{"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/extracting-biomolecular-interactions-using","title":"Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text","arxiv_id":"1512.01587","date":"2015-12-04","proceeding":null,"authors":["Sahil Garg","Aram Galstyan","Ulf Hermjakob","Daniel Marcu"],"abstract":"We advance the state of the art in biomolecular interaction extraction with\nthree contributions: (i) We show that deep, Abstract Meaning Representations\n(AMR) significantly improve the accuracy of a biomolecular interaction\nextraction system when compared to a baseline that relies solely on surface-\nand syntax-based features; (ii) In contrast with previous approaches that infer\nrelations on a sentence-by-sentence basis, we expand our framework to enable\nconsistent predictions over sets of sentences (documents); (iii) We further\nmodify and expand a graph kernel learning framework to enable concurrent\nexploitation of automatically induced AMR (semantic) and dependency structure\n(syntactic) representations. Our experiments show that our approach yields\ninteraction extraction systems that are more robust in environments where there\nis a significant mismatch between training and test conditions.","url_abs":"http://arxiv.org/abs/1512.01587v1","url_pdf":"http://arxiv.org/pdf/1512.01587v1.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":"extracting-biomolecular-interactions-using","repo_url":"https://github.com/sgarg87/big_mech_isi_gg","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"semantic-parsing","task_name":"Semantic Parsing"},{"task_slug":"sentence","task_name":"Sentence"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=1512.01587","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}