Abstract
Although biomedical entity linking (BioEL) has made significant progress with pre-trained language models, challenges still exist for fine-grained and long-tailed entities. To address these challenges, we present BioELQA, a novel model that treats Biomedical Entity Linking as Multiple Choice Question Answering. BioELQA first obtains candidate entities with a fast retriever, jointly presents the mention and candidate entities to a generator, and then outputs the predicted symbol associated with its chosen entity. This formulation enables explicit comparison of different candidate entities, thus capturing fine-grained interactions between mentions and entities, as well as among entities themselves. To improve generalization for long-tailed entities, we retrieve similar labeled training instances as clues and concatenate the input with retrieved instances for the generator. Extensive experimental results show that BioELQA outperforms state-of-the-art baselines on several datasets.- Anthology ID:
- 2024.lrec-main.214
- Volume:
- Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)
- Month:
- May
- Year:
- 2024
- Address:
- Torino, Italia
- Editors:
- Nicoletta Calzolari, Min-Yen Kan, Veronique Hoste, Alessandro Lenci, Sakriani Sakti, Nianwen Xue
- Venues:
- LREC | COLING
- SIG:
- Publisher:
- ELRA and ICCL
- Note:
- Pages:
- 2390–2396
- Language:
- URL:
- https://aclanthology.org/2024.lrec-main.214
- DOI:
- Cite (ACL):
- Zhenxi Lin, Ziheng Zhang, Xian Wu, and Yefeng Zheng. 2024. Biomedical Entity Linking as Multiple Choice Question Answering. In Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), pages 2390–2396, Torino, Italia. ELRA and ICCL.
- Cite (Informal):
- Biomedical Entity Linking as Multiple Choice Question Answering (Lin et al., LREC-COLING 2024)
- PDF:
- https://preview.aclanthology.org/nschneid-patch-4/2024.lrec-main.214.pdf