@inproceedings{lin-etal-2024-biomedical-entity,
title = "Biomedical Entity Linking as Multiple Choice Question Answering",
author = "Lin, Zhenxi and
Zhang, Ziheng and
Wu, Xian and
Zheng, Yefeng",
editor = "Calzolari, Nicoletta and
Kan, Min-Yen and
Hoste, Veronique and
Lenci, Alessandro and
Sakti, Sakriani and
Xue, Nianwen",
booktitle = "Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)",
month = may,
year = "2024",
address = "Torino, Italia",
publisher = "ELRA and ICCL",
url = "https://aclanthology.org/2024.lrec-main.214",
pages = "2390--2396",
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.",
}
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<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.</abstract>
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%0 Conference Proceedings
%T Biomedical Entity Linking as Multiple Choice Question Answering
%A Lin, Zhenxi
%A Zhang, Ziheng
%A Wu, Xian
%A Zheng, Yefeng
%Y Calzolari, Nicoletta
%Y Kan, Min-Yen
%Y Hoste, Veronique
%Y Lenci, Alessandro
%Y Sakti, Sakriani
%Y Xue, Nianwen
%S Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)
%D 2024
%8 May
%I ELRA and ICCL
%C Torino, Italia
%F lin-etal-2024-biomedical-entity
%X 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.
%U https://aclanthology.org/2024.lrec-main.214
%P 2390-2396
Markdown (Informal)
[Biomedical Entity Linking as Multiple Choice Question Answering](https://aclanthology.org/2024.lrec-main.214) (Lin et al., LREC-COLING 2024)
ACL