{"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/negbio-a-high-performance-tool-for-negation","title":"NegBio: a high-performance tool for negation and uncertainty detection in radiology reports","arxiv_id":"1712.05898","date":"2017-12-16","proceeding":null,"authors":["Yifan Peng","Xiaosong Wang","Le Lu","Mohammadhadi Bagheri","Ronald Summers","Zhiyong Lu"],"abstract":"Negative and uncertain medical findings are frequent in radiology reports,\nbut discriminating them from positive findings remains challenging for\ninformation extraction. Here, we propose a new algorithm, NegBio, to detect\nnegative and uncertain findings in radiology reports. Unlike previous\nrule-based methods, NegBio utilizes patterns on universal dependencies to\nidentify the scope of triggers that are indicative of negation or uncertainty.\nWe evaluated NegBio on four datasets, including two public benchmarking corpora\nof radiology reports, a new radiology corpus that we annotated for this work,\nand a public corpus of general clinical texts. Evaluation on these datasets\ndemonstrates that NegBio is highly accurate for detecting negative and\nuncertain findings and compares favorably to a widely-used state-of-the-art\nsystem NegEx (an average of 9.5% improvement in precision and 5.1% in\nF1-score).","url_abs":"http://arxiv.org/abs/1712.05898v2","url_pdf":"http://arxiv.org/pdf/1712.05898v2.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":"negbio-a-high-performance-tool-for-negation","repo_url":"https://github.com/ncbi-nlp/NegBio","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"negation","task_name":"Negation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=1712.05898","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"1712.05898"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+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/ncbi-nlp/NegBio","reach":null}],"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":2,"samples":[{"code_sha256_prefix":"dca18b90e8ef9e7a","entry":"get_absolute_path","repo":"ncbi-nlp/NegBio","repo_kind":"official","path":"negbio/cli_utils.py","file_url":"https://github.com/ncbi-nlp/NegBio/blob/HEAD/negbio/cli_utils.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":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"dca18b90e8ef9e7a"}},{"code_sha256_prefix":"7bb3643e2f4c8af6","entry":"get_args","repo":"ncbi-nlp/NegBio","repo_kind":"official","path":"negbio/cli_utils.py","file_url":"https://github.com/ncbi-nlp/NegBio/blob/HEAD/negbio/cli_utils.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":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"7bb3643e2f4c8af6"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}