pubmed-embedding

A tool to work with pre-computed large pubmed embedding.

Project description

Building PubMed embedding, automatically.

Install the package

As usual, just install from Pypi:

pip install pubmed_embedding

Usage examples

You can retrieve embedding for PubMed IDs of interest as such:

BERT

from pubmed_embedding import get_pubmed_embedding_from_curies

pubmed_ids = ["PMID:24774509", "PMID:15170967", "PMID:7850793"]

bert_features = get_pubmed_embedding_from_curies(
    curies=pubmed_ids,
    version="pubmed_bert_30_11_2022"
)

And the result is:

BERT

SciBERT

scibert_features = get_pubmed_embedding_from_curies(
    curies=pubmed_ids,
    version="pubmed_scibert_30_11_2022"
)

And the result is:

SciBERT

Specter

spected_features = get_pubmed_embedding_from_curies(
    curies=pubmed_ids,
    version="pubmed_specter_30_11_2022"
)

And the result is:

Specter

Citing this work

If you have found these datasets useful, please do cite:

@software{cappellettiPubMed2022,
    author = {Cappelletti, Luca and Fontana, Tommaso and Reese, Justin},
    month = {12},
    title = {{BM25-weighted BERT-based embedding of PubMed}},
    url = {https://github.com/LucaCappelletti94/pubmed_embedding},
    version = {1.0.14},
    year = {2022}
}

Project details

Release history Release notifications | RSS feed

This version

1.0.14

Dec 2, 2022

1.0.13

Dec 2, 2022

1.0.12

Dec 2, 2022

1.0.11

Nov 30, 2022

1.0.10

Nov 30, 2022

1.0.9

Nov 30, 2022

1.0.8

Nov 29, 2022

1.0.7

Nov 29, 2022

1.0.6

Nov 29, 2022

1.0.5

Nov 29, 2022

1.0.4

Nov 29, 2022

1.0.3

Nov 29, 2022

1.0.2

Nov 29, 2022

1.0.1

Nov 29, 2022

1.0.0

Nov 29, 2022

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