Multi-center clinical studies and biomedical research collaborations increasingly seek to utilize data across centers to build models that generalize beyond any single center. This creates two distinct challenges: data protection regulations may restrict the sharing of raw patient data across institutions, while centers may collect only partially overlapping sets of features under different protocols. Federated learning enables collaborative model training without centralizing raw data. However, existing federated imputation methods rarely evaluate feature-level missingness, in which entire features are unobserved at some centers. To address this setting, we adapt the ReMasker masked autoencoder to federated learning (Fed-ReMasker), enabling centers to impute features never observed locally by leveraging knowledge learned across collaborating centers. We evaluate Fed-ReMasker in a benchmark spanning synthetic datasets with linear and nonlinear relationships and real-world tabular datasets, including clinical data. The benchmark varies the number of centers, the missingness ratios, and client heterogeneity. Fed-ReMasker achieves the lowest imputation error in 93.2% of value-level and 96.7% of feature-level scenarios in the homogeneous benchmark. It also remains robust to client heterogeneity using simple federated averaging, outperforming all baselines in all 36 value-level scenarios and each baseline in at least 35 of 36 feature-level scenarios, and comes within 3.0% on average of a centralized model trained on the pooled data.
Federated Learning (FL) enables collaborative training across decentralized clients, but most methods assume aligned feature schemas, an assumption that rarely holds in tabular settings where clients observe only partially overlapping feature subsets. In these heterogeneous feature spaces, parameter-averaging methods (e.g., FedAvg) transfer little information across weakly overlapping or disjoint feature groups, limiting their effectiveness for federated imputation. To overcome this, we propose \textbf{FedHF-Impute}, a federated imputation framework that separates structural feature unavailability from conventional missingness and uses a shared global feature graph to propagate information across statistically related features through message passing. This enables indirect cross-client knowledge transfer, even when features are never jointly observed locally, while preserving standard federated communication. Under simulated partial schema overlap on the SECOM and AirQuality datasets, FedHF-Impute improves imputation accuracy (RMSE) over FL baselines by 26.9%, and 8.4% respectively, while achieving comparable performance on PhysioNET, with only a 0.3% difference relative to the best baseline.
Multimodal Federated Learning (MMFL) enables privacy-preserving collaborative training, but real-world clinical applications often suffer from within-modality missingness caused by sensor intermittency or irregular sampling. Existing methods implicitly represent unobserved data via architectural alignment or missing embeddings, often failing to recover the true distribution and yielding sub-optimal performance. We propose CondI, a federated framework explicitly addressing this missingness using conditional diffusion models. CondI employs a two-phase training pipeline: first, imputing unobserved temporal components using available multimodal context and conditional embeddings; second, optimizing modality-specific extractors and joint embedding spaces. During inference, imputed raw data pass through trained extractors to generate robust features, providing a holistic representation for downstream tasks. Explicit data imputation ensures models operate on complete semantic structures, significantly enhancing resilience against severe data incompleteness. Experiments on three clinical datasets (PTB-XL, SLEEP-EDF, MIMIC-IV) demonstrate CondI achieves comparable results to state-of-the-art baselines. Code: https://github.com/ZhengWugeng/CondI
Federated learning (FL) enables collaborative analysis of biomedical data without exchanging sensitive patient-level information, but its performance in multi-center studies may be compromised by batch effects which can obscure biological signals. Here, we systematically assess the impact of uncorrected batch effects on FL outcomes using four multi-center omics datasets, including transcriptomic, proteomic, and metabolomic data, and two representative algorithms: federated k-means clustering and federated random forest classification. Our results demonstrate that uncorrected batch effects undermine unsupervised FL and can substantially degrade supervised FL performance, indicating that privacy-aware batch-effect correction is essential for reliable FL. To enable privacy-preserving BEC in distributed bulk omics data, we introduce fedRBE ( https://featurecloud.ai/app/fedrbe ), a federated implementation of limma's removeBatchEffect() method enhanced by secure multi-party computation, suitable for datasets with missing values and non-identical feature sets across clients, including proteomics and metabolomics data.
Yuliya Burankova, Julian Klemm, Jens J. G. Lohmann +5