Guiding Clinical Reasoning with Large Language Models via Knowledge Seeds
Open accessAbstract
Clinical reasoning refers to the cognitive process that physicians employ in evaluating and managing patients. This process typically involves suggesting necessary examinations, diagnosing patients’ diseases, and selecting appropriate therapies, etc. Accurate clinical reasoning requires extensive medical knowledge and rich clinical experience, setting a high bar for physicians. This is particularly challenging in developing countries due to the overwhelming number of patients and limited physician resources, contributing significantly to global health inequity and necessitating automated clinical reasoning approaches. Recently, the emergence of large language models (LLMs) such as ChatGPT and GPT-4 have demonstrated their potential in clinical reasoning. However, these LLMs are prone to hallucination problems, and the reasoning process of LLMs may not align with the clinical decision pathways of physicians. In this study, we introduce a novel framework, In-Context Padding (ICP), to enhance LLMs reasoning with medical knowledge. Specifically, we infer critical clinical reasoning elements (referred to as knowledge seeds) and use these as anchors to guide the generation process of LLMs. Experiments on two clinical question datasets validate that ICP significantly improves the clinical reasoning ability of LLMs.
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Advanced LLMs often rely on general domain datasets and lack exposure to real-world EHR notes, which limits their effectiveness in clinical settings.
“Furthermore, due to data access and privacy concerns34, advanced LLMs often rely on general domain datasets and lack exposure to real-world EHR notes, which limits their effectiveness in clinical settings24,36.”
From Probabilistic medical predictions of large language models (2024) · cites this paper as [36]
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- Isaac A Bernstein, Youchen Victor Zhang, et al. Comparison of ophthalmologist and large language model chatbot responses to online patient eye care questions. JAMA Network Open, 6(8):e2330320- e2330320, 2023.
- Maciej Besta, Nils Blach, et al. Graph of thoughts: Solving elaborate problems with large language models. arXiv preprint arXiv:2308.09687, 2023. · arXiv
- Yanjun Gao, Ruizhe Li, John Caskey, Dmitriy Dligach, Timothy Miller, Matthew M Churpek, and Majid Afshar. Leveraging a medical knowledge graph into large language models for diagnosis prediction. arXiv preprint arXiv:2308.14321, 2023. · arXiv
- Peter Lee, Sebastien Bubeck, and Joseph Petro. Benefits, limits, and risks of gpt-4 as an ai chat- bot for medicine. New England Journal of Medicine, 388(13):1233-1239, 2023.
- Chin-Yew Lin. Rouge: A package for automatic evaluation of summaries. In Text summarization branches out, pages 74-81, 2004.
- Fenglin Liu, Xian Wu, Shen Ge, Wei Fan, and Yuexian Zou. Exploring and distilling posterior and prior knowledge for radiology report generation. In Pro- ceedings of the IEEE/CVF conference on computer vision and pattern recognition, pages 13753-13762, 2021.
- Liu et al., 2024] Xiaocong Liu, Jiageng Wu, and et al. Un- covering language disparity of chatgpt on retinal vascular disease classification: Cross-sectional study. Journal of Medical Internet Research, 26:e51926, 2024.
- Qing Lyu, Josh Tan, Mike E Zapadka, Janardhana Ponnatapuram, Chuang Niu, Ge Wang, and Christopher T Whitlow. Translating radiology reports into plain language using chatgpt and gpt-4 with prompt learn- ing: Promising results, limitations, and potential. arXiv preprint arXiv:2303.09038, 2023. · arXiv
- Erwin B Montgomery Jr. Medical reasoning: the nature and use of medical knowledge. Ox- ford University Press, 2018.
- Ashwin Nayak, Matthew S Alkaitis, Kristen Nayak, Margaret Nikolov, Kevin P Weinfurt, and Kevin Schulman. Comparison of history of present ill- ness summaries generated by a chatbot and senior in- ternal medicine residents. JAMA Internal Medicine, 183(9):1026-1027, 2023.
- Kishore Papineni, Salim Roukos, Todd Ward, and Wei-Jing Zhu. Bleu: a method for au- tomatic evaluation of machine translation. In Proceedings of the 40th annual meeting of the Association for Compu- tational Linguistics, pages 311-318, 2002.
- Colin Raffel, Noam Shazeer, and others J. Exploring the limits of transfer learning with a unified text-to-text transformer. The Journal of Machine Learning Research, 21(1):5485-5551, 2020.
- Karan Singhal, Shekoofeh Azizi, Tao Tu, S Sara Mahdavi, Jason Wei, Hyung Won Chung, Nathan Scales, Ajay Tanwani, Heather Cole-Lewis, Stephen Pfohl, et al. Large language models encode clini- cal knowledge. Nature, 620(7972):172-180, 2023.
- Touvron et al., 2023] Hugo Touvron, Thibaut Lavril, and et al. Llama: Open and efficient foundation language mod- els. arXiv preprint arXiv:2302.13971, 2023. · arXiv
- Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin. Attention is all you need. Advances in neural information processing systems, 30, 2017.
- Wu et al., 2024a] Jiageng Wu, Xiaocong Liu, and et al. Clinical text datasets for medical artificial intelligence and large language models-a systematic review. NEJM AI, page AIra2400012, 2024.
- Wu et al., 2024b] Jiageng Wu, Xian Wu, and et al. Large language models leverage external knowledge to extend clinical insight beyond language boundaries. Journal of the American Medical Informatics Association, page ocae079, 2024.
- Meredith Young, Aliki Thomas, Stu- art Lubarsky, Tiffany Ballard, David Gordon, Larry D Gruppen, Eric Holmboe, Temple Ratcliffe, Joseph Rencic, Lambert Schuwirth, et al. Drawing boundaries: the diffi- culty in defining clinical reasoning. Academic Medicine, 93(7):990-995, 2018.
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Self-citation
- Authors
- Wu, J., Wu, X., & Yang, J.
- Affiliations
- Zhejiang University, Hangzhou, China
- Tencent Youtu Lab, Jarvis Research Center, Beijing, China
- Brigham and Women's Hospital (US)
- Venue
- Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence
- Published
- 2024-08
- Pages
- 7491-7499
- OpenAlex
- W4401024268
- Cited by
- 7
- References
- 0
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 3
- FWCI
- 1.88
- Type
- conference paper
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- International Joint Conference on Artificial Intelligence (publishedVersion)
- arXiv (Cornell University) (submittedVersion, cc-by)
- arXiv (Cornell University) (cc-by)
- Topics
- Health Sciences › Medicine › Health Informatics › Artificial Intelligence in Healthcare and Education
- Physical Sciences › Computer Science › Artificial Intelligence › Machine Learning in Healthcare
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Multimodal Machine Learning Applications
- Keywords
- clinical reasoning, large language models, hallucination mitigation, medical question answering, clinical decision support
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