# Dissecting Clinical Reasoning in Language Models: A Comparative Study of Prompts and Model Adaptation Strategies

arXiv: https://arxiv.org/abs/2507.04142 · HTML: https://mlsanity.com/paper/2507.04142/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 16 of its 31 references that are in the map.
- First posted on arXiv 5 Jul 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 16 of 16)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Qwen2 Technical Report](https://mlsanity.com/paper/2407.10671/) (2024)
- [Measuring and Narrowing the Compositionality Gap in Language Models](https://mlsanity.com/paper/2210.03350/) (2022)
- [Automatic Chain of Thought Prompting in Large Language Models](https://mlsanity.com/paper/2210.03493/) (2022)
- [Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine](https://mlsanity.com/paper/2311.16452/) (2023)
- [To CoT or not to CoT? Chain-of-thought helps mainly on math and symbolic reasoning](https://mlsanity.com/paper/2409.12183/) (2024)
- [Beyond Accuracy: Evaluating the Reasoning Behavior of Large Language Models -- A Survey](https://mlsanity.com/paper/2404.01869/) (2024)
- [Phi-4-Mini-Reasoning: Exploring the Limits of Small Reasoning Language Models in Math](https://mlsanity.com/paper/2504.21233/) (2025)
- [Benchmarking Reasoning Robustness in Large Language Models](https://mlsanity.com/paper/2503.04550/) (2025)
- [Improving Chain-of-Thought Reasoning via Quasi-Symbolic Abstractions](https://mlsanity.com/paper/2502.12616/) (2025)
- [ThinkPatterns-21k: A Systematic Study on the Impact of Thinking Patterns in LLMs](https://mlsanity.com/paper/2503.12918/) (2025)
- [Large Language and Reasoning Models are Shallow Disjunctive Reasoners](https://mlsanity.com/paper/2503.23487/) (2025)

## Abstract (arXiv)

Recent works on large language models (LLMs) have demonstrated the impact of prompting strategies and fine-tuning techniques on their reasoning capabilities. Yet, their effectiveness on clinical natural language inference (NLI) remains underexplored. This study presents the first controlled evaluation of how prompt structure and efficient fine-tuning jointly shape model performance in clinical NLI. We inspect four classes of prompting strategies to elicit reasoning in LLMs at different levels of abstraction, and evaluate their impact on a range of clinically motivated reasoning types. For each prompting strategy, we construct high-quality demonstrations using a frontier model to distil multi-step reasoning capabilities into smaller models (4B parameters) via Low-Rank Adaptation (LoRA). Across different language models fine-tuned on the NLI4CT benchmark, we found that prompt type alone accounts for up to 44% of the variance in macro-F1. Moreover, LoRA fine-tuning yields consistent gains of +8 to 12 F1, raises output alignment above 97%, and narrows the performance gap to GPT-4o-mini to within 7.1%. Additional experiments on reasoning generalisation reveal that LoRA improves performance in 75% of the models on MedNLI and TREC Clinical Trials Track. Overall, these findings demonstrate that (i) prompt structure is a primary driver of clinical reasoning performance, (ii) compact models equipped with strong prompts and LoRA can rival frontier-scale systems, and (iii) reasoning-type-aware evaluation is essential to uncover prompt-induced trade-offs. Our results highlight the promise of combining prompt design and lightweight adaptation for more efficient and trustworthy clinical NLP systems, providing insights on the strengths and limitations of widely adopted prompting and parameter-efficient techniques in highly specialised domains.