Anatomically-aware conformal prediction for medical image segmentation with random walks

The reliable deployment of deep learning in medical imaging requires uncertainty quantification that provides rigorous error guarantees while remaining anatomically meaningful. Conformal prediction (CP) is a powerful distribution-free framework for constructing statistically valid prediction intervals. However, standard applications in segmentation often ignore anatomical context, resulting in fragmented, spatially incoherent, and over-segmented prediction sets that limit clinical utility. To bridge this gap, this paper proposes Random-Walk Conformal Prediction (RW-CP), a model-agnostic framework which can be added on top of any segmentation method. RW-CP enforces spatial coherence to generate anatomically valid sets. Our method constructs a k-nearest neighbour graph from pre-trained vision foundation model features and applies a random walk to diffuse uncertainty. The random walk diffusion regularizes the non-conformity scores, making the prediction sets less sensitive to the conformal calibration parameter $λ$, ensuring more stable and continuous anatomical boundaries. RW-CP maintains rigorous marginal coverage while significantly improving segmentation quality. Evaluations on multi-modal public datasets show improvements of up to $35.4\%$ compared to standard CP baselines, given an allowable error rate of $α=0.1$.