@inproceedings{laskar-etal-2025-improving,
title = "Improving Automatic Evaluation of Large Language Models ({LLM}s) in Biomedical Relation Extraction via {LLM}s-as-the-Judge",
author = "Laskar, Md Tahmid Rahman and
Jahan, Israt and
Dolatabadi, Elham and
Peng, Chun and
Hoque, Enamul and
Huang, Jimmy",
editor = "Che, Wanxiang and
Nabende, Joyce and
Shutova, Ekaterina and
Pilehvar, Mohammad Taher",
booktitle = "Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)",
month = jul,
year = "2025",
address = "Vienna, Austria",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2025.acl-long.1238/",
doi = "10.18653/v1/2025.acl-long.1238",
pages = "25483--25497",
ISBN = "979-8-89176-251-0",
abstract = "Large Language Models (LLMs) have demonstrated impressive performance in biomedical relation extraction, even in zero-shot scenarios. However, evaluating LLMs in this task remains challenging due to their ability to generate human-like text, often producing synonyms or abbreviations of gold-standard answers, making traditional automatic evaluation metrics unreliable. On the other hand, while human evaluation is more reliable, it is costly and time-consuming, making it impractical for real-world applications. This paper investigates the use of LLMs-as-the-Judge as an alternative evaluation method for biomedical relation extraction. We benchmark 8 LLMs as judges to evaluate the responses generated by 5 other LLMs across 3 biomedical relation extraction datasets. Unlike other text-generation tasks, we observe that LLM-based judges perform quite poorly (usually below 50{\%} accuracy) in the biomedical relation extraction task. Our findings reveal that it happens mainly because relations extracted by LLMs do not adhere to any standard format. To address this, we propose structured output formatting for LLM-generated responses that helps LLM-Judges to improve their performance by about 15{\%} (on average). We also introduce a domain adaptation technique to further enhance LLM-Judge performance by effectively transferring knowledge between datasets. We release both our human-annotated and LLM-annotated judgment data (36k samples in total) for public use here: https://github.com/tahmedge/llm{\_}judge{\_}biomedical{\_}re."
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<abstract>Large Language Models (LLMs) have demonstrated impressive performance in biomedical relation extraction, even in zero-shot scenarios. However, evaluating LLMs in this task remains challenging due to their ability to generate human-like text, often producing synonyms or abbreviations of gold-standard answers, making traditional automatic evaluation metrics unreliable. On the other hand, while human evaluation is more reliable, it is costly and time-consuming, making it impractical for real-world applications. This paper investigates the use of LLMs-as-the-Judge as an alternative evaluation method for biomedical relation extraction. We benchmark 8 LLMs as judges to evaluate the responses generated by 5 other LLMs across 3 biomedical relation extraction datasets. Unlike other text-generation tasks, we observe that LLM-based judges perform quite poorly (usually below 50% accuracy) in the biomedical relation extraction task. Our findings reveal that it happens mainly because relations extracted by LLMs do not adhere to any standard format. To address this, we propose structured output formatting for LLM-generated responses that helps LLM-Judges to improve their performance by about 15% (on average). We also introduce a domain adaptation technique to further enhance LLM-Judge performance by effectively transferring knowledge between datasets. We release both our human-annotated and LLM-annotated judgment data (36k samples in total) for public use here: https://github.com/tahmedge/llm_judge_biomedical_re.</abstract>
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%0 Conference Proceedings
%T Improving Automatic Evaluation of Large Language Models (LLMs) in Biomedical Relation Extraction via LLMs-as-the-Judge
%A Laskar, Md Tahmid Rahman
%A Jahan, Israt
%A Dolatabadi, Elham
%A Peng, Chun
%A Hoque, Enamul
%A Huang, Jimmy
%Y Che, Wanxiang
%Y Nabende, Joyce
%Y Shutova, Ekaterina
%Y Pilehvar, Mohammad Taher
%S Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)
%D 2025
%8 July
%I Association for Computational Linguistics
%C Vienna, Austria
%@ 979-8-89176-251-0
%F laskar-etal-2025-improving
%X Large Language Models (LLMs) have demonstrated impressive performance in biomedical relation extraction, even in zero-shot scenarios. However, evaluating LLMs in this task remains challenging due to their ability to generate human-like text, often producing synonyms or abbreviations of gold-standard answers, making traditional automatic evaluation metrics unreliable. On the other hand, while human evaluation is more reliable, it is costly and time-consuming, making it impractical for real-world applications. This paper investigates the use of LLMs-as-the-Judge as an alternative evaluation method for biomedical relation extraction. We benchmark 8 LLMs as judges to evaluate the responses generated by 5 other LLMs across 3 biomedical relation extraction datasets. Unlike other text-generation tasks, we observe that LLM-based judges perform quite poorly (usually below 50% accuracy) in the biomedical relation extraction task. Our findings reveal that it happens mainly because relations extracted by LLMs do not adhere to any standard format. To address this, we propose structured output formatting for LLM-generated responses that helps LLM-Judges to improve their performance by about 15% (on average). We also introduce a domain adaptation technique to further enhance LLM-Judge performance by effectively transferring knowledge between datasets. We release both our human-annotated and LLM-annotated judgment data (36k samples in total) for public use here: https://github.com/tahmedge/llm_judge_biomedical_re.
%R 10.18653/v1/2025.acl-long.1238
%U https://aclanthology.org/2025.acl-long.1238/
%U https://doi.org/10.18653/v1/2025.acl-long.1238
%P 25483-25497
Markdown (Informal)
[Improving Automatic Evaluation of Large Language Models (LLMs) in Biomedical Relation Extraction via LLMs-as-the-Judge](https://aclanthology.org/2025.acl-long.1238/) (Laskar et al., ACL 2025)
ACL