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.

Large Language Models (LLMs) have recently gained significant attention due to their remarkable capabilities in performing diverse tasks across various domains. However, a thorough evaluation of these models is crucial before deploying them in real-world applications to ensure they produce reliable performance. Despite the well-established importance of evaluating LLMs in the community, the complexity of the evaluation process has led to varied evaluation setups, causing inconsistencies in findings and interpretations. To address this, we systematically review the primary challenges and limitations causing these inconsistencies and unreliable evaluations in various steps of LLM evaluation. Based on our critical review, we present our perspectives and recommendations to ensure LLM evaluations are reproducible, reliable, and robust.

ChatGPT is a large language model developed by OpenAI. Despite its impressive performance across various tasks, no prior work has investigated its capability in the biomedical domain yet. To this end, this paper aims to evaluate the performance of ChatGPT on various benchmark biomedical tasks, such as relation extraction, document classification, question answering, and summarization. To the best of our knowledge, this is the first work that conducts an extensive evaluation of ChatGPT in the biomedical domain. Interestingly, we find based on our evaluation that in biomedical datasets that have smaller training sets, zero-shot ChatGPT even outperforms the state-of-the-art fine-tuned generative transformer models, such as BioGPT and BioBART. This suggests that ChatGPT’s pre-training on large text corpora makes it quite specialized even in the biomedical domain. Our findings demonstrate that ChatGPT has the potential to be a valuable tool for various tasks in the biomedical domain that lack large annotated data.

Debatepedia is a publicly available dataset consisting of arguments and counter-arguments on controversial topics that has been widely used for the single-document query-focused abstractive summarization task in recent years. However, it has been recently found that this dataset is limited by noise and even most queries in this dataset do not have any relevance to the respective document. In this paper, we study whether large language models (LLMs) can be utilized to clean the Debatepedia dataset to make it suitable for query-focused abstractive summarization. More specifically, we harness the language generation capabilities of two LLMs, namely, ChatGPT and PaLM to regenerate its queries. Based on our experiments, we find that solely depending on large language models for query correction may not be very useful for data cleaning. However, we observe that leveraging a rule-based approach for data sampling followed by query regeneration using LLMs (especially ChatGPT) for the sampled instances may ensure a higher quality version of this dataset suitable for the development of more generalized query-focused text summarization models.