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This paper introduces FedTGNN-SS, a federated semi-supervised framework designed to address label scarcity and privacy constraints in predicting gestational diabetes using electronic health records. By combining prototype-guided pseudo-labeling with adaptive graph refinement, the method effectively leverages unlabeled data across hospital silos while exchanging only class-level centroids to preserve patient privacy. The approach demonstrates significant performance gains over existing baselines under extreme data scarcity conditions, offering a viable pathway for deploying robust clinical AI models without compromising data sovereignty.
Federated Semi-Supervised Graph Neural Networks with Prototype-Guided Pseudo-Labeling for Privacy-Preserving Gestational Diabetes Mellitus Prediction
arXiv:2605.01810v2 Announce Type: replace Abstract: Gestational Diabetes Mellitus (GDM) is a high-prevalence pregnancy complication that requires accurate early risk stratification to reduce maternal and fetal morbidity. However, real-world clinical deployment of machine learning is hindered by two coupled constraints: (i) label scarcity, where a large fraction of electronic health records (EHR) lack confirmed diagnostic labels, and (ii) data privacy, which prevents sharing patient-level data across hospitals. This paper proposes FedTGNN-SS, a privacy-preserving federated semi-supervised framework for clinical tabular EHR. Each hospital builds a local k-nearest-neighbor patient similarity graph and trains a topology-adaptive GNN encoder. To robustly exploit unlabeled records, FedTGNN-SS combines (1) prototype-guided pseudo-labeling with neighborhood agreement, (2) adaptive graph refinement that periodically updates the k-NN graph using learned embeddings, (3) clinical-aware consistency augmentation applied only to continuous variables, and (4) privacy-safe prototype sharing that exchanges only class-level centroids. Across three diabetes-related datasets (GDM: N = 3,525; Pima: N = 768; Early Stage: N = 520) under 10\%-80\% missing labels per silo, FedTGNN-SS achieves 56 significant wins ($p < 0.05$) against 11 federated baselines and attains strong AUROC under extreme scarcity (Pima: 0.8037 at 80\% missing, Early Stage: 0.9634 at 80\% missing).
Abstract:Gestational Diabetes Mellitus (GDM) is a high-prevalence pregnancy complication that requires accurate early risk stratification to reduce maternal and fetal morbidity. However, real-world clinical deployment of machine learning is hindered by two coupled constraints: (i) label scarcity, where a large fraction of electronic health records (EHR) lack confirmed diagnostic labels, and (ii) data privacy, which prevents sharing patient-level data across hospitals. This paper proposes FedTGNN-SS, a privacy-preserving federated semi-supervised framework for clinical tabular EHR. Each hospital builds a local k-nearest-neighbor patient similarity graph and trains a topology-adaptive GNN encoder. To robustly exploit unlabeled records, FedTGNN-SS combines (1) prototype-guided pseudo-labeling with neighborhood agreement, (2) adaptive graph refinement that periodically updates the k-NN graph using learned embeddings, (3) clinical-aware consistency augmentation applied only to continuous variables, and (4) privacy-safe prototype sharing that exchanges only class-level centroids. Across three diabetes-related datasets (GDM: N = 3,525; Pima: N = 768; Early Stage: N = 520) under 10\%-80\% missing labels per silo, FedTGNN-SS achieves 56 significant wins ($p < 0.05$) against 11 federated baselines and attains strong AUROC under extreme scarcity (Pima: 0.8037 at 80\% missing, Early Stage: 0.9634 at 80\% missing).
Machine Learning (cs.LG); Artificial Intelligence (cs.AI)
arXiv:2605.01810 [cs.LG]
(or arXiv:2605.01810v2 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2605.01810 Focus to learn more arXiv-issued DOI via DataCite
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