Different Questions, Different Models: Fine-Grained Evaluation of Uncertainty and Calibration in Clinical QA with LLMs

Accurate and well-calibrated uncertainty estimates are essential for deploying large language models (LLMs) in high-stakes domains such as clinical decision support. We present a fine-grained evaluation of uncertainty estimation methods for clinical multiple-choice question answering, covering ten open-source LLMs (general-purpose, biomedical, and reasoning models) across two datasets, eleven medical specialties, and six question types. We compare standard single-generation and sampling-based methods, and present a case study exploring simple, single-pass estimators based on behavioral signals in reasoning traces. These lightweight methods approach the performance of Semantic Entropy while requiring only one generation. Our results reveal substantial variation across specialties and question types, underscoring the importance of selecting models based on both the nature of the question and model-specific strengths.