Decouple, Purify and Unite: Semantic-Structural Prototype Learning for Federated Medical Segmentation

Federated learning (FL) is severely hindered by statistical heterogeneity due to variations in scanners, acquisition protocols, and patient populations. Such non-IID data induces client drift during local optimization, leading to unstable convergence and suboptimal global models when parameter-based aggregation is applied. We propose a prototype-based, influence-aware federated learning framework (FedProIn) that uses multiple learnable class prototypes to capture shared semantic structures across heterogeneous clients. We introduce feature divergence loss and prototype contrastive loss to mitigate client drift by decomposing it into feature drift and prototype drift. In addition, we propose a normalized influence aggregation strategy that adaptively weights client prototypes according to their contribution to the global representation, reducing the impact of biased or low-quality updates. Experimental results on two publicly available medical datasets, HAM10000 and Matek-19, demonstrate that FedProIn achieves accuracies of (83.5% IID, 81.1% non-IID) on HAM10000 and (96.2% IID, 95.8% non-IID) on Matek-19, respectively, outperforming existing baselines in both conditions. Our code is available at https://github.com/harsh-kmr/FedProIn.

Purpose: Developing generalizable medical image segmentation models is challenging because imaging data are distributed across institutions and differ in modality and acquisition protocol. Federated learning (FL) enables collaborative training without centralizing raw medical images, but cross-modality domain shifts between computed tomography (CT) and magnetic resonance imaging (MRI) can substantially reduce model performance. This study investigates augmentation-driven cross-modality FL for abdominal organ and whole-heart segmentation. Methods: We evaluate convolution-based spatial augmentation, frequency-domain argumentation, domain-specific normalization, and global intensity nonlinear (GIN) augmentation for multimodal segmentation. Abdominal organ segmentation and whole-heart segmentation are first evaluated using a 2D U-Net framework. For whole-heart segmentation, we additionally perform native 3D experiments using a self-configuring nnU-Net architecture on the CARE-WHS 2026 dataset, enabling evaluation of whether the observed cross-modality FL behavior persists when moving from slice-based 2D segmentation to volumetric 3D segmentation. Results: GIN provides the most consistent cross-modality performance among the evaluated approaches in the original 2D experiments. For pancreas segmentation, the Dice similarity coefficient (DSC) improved from 0.073 to 0.437 when CT data were incorporated through federated cross-modality training. In 3D whole-heart segmentation, FedGIN improved mean DSC over FedAvg from 0.8696 to 0.8901 on the unseen CT center and from 0.7160 to 0.7956 on the unseen MRI center. Relative to centralized GIN training, FedGIN retained 92.4% of performance on unseen CT data and achieved comparable performance on unseen MRI data (0.7956 versus 0.7937).

Learning discriminative visual representations from distributed, heterogeneous data is a fundamental challenge in Federated Learning (FL). Prototype-based methods address statistical heterogeneity by sharing class-level representations across clients but create a distance-dependent gradient pressure that is particularly severe during early training rounds: alignment pressure applied to immature global prototypes, aggregated from noisy local representations, generates large gradients that suppress the emergence of local discriminative structure. The result is a poorly organized embedding space and degraded recognition performance, particularly under severe non-IID conditions. We propose FedSAP, a framework that stabilises federated representation learning through two complementary mechanisms: a deterministic alignment curriculum that delays global alignment until local representations become stable and a geometry-driven proxy separation loss that enforces inter-class structure on the unit hypersphere using the existing prototype bank without introducing additional parameters or communication overhead. Together, these mechanisms produce compact, well-separated class clusters without altering the underlying communication protocol between federation's participants. Experiments across three benchmarks and varying degrees of heterogeneity show gains of up to 4 percentage points over the prototype-based baselines evaluated, with improvements most pronounced under high heterogeneity. The representational nature of our framework further enables a straightforward extension to semi-supervised settings, where unlabelled data is incorporated with minimal modification, underscoring the generality of scheduled alignment as a design principle.