{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/multi-domain-clinical-natural-language","title":"Multi-domain Clinical Natural Language Processing with MedCAT: the Medical Concept Annotation Toolkit","arxiv_id":"2010.01165","date":"2020-10-02","proceeding":null,"authors":["Zeljko Kraljevic","Thomas Searle","Anthony Shek","Lukasz Roguski","Kawsar Noor","Daniel Bean","Aurelie Mascio","Leilei Zhu","Amos A Folarin","Angus Roberts","Rebecca Bendayan","Mark P Richardson","Robert Stewart","Anoop D Shah","Wai Keong Wong","Zina Ibrahim","James T Teo","Richard JB Dobson"],"abstract":"Electronic health records (EHR) contain large volumes of unstructured text, requiring the application of Information Extraction (IE) technologies to enable clinical analysis. We present the open-source Medical Concept Annotation Toolkit (MedCAT) that provides: a) a novel self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT; b) a feature-rich annotation interface for customising and training IE models; and c) integrations to the broader CogStack ecosystem for vendor-agnostic health system deployment. We show improved performance in extracting UMLS concepts from open datasets (F1:0.448-0.738 vs 0.429-0.650). Further real-world validation demonstrates SNOMED-CT extraction at 3 large London hospitals with self-supervised training over ~8.8B words from ~17M clinical records and further fine-tuning with ~6K clinician annotated examples. We show strong transferability (F1 > 0.94) between hospitals, datasets, and concept types indicating cross-domain EHR-agnostic utility for accelerated clinical and research use cases.","url_abs":"https://arxiv.org/abs/2010.01165v2","url_pdf":"https://arxiv.org/pdf/2010.01165v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"multi-domain-clinical-natural-language","repo_url":"https://github.com/CogStack/MedCAT","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2010.01165","atlas_url":"https://app.syntology.ai/?focus=2010.01165","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2010.01165"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/CogStack/MedCAT","reach":null}],"summary":{"ran_draft_wrong":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"5723803d0a82274b","entry":"get_fixed_meta_cat_data","repo":"CogStack/MedCAT","repo_kind":"official","path":"tests/test_cat.py","file_url":"https://github.com/CogStack/MedCAT/blob/HEAD/tests/test_cat.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"5723803d0a82274b"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}