# A Comprehensive Evaluation of Large Language Models on Benchmark Biomedical Text Processing Tasks

arXiv: https://arxiv.org/abs/2310.04270 · HTML: https://mlsanity.com/paper/2310.04270/

## Key facts

- Cited by 36 papers in the map (data through 14 Oct 2026).
- Builds on 55 of its 126 references that are in the map.
- First posted on arXiv 6 Oct 2023.

## Builds on (most cited first, 30 of 55)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [PaLM 2 Technical Report](https://mlsanity.com/paper/2305.10403/) (2023)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [A Multitask, Multilingual, Multimodal Evaluation of ChatGPT on Reasoning, Hallucination, and Interactivity](https://mlsanity.com/paper/2302.04023/) (2023)
- [A Primer in BERTology: What we know about how BERT works](https://mlsanity.com/paper/2002.12327/) (2020)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Is ChatGPT a General-Purpose Natural Language Processing Task Solver?](https://mlsanity.com/paper/2302.06476/) (2023)
- [Med-Flamingo: a Multimodal Medical Few-shot Learner](https://mlsanity.com/paper/2307.15189/) (2023)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [A Comprehensive Capability Analysis of GPT-3 and GPT-3.5 Series Models](https://mlsanity.com/paper/2303.10420/) (2023)
- [A Systematic Study and Comprehensive Evaluation of ChatGPT on Benchmark Datasets](https://mlsanity.com/paper/2305.18486/) (2023)

## Built on by (most cited first, 30 of 36)

- [A Systematic Survey and Critical Review on Evaluating Large Language Models: Challenges, Limitations, and Recommendations](https://mlsanity.com/paper/2407.04069/) (2024)
- [Tiny Titans: Can Smaller Large Language Models Punch Above Their Weight in the Real World for Meeting Summarization?](https://mlsanity.com/paper/2402.00841/) (2024)
- [ClinicalBench: Can LLMs Beat Traditional ML Models in Clinical Prediction?](https://mlsanity.com/paper/2411.06469/) (2024)
- [AfriMed-QA: A Pan-African, Multi-Specialty, Medical Question-Answering Benchmark Dataset](https://mlsanity.com/paper/2411.15640/) (2024)
- [Reading Subtext: Evaluating Large Language Models on Short Story Summarization with Writers](https://mlsanity.com/paper/2403.01061/) (2024)
- [Unveiling LLM Evaluation Focused on Metrics: Challenges and Solutions](https://mlsanity.com/paper/2404.09135/) (2024)
- [Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey](https://mlsanity.com/paper/2403.01528/) (2024)
- [A Comprehensive Survey on Evaluating Large Language Model Applications in the Medical Industry](https://mlsanity.com/paper/2404.15777/) (2024)
- [Exploring the Effectiveness of Instruction Tuning in Biomedical Language Processing](https://mlsanity.com/paper/2401.00579/) (2023)
- [Assessing and Enhancing Large Language Models in Rare Disease Question-answering](https://mlsanity.com/paper/2408.08422/) (2024)
- [Probabilistic Medical Predictions of Large Language Models](https://mlsanity.com/paper/2408.11316/) (2024)
- [BioProBench: A Corpus and Benchmark for Biological Protocol Reasoning in Autonomous Science](https://mlsanity.com/paper/2505.07889/) (2025)
- [ChemSafetyBench: Benchmarking LLM Safety on Chemistry Domain](https://mlsanity.com/paper/2411.16736/) (2024)
- [Large Language Models in the Clinic: A Comprehensive Benchmark](https://mlsanity.com/paper/2405.00716/) (2024)
- [Improving Automatic Evaluation of Large Language Models (LLMs) in Biomedical Relation Extraction via LLMs-as-the-Judge](https://mlsanity.com/paper/2506.00777/) (2025)
- [Zodiac: A Cardiologist-Level LLM Framework for Multi-Agent Diagnostics](https://mlsanity.com/paper/2410.02026/) (2024)
- [Performance Evaluation of Large Language Models in Bangla Consumer Health Query Summarization](https://mlsanity.com/paper/2505.05070/) (2025)
- [An Evaluation of Large Language Models in Bioinformatics Research](https://mlsanity.com/paper/2402.13714/) (2024)
- [RAmBLA: A Framework for Evaluating the Reliability of LLMs as Assistants in the Biomedical Domain](https://mlsanity.com/paper/2403.14578/) (2024)
- [Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review](https://mlsanity.com/paper/2403.15274/) (2024)
- [A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification](https://mlsanity.com/paper/2401.13887/) (2024)
- [Position: Beyond Assistance -- Reimagining LLMs as Ethical and Adaptive Co-Creators in Mental Health Care](https://mlsanity.com/paper/2503.16456/) (2025)
- [Ontology- and LLM-based Data Harmonization for Federated Learning in Healthcare](https://mlsanity.com/paper/2505.20020/) (2025)
- [Biomedical Entity Linking as Multiple Choice Question Answering](https://mlsanity.com/paper/2402.15189/) (2024)
- [Evaluation of Language Models in the Medical Context Under Resource-Constrained Settings](https://mlsanity.com/paper/2406.16611/) (2024)
- [EvidenceBench: A Benchmark for Extracting Evidence from Biomedical Papers](https://mlsanity.com/paper/2504.18736/) (2025)
- [Evaluating the Effectiveness of Cost-Efficient Large Language Models in Benchmark Biomedical Tasks](https://mlsanity.com/paper/2507.14045/) (2025)
- [Exploring AI-based System Design for Pixel-level Protected Health Information Detection in Medical Images](https://mlsanity.com/paper/2501.09552/) (2025)
- [Can Frontier LLMs Replace Annotators in Biomedical Text Mining? Analyzing Challenges and Exploring Solutions](https://mlsanity.com/paper/2503.03261/) (2025)
- [Classification of User Reports for Detection of Faulty Computer Components using NLP Models: A Case Study](https://mlsanity.com/paper/2503.16614/) (2025)

## Abstract (arXiv)

Recently, Large Language Models (LLM) have demonstrated impressive capability to solve a wide range of tasks. However, despite their success across various tasks, no prior work has investigated their capability in the biomedical domain yet. To this end, this paper aims to evaluate the performance of LLMs on benchmark biomedical tasks. For this purpose, we conduct a comprehensive evaluation of 4 popular LLMs in 6 diverse biomedical tasks across 26 datasets. To the best of our knowledge, this is the first work that conducts an extensive evaluation and comparison of various LLMs in the biomedical domain. Interestingly, we find based on our evaluation that in biomedical datasets that have smaller training sets, zero-shot LLMs even outperform the current state-of-the-art fine-tuned biomedical models. This suggests that pretraining on large text corpora makes LLMs quite specialized even in the biomedical domain. We also find that not a single LLM can outperform other LLMs in all tasks, with the performance of different LLMs may vary depending on the task. While their performance is still quite poor in comparison to the biomedical models that were fine-tuned on large training sets, our findings demonstrate that LLMs have the potential to be a valuable tool for various biomedical tasks that lack large annotated data.