Federated Semi-Supervised Graph Neural Networks with Prototype-Guided Pseudo-Labeling for Privacy-Preserving Gestational Diabetes Mellitus Prediction

Graph neural networks (GNNs) achieve strong performance on relational data, but real-world graphs are often distributed across organizations that cannot share raw data due to privacy and policy constraints. Existing federated GNN methods either ignore cross-client links, leading to degraded accuracy, or require frequent embedding exchanges, incurring substantial communication and privacy costs. We propose CE-FedGNN, a communication-efficient and privacy-preserving federated GNN framework for learning over such coupled graphs. Our approach avoids sharing raw data or per-round embeddings by infrequently exchanging aggregated node representations. To handle cross-client dependency and staleness, we introduce a moving-average estimator that continuously tracks node representations and enables their stable reuse across rounds. To provide formal privacy guarantees for the released representations, we adopt the metric differential privacy (metric-DP) framework, which measures privacy with respect to distances in the learned embedding space rather than worst-case input perturbations. This yields meaningful guarantees at noise levels where standard differential privacy becomes overly conservative. We establish convergence to a stationary point at a rate of $O(1/\sqrt{T})$ with $O(T^{3/4})$ communication complexity. In addition, we derive $(\varepsilon,δ)$-metric-DP guarantees via Rényi differential privacy composition under a public-cohort threat model. Experiments on synthetic interbank anti-money laundering benchmarks and citation networks demonstrate that CE-FedGNN achieves strong performance while significantly reducing communication and maintaining robustness under privacy-preserving noise.

Federated learning (FL) offers a promising approach to privacy-preserving clinical risk prediction, but its deployment remains limited by restricted data sharing, client heterogeneity, class imbalance, and the lack of realistic tabular electronic health record (EHR) benchmarks. Synthetic data generation may alleviate data scarcity, yet its integration with federated optimisation has received limited systematic study. We propose SynPre-FL, a unified framework combining high-fidelity synthetic EHR generation with synthetic-pretrained FL for robust prediction under non-IID conditions. A latent autoencoder-diffusion model generates privacy-preserving synthetic cohorts, which are used to warm-start federated training. This pretraining is followed by heterogeneity-aware optimisation using class-balanced local objectives, proximal regularisation, and adaptive server aggregation. Post-hoc calibration and federated-safe explainability support reliable and interpretable risk estimates. Experiments show that the synthetic generator preserves univariate, bivariate, and multivariate structure while protecting against membership-inference and reconstruction attacks. The generated data achieve strong downstream utility under TSTR, TRTS, and model-based evaluations. Across federated settings with 5, 10, and 15 heterogeneous clients, SynPre-FL consistently improves robustness and scalability over baseline methods, especially under severe non-IID fragmentation. Calibration improves probability reliability, while SHAP analysis produces stable and clinically coherent feature attributions across federation sizes. SynPre-FL therefore provides a practical and reproducible framework for combining synthetic data with FL to enable privacy-aware, interpretable, and robust clinical prediction from distributed tabular EHR data.

Protecting sensitive health data while enabling collaborative analysis is a central challenge in healthcare. Traditional machine learning (ML) requires institutions to pool anonymized patient records, centralizing analytical development and privacy risks at a single site. Privacy-enhancing technologies (PETs), including Differential Privacy (DP) and Homomorphic Encryption (HE), can mitigate these risks. However, they are mainly studied in conventional data-sharing settings and often introduce trade-offs, including reduced model utility, higher computational cost, and increased implementation complexity. Federated Learning (FL) reduces data centralization by enabling institutions to train models locally and share only model updates. Nevertheless, FL does not eliminate privacy risks, as shared parameters or gradients may still reveal sensitive information. Integrating DP or HE into FL can strengthen privacy guarantees, yet their comparative performance and deployment implications in real-world healthcare settings remain unclear. We systematically evaluated DP and HE integration in FL under real-world conditions, comparing them with standard FL and centralized ML (cML) to quantify privacy-utility trade-offs in multi-institutional settings. Using nationwide Swedish healthcare data, we evaluated cardiovascular disease risk prediction using logistic regression (LR) and neural network (NN) learners. FL with HE achieved performance comparable to cML but introduced measurable cryptographic overhead, particularly in the NN implementation. FL with DP incurred lower computational cost; however, LR was more sensitive to calibrated noise than the NN, resulting in greater performance degradation. Our findings provide practical guidance for deploying privacy-preserving FL in fragmented healthcare systems.