{"id":15904105,"url":"https://github.com/dermatologist/cui-embed","last_synced_at":"2025-10-27T04:11:54.759Z","repository":{"id":88878268,"uuid":"248640580","full_name":"dermatologist/cui-embed","owner":"dermatologist","description":"Gensim wrapper for the clinical (CUI) embeddings","archived":false,"fork":false,"pushed_at":"2023-11-13T20:49:58.000Z","size":16,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-08-14T12:41:39.611Z","etag":null,"topics":["cui","embeddings","gensim","health-informatics"],"latest_commit_sha":null,"homepage":"http://nuchange.ca","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dermatologist.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-03-20T01:22:40.000Z","updated_at":"2023-07-11T21:38:48.000Z","dependencies_parsed_at":"2024-10-28T08:04:43.257Z","dependency_job_id":"92958135-3caf-49d9-9d46-3928493e3a22","html_url":"https://github.com/dermatologist/cui-embed","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/dermatologist/cui-embed","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dermatologist%2Fcui-embed","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dermatologist%2Fcui-embed/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dermatologist%2Fcui-embed/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dermatologist%2Fcui-embed/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dermatologist","download_url":"https://codeload.github.com/dermatologist/cui-embed/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dermatologist%2Fcui-embed/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278165677,"owners_count":25940956,"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","status":"online","status_checked_at":"2025-10-03T02:00:06.070Z","response_time":53,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["cui","embeddings","gensim","health-informatics"],"created_at":"2024-10-06T12:21:26.689Z","updated_at":"2025-10-03T12:51:14.179Z","avatar_url":"https://github.com/dermatologist.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# cui-embed\n\n## Update 2/16/2023\n* Added support for LOINC embedding from [this repo](https://github.com/elleros/DSHealth2019_loinc_embeddings). Please cite [the paper](https://arxiv.org/abs/1907.09600) in the above repo if you use LOINC embedding.\n\nThis is a gensim wrapper for the Concept Unique Identifier (CUI) embeddings from the model presented [here](https://github.com/beamandrew/cui2vec). The paper describing the model creation is [here](https://arxiv.org/abs/1804.01486). This can be used with [pyomop](https://github.com/dermatologist/pyomop) for efficient electronic phenotyping from [OHDSI](https://www.ohdsi.org/) CDM databases.\n\nYou can use [cui-cdm](https://github.com/E-Health/cui-cdm) for mapping CUI to OHDSI OMOP concepts and [umlsjs](https://github.com/dermatologist/umlsjs) for accessing UMLS REST APIs for CUI and other terminology management.\n\n* This does not include data/model.\n* Model is downloaded on first use\n\n### Install\n\n```\npip install git+https://github.com/dermatologist/cui-embed.git\n\n```\n### Use\n\n```\n# CUI embedding\nfrom cui_embed import Cuimodel\ncm = Cuimodel('cui')\nm = cm.model()\nprint(m.most_similar_cosmul(['C0002268']))\n\n# LOINC embedding\nlm = Cuimodel('loinc')\nlm = cm.model()\nprint(lm.most_similar_cosmul(['2324-2']))\n\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdermatologist%2Fcui-embed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdermatologist%2Fcui-embed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdermatologist%2Fcui-embed/lists"}