', 'O', 'O', 'O',
- 'O',
- 'O', 'O',
- 'O',
- 'B-LOC', 'I-LOC', 'I-LOC', 'I-LOC', 'I-LOC',
- 'O',
- 'O', 'O',
- 'O',
- 'B-DAT', 'I-DAT', 'I-DAT', 'I-DAT',
- 'O',
- 'O'
+ "entity_count": {"All": 3, "DAT": 1, "LOC": 1, "PER": 1},
+ "labels": [
+ "B-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "B-LOC",
+ "I-LOC",
+ "I-LOC",
+ "I-LOC",
+ "I-LOC",
+ "O",
+ "O",
+ "O",
+ "O",
+ "B-DAT",
+ "I-DAT",
+ "I-DAT",
+ "I-DAT",
+ "O",
+ "O",
],
- 'words': 'Gérard de Nerval was born in Paris in 1808 .'
+ "words": "Gérard de Nerval was born in Paris in 1808 .",
}
expected_parsed_predict = {
- 'entity_count': {'All': 3, 'DAT': 1, '***': 1, 'PER': 1},
- 'labels': [
- 'B-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER',
- 'I-PER',
- 'I-PER', 'I-PER',
- 'I-PER',
- 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER', 'I-PER',
- 'O',
- 'O', 'O', 'O', 'O', 'O',
- 'O',
- 'O', 'O',
- 'O',
- 'B-***', 'I-***', 'I-***', 'I-***', 'I-***',
- 'O',
- 'O', 'O',
- 'O',
- 'B-DAT', 'I-DAT', 'I-DAT', 'I-DAT',
- 'O',
- 'O', 'O'
+ "entity_count": {"All": 3, "DAT": 1, "***": 1, "PER": 1},
+ "labels": [
+ "B-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "I-PER",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "O",
+ "B-***",
+ "I-***",
+ "I-***",
+ "I-***",
+ "I-***",
+ "O",
+ "O",
+ "O",
+ "O",
+ "B-DAT",
+ "I-DAT",
+ "I-DAT",
+ "I-DAT",
+ "O",
+ "O",
+ "O",
],
- 'words': 'G*rard de *N*erval bo*rn in Paris in 1833 *.'
+ "words": "G*rard de *N*erval bo*rn in Paris in 1833 *.",
}
-# fmt: on
@pytest.mark.parametrize(
@@ -68,6 +120,7 @@ expected_parsed_predict = {
(FAKE_ANNOT_BIO, expected_parsed_annot),
(FAKE_PREDICT_BIO, expected_parsed_predict),
(EMPTY_BIO, None),
+ (BIOUES_BIO, expected_parsed_annot),
],
)
def test_parse_bio(test_input, expected):
--
GitLab