https://github.com/lucacappelletti94/pubmed_embedding

Building a pubmed graph, automatically.
https://github.com/lucacappelletti94/pubmed_embedding

Last synced: 4 days ago
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Building a pubmed graph, automatically.

• Host: GitHub
• URL: https://github.com/lucacappelletti94/pubmed_embedding
• Owner: LucaCappelletti94
• License: mit
• Created: 2022-06-01T18:15:48.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2024-05-14T11:10:37.000Z (6 months ago)
• Last Synced: 2024-10-24T18:15:32.965Z (12 days ago)
• Language: Rust
• Size: 534 KB
• Stars: 5
• Watchers: 1
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE
  • Citation: CITATION.cff

Awesome Lists containing this project

README

        
PubMed embedding

===================================

|pip| |downloads| |paper|

Building PubMed embedding, automatically.

Install the package

----------------------------------

As usual, just install from Pypi:

.. code:: shell

    pip install pubmed_embedding

Usage examples

----------------------------------

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

BERT

~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

    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

~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

    scibert_features = get_pubmed_embedding_from_curies(

        curies=pubmed_ids,

        version="pubmed_scibert_30_11_2022"

    )

   

And the result is:

|SciBERT|

Specter

~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: python

    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:

.. code:: bib

    @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}

    }

.. |BERT| image:: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/bert.png?raw=true

.. |SciBERT| image:: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/scibert.png?raw=true

.. |Specter| image:: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/specter.png?raw=true

.. |pip| image:: https://badge.fury.io/py/pubmed-embedding.svg

    :target: https://badge.fury.io/py/pubmed-embedding

    :alt: Pypi project

.. |downloads| image:: https://pepy.tech/badge/pubmed-embedding

    :target: https://pepy.tech/badge/pubmed-embedding

    :alt: Pypi total project downloads 

.. |paper| image:: https://img.shields.io/badge/Paper-BM25_weighted_BERT_based_embedding_of_PubMed-blue.svg

    :target: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/BM25_weighted_BERT_based_embedding_of_PubMed.pdf

    :alt: Paper