{"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/enhancing-biomedical-relation-extraction-with-1","title":"Enhancing Biomedical Relation Extraction with Directionality","arxiv_id":"2501.14079","date":"2025-01-23","proceeding":null,"authors":["Po-Ting Lai","Chih-Hsuan Wei","Shubo Tian","Robert Leaman","Zhiyong Lu"],"abstract":"Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, proteins, diseases, and chemicals. The vast growth of biomedical literature poses significant challenges updating the network knowledge. The recent Biomedical Relation Extraction Dataset (BioRED) provides valuable manual annotations, facilitating the develop-ment of machine-learning and pre-trained language model approaches for automatically identifying novel document-level (inter-sentence context) relationships. Nonetheless, its annotations lack directionality (subject/object) for the entity roles, essential for studying complex biological networks. Herein we annotate the entity roles of the relationships in the BioRED corpus and subsequently propose a novel multi-task language model with soft-prompt learning to jointly identify the relationship, novel findings, and entity roles. Our results in-clude an enriched BioRED corpus with 10,864 directionality annotations. Moreover, our proposed method outperforms existing large language models such as the state-of-the-art GPT-4 and Llama-3 on two benchmarking tasks. Our source code and dataset are available at https://github.com/ncbi-nlp/BioREDirect.","url_abs":"https://arxiv.org/abs/2501.14079v1","url_pdf":"https://arxiv.org/pdf/2501.14079v1.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":"enhancing-biomedical-relation-extraction-with-1","repo_url":"https://github.com/ncbi-nlp/bioredirect","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"document-level-relation-extraction","task_name":"Document-level Relation Extraction"},{"task_slug":"language-modeling","task_name":"Language Modeling"},{"task_slug":"language-modelling","task_name":"Language Modelling"},{"task_slug":"prompt-learning","task_name":"Prompt Learning"},{"task_slug":null,"task_name":"Relation"},{"task_slug":"relation-extraction","task_name":"Relation Extraction"},{"task_slug":"sentence","task_name":"Sentence"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"gpt-4","method_name":"GPT-4"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"}],"datasets_introduced":[{"slug":"bc8","name":"Bc8","full_name":"Bc8BioRED"}],"methods_introduced":[],"results":[{"leaderboard":"/sota/document-level-relation-extraction-on-bc8","task":"Document-level Relation Extraction","dataset":"Bc8","model":"BioRex+Directionality","rank_in_archive_order":1,"of":1,"metrics":{"Evaluation Macro F1":"56.06"},"uses_additional_data":true}],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}