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pubmed_embedding

Building a pubmed graph, automatically.

https://github.com/lucacappelletti94/pubmed_embedding

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Found codemeta.json file
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    Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Building a pubmed graph, automatically.

Basic Info
  • Host: GitHub
  • Owner: LucaCappelletti94
  • License: mit
  • Language: Rust
  • Default Branch: main
  • Size: 534 KB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 2
  • Open Issues: 3
  • Releases: 0
Created almost 4 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License Citation

README.rst 

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

Owner

  • Name: Luca Cappelletti
  • Login: LucaCappelletti94
  • Kind: user
  • Location: Milano, Italy
  • Company: University of Fribourg

I am but an egg 🥚 - "Stranger in a Strange Land"

Citation (CITATION.cff) 

@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 = {1.0.12},
  year = {2022}
}

GitHub Events

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Last synced: over 1 year ago

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  • Development Distribution Score (DDS): 0.0
Top Committers
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LucaCappelletti94 c****4@g****m 79

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Last synced: 11 months ago

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Past Year
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Top Authors
Issue Authors
  • cthoyt (1)
  • LucaCappelletti94 (1)
Pull Request Authors
  • cthoyt (2)
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Dependencies

pubmed_parser/Cargo.lock cargo
  • adler 1.0.2
  • autocfg 1.1.0
  • cfg-if 1.0.0
  • console 0.15.0
  • crc32fast 1.3.2
  • crossbeam-channel 0.5.4
  • crossbeam-deque 0.8.1
  • crossbeam-epoch 0.9.8
  • crossbeam-utils 0.8.8
  • either 1.6.1
  • encode_unicode 0.3.6
  • flate2 1.0.24
  • hermit-abi 0.1.19
  • indicatif 0.16.2
  • lazy_static 1.4.0
  • libc 0.2.126
  • memoffset 0.6.5
  • miniz_oxide 0.5.3
  • num_cpus 1.13.1
  • number_prefix 0.4.0
  • once_cell 1.12.0
  • rayon 1.5.3
  • rayon-core 1.9.3
  • regex 1.5.6
  • regex-syntax 0.6.26
  • scopeguard 1.1.0
  • terminal_size 0.1.17
  • winapi 0.3.9
  • winapi-i686-pc-windows-gnu 0.4.0
  • winapi-x86_64-pc-windows-gnu 0.4.0
pubmed_parser/Cargo.toml cargo
setup.py pypi
  • compress_json *
  • downloaders *
  • numpy *
  • pandas *
  • tqdm *
  • userinput *