{"id":15706367,"url":"https://github.com/lucacappelletti94/pubmed_embedding","last_synced_at":"2025-05-12T13:46:01.590Z","repository":{"id":98555443,"uuid":"498850000","full_name":"LucaCappelletti94/pubmed_embedding","owner":"LucaCappelletti94","description":"Building a pubmed graph, automatically.","archived":false,"fork":false,"pushed_at":"2024-05-14T11:10:37.000Z","size":547,"stargazers_count":5,"open_issues_count":3,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-12T08:54:24.655Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Rust","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LucaCappelletti94.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-06-01T18:15:48.000Z","updated_at":"2023-04-28T13:19:05.000Z","dependencies_parsed_at":"2024-10-24T07:42:22.730Z","dependency_job_id":"463f88a9-9c5d-419f-86ba-e44828e05adb","html_url":"https://github.com/LucaCappelletti94/pubmed_embedding","commit_stats":null,"previous_names":["lucacappelletti94/pubmed_graph"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpubmed_embedding","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpubmed_embedding/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpubmed_embedding/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fpubmed_embedding/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LucaCappelletti94","download_url":"https://codeload.github.com/LucaCappelletti94/pubmed_embedding/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253749963,"owners_count":21958227,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-03T20:22:27.435Z","updated_at":"2025-05-12T13:46:01.562Z","avatar_url":"https://github.com/LucaCappelletti94.png","language":"Rust","readme":"PubMed embedding\n===================================\n|pip| |downloads| |paper|\n\nBuilding PubMed embedding, automatically.\n\n\nInstall the package\n----------------------------------\nAs usual, just install from Pypi:\n\n.. code:: shell\n\n    pip install pubmed_embedding\n\n\nUsage examples\n----------------------------------\nYou can retrieve embedding for PubMed IDs of interest as such:\n\nBERT\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. code:: python\n\n    from pubmed_embedding import get_pubmed_embedding_from_curies\n\n    pubmed_ids = [\"PMID:24774509\", \"PMID:15170967\", \"PMID:7850793\"]\n\n    bert_features = get_pubmed_embedding_from_curies(\n        curies=pubmed_ids,\n        version=\"pubmed_bert_30_11_2022\"\n    )\n\nAnd the result is:\n\n|BERT|\n\n\nSciBERT\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. code:: python\n\n    scibert_features = get_pubmed_embedding_from_curies(\n        curies=pubmed_ids,\n        version=\"pubmed_scibert_30_11_2022\"\n    )\n   \nAnd the result is:\n\n|SciBERT|\n\nSpecter\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n.. code:: python\n\n    spected_features = get_pubmed_embedding_from_curies(\n        curies=pubmed_ids,\n        version=\"pubmed_specter_30_11_2022\"\n    )\n\nAnd the result is:\n\n|Specter|\n\nCiting this work\n-----------------------------\nIf you have found these datasets useful, please do cite:\n\n.. code:: bib\n\n    @software{cappellettiPubMed2022,\n        author = {Cappelletti, Luca and Fontana, Tommaso and Reese, Justin},\n        month = {12},\n        title = {{BM25-weighted BERT-based embedding of PubMed}},\n        url = {https://github.com/LucaCappelletti94/pubmed_embedding},\n        version = {1.0.14},\n        year = {2022}\n    }\n\n\n\n.. |BERT| image:: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/bert.png?raw=true\n.. |SciBERT| image:: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/scibert.png?raw=true\n.. |Specter| image:: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/specter.png?raw=true\n\n.. |pip| image:: https://badge.fury.io/py/pubmed-embedding.svg\n    :target: https://badge.fury.io/py/pubmed-embedding\n    :alt: Pypi project\n\n.. |downloads| image:: https://pepy.tech/badge/pubmed-embedding\n    :target: https://pepy.tech/badge/pubmed-embedding\n    :alt: Pypi total project downloads \n\n.. |paper| image:: https://img.shields.io/badge/Paper-BM25_weighted_BERT_based_embedding_of_PubMed-blue.svg\n    :target: https://github.com/LucaCappelletti94/pubmed_embedding/blob/main/BM25_weighted_BERT_based_embedding_of_PubMed.pdf\n    :alt: Paper\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fpubmed_embedding","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flucacappelletti94%2Fpubmed_embedding","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fpubmed_embedding/lists"}