{"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/improving-biomedical-entity-linking-with","title":"Improving Biomedical Entity Linking with Retrieval-enhanced Learning","arxiv_id":"2312.09806","date":"2023-12-15","proceeding":null,"authors":["Zhenxi Lin","Ziheng Zhang","Xian Wu","Yefeng Zheng"],"abstract":"Biomedical entity linking (BioEL) has achieved remarkable progress with the help of pre-trained language models. However, existing BioEL methods usually struggle to handle rare and difficult entities due to long-tailed distribution. To address this limitation, we introduce a new scheme $k$NN-BioEL, which provides a BioEL model with the ability to reference similar instances from the entire training corpus as clues for prediction, thus improving the generalization capabilities. Moreover, we design a contrastive learning objective with dynamic hard negative sampling (DHNS) that improves the quality of the retrieved neighbors during inference. Extensive experimental results show that $k$NN-BioEL outperforms state-of-the-art baselines on several datasets.","url_abs":"https://arxiv.org/abs/2312.09806v1","url_pdf":"https://arxiv.org/pdf/2312.09806v1.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":"improving-biomedical-entity-linking-with","repo_url":"https://github.com/lzxlin/knn-bioel","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"contrastive-learning","task_name":"Contrastive Learning"},{"task_slug":"entity-linking","task_name":"Entity Linking"},{"task_slug":"retrieval","task_name":"Retrieval"}],"methods":[{"method_slug":"contrastive-learning","method_name":"Contrastive Learning"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}