Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Wrong entity offsets in the tmvar_v3 datasets #873

Closed
WangXII opened this issue Feb 15, 2023 · 0 comments · Fixed by #874 · May be fixed by #876
Closed

Wrong entity offsets in the tmvar_v3 datasets #873

WangXII opened this issue Feb 15, 2023 · 0 comments · Fixed by #874 · May be fixed by #876
Labels
bug Something isn't working

Comments

@WangXII
Copy link
Contributor

WangXII commented Feb 15, 2023

Describe the bug

Some entities in the tmvar_v3 dataset have wrong entity offsets

Steps to reproduce the bug

Python Code
from datasets import load_dataset

dataset_name= "tmvar_v3"
dataset = load_dataset(f"bigbio/{dataset_name}", name=f"{dataset_name}_bigbio_kb")

doc_id = "21904390"

def check_offsets(doc_id):
    text = dataset[split].filter(lambda x: x["document_id"] == doc_id)[0]["passages"][0]["text"][0] \
        + " " + dataset[split].filter(lambda x: x["document_id"] == doc_id)[0]["passages"][1]["text"][0]

    sentences = text.split(". ")

    sentence_indexes = [m.start() + 2 for m in re.finditer("\. ", text)]  # because the suffix is ". "
    sentence_indexes = [0] + sentence_indexes

    doc_entities = dataset[split].filter(lambda x: x["document_id"] == doc_id)[:]["entities"][0]

    print(sentence_indexes)
    print(len(sentences))
    print(text)
    print(doc_entities)

    sentence_index = 0
    entity_index = 0
    current_offset = 0
    next_sentence_offset = 0
    next_entity_offset = text[current_offset:].find(doc_entities[entity_index]["text"][0])
    while True:
        if sentence_index >= len(sentence_indexes) and entity_index >= len(doc_entities):
            break
        if next_sentence_offset <= next_entity_offset:
            sentence_end = sentence_indexes[sentence_index] + len(sentences[sentence_index]) + 2
            print(f"Sentence {sentence_index} @ offsets {sentence_indexes[sentence_index]} to {sentence_end}")
            print(sentences[sentence_index] + ". ")
            sentence_index += 1
            if sentence_index >= len(sentence_indexes):
                next_sentence_offset = len(text)
            else:
                next_sentence_offset = sentence_indexes[sentence_index]
            # print(f"DEBUG next_sentence_offset: {next_sentence_offset}")
        else:  # next_entity_offset < next_sentence_offset
            entity = doc_entities[entity_index]
            entity_name = entity["text"][0]
            given_offset_start = entity["offsets"][0][0]
            given_offset_end = entity["offsets"][0][1]
            print(f"  {entity_name} @ offsets (real) {next_entity_offset} to {next_entity_offset + len(entity_name)}")
            print(f"  {text[given_offset_start:given_offset_end]} @ offset (given) {given_offset_start} to {given_offset_end}")
            current_offset = next_entity_offset + len(entity_name)
            entity_index += 1
            if entity_index >= len(doc_entities):
                next_entity_offset = len(text)
            else:
                next_entity_offset = current_offset + text[current_offset:].find(doc_entities[entity_index]["text"][0])
            # print(f"DEBUG next_entity_offset: {next_entity_offset}")

check_offsets(doc_id)

Expected results

In Pubmed ID 21904390, expected offsets for these seven entities "entity name, (offset_start, offset_end)" are as follows:

PAX6 (342, 346)
PAX6 (751, 755)
PAX6 (1153, 1157)
PAX6 (1483, 1487)
PAX6 (1627, 1631)
DKFZ p686k1684 (1640, 1654)
PAX6 (2037, 2041).

Actual results

Offsets in the tmvar_v3 dataset for the seven entities are as follows:

PAX6 (343, 347)
PAX6 (753, 757)
PAX6 (1156, 1160)
PAX6 (1487, 1491)
PAX6 (1631, 1635)
DKFZ p686k1684 (1645, 1659)
PAX6 (2043, 2047)

All the remaining entity offsets in the tmvar_v3 dataset seem to be correct.

@WangXII WangXII added the bug Something isn't working label Feb 15, 2023
@WangXII WangXII mentioned this issue Feb 15, 2023
3 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant