{"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/bern2-an-advanced-neural-biomedical-named","title":"BERN2: an advanced neural biomedical named entity recognition and normalization tool","arxiv_id":"2201.02080","date":"2022-01-06","proceeding":null,"authors":["Mujeen Sung","Minbyul Jeong","Yonghwa Choi","Donghyeon Kim","Jinhyuk Lee","Jaewoo Kang"],"abstract":"In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.","url_abs":"https://arxiv.org/abs/2201.02080v3","url_pdf":"https://arxiv.org/pdf/2201.02080v3.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":"bern2-an-advanced-neural-biomedical-named","repo_url":"https://github.com/dmis-lab/bern2","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"BSD-2-Clause"}}],"tasks":[{"task_slug":"cg","task_name":"NER"},{"task_slug":"named-entity-recognition-1","task_name":"Named Entity Recognition"},{"task_slug":"named-entity-recognition-ner","task_name":"Named Entity Recognition (NER)"},{"task_slug":"graph-construction","task_name":"graph construction"},{"task_slug":"named-entity-recognition","task_name":"named-entity-recognition"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[{"leaderboard":"/sota/named-entity-recognition-on-bc2gm","task":"Named Entity Recognition (NER)","dataset":"BC2GM","model":"BERN2","rank_in_archive_order":11,"of":13,"metrics":{"F1":"83.7"},"uses_additional_data":false},{"leaderboard":"/sota/named-entity-recognition-on-bc4chemd","task":"Named Entity Recognition (NER)","dataset":"BC4CHEMD","model":"BERN2","rank_in_archive_order":3,"of":7,"metrics":{"F1":"92.8"},"uses_additional_data":false},{"leaderboard":"/sota/named-entity-recognition-on-linnaeus","task":"Named Entity Recognition (NER)","dataset":"LINNAEUS","model":"BERN2","rank_in_archive_order":6,"of":6,"metrics":{"F1":"92.7"},"uses_additional_data":false},{"leaderboard":"/sota/named-entity-recognition-ner-on-ncbi-disease","task":"Named Entity Recognition (NER)","dataset":"NCBI-disease","model":"BERN2","rank_in_archive_order":12,"of":26,"metrics":{"F1":"88.6"},"uses_additional_data":false}],"syntology":{"syntology_url":"https://syntology.ai/paper/2201.02080","atlas_url":"https://app.syntology.ai/?focus=2201.02080","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2201.02080"}},"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/dmis-lab/bern2","reach":{"status":"ok","spdx":"BSD-2-Clause"}}],"summary":{"ran_draft_wrong":2},"by_repo_kind":{"official":{"samples":2,"ran":2,"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":"7ed778480bbe602e","entry":"async_tell_inputfile","repo":"dmis-lab/bern2","repo_kind":"official","path":"bern2/bern2.py","file_url":"https://github.com/dmis-lab/bern2/blob/HEAD/bern2/bern2.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"BSD-2-Clause","inline_ok":true,"mcp_get_code":{"code_sha256":"7ed778480bbe602e"}},{"code_sha256_prefix":"171bca6004f4681e","entry":"sync_tell_inputfile","repo":"dmis-lab/bern2","repo_kind":"official","path":"bern2/bern2.py","file_url":"https://github.com/dmis-lab/bern2/blob/HEAD/bern2/bern2.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":true,"licence":"BSD-2-Clause","inline_ok":true,"mcp_get_code":{"code_sha256":"171bca6004f4681e"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}