Embedding-Based Federated Learning with Runtime Governance for Iron Deficiency Prediction

Recent reviews find that the vast majority of published healthcare federated learning (FL) studies never reach real-world deployment. We developed an embedding-based FL pipeline for iron deficiency prediction from routine full blood count (FBC) data and deployed it across real institutional environments at Amsterdam University Medical Centre (AUMC) and NHS Blood and Transplant (NHSBT), two clinical environments that differ markedly in iron deficiency prevalence, ferritin distribution, and subject populations. A frozen domain-specific haematology foundation model, DeepCBC, performs site-local representation extraction, restricting federated training to a compact downstream classifier and substantially reducing recurrent communication relative to full-encoder federation. The two clinical datasets are structurally not independent and identically distributed (non-IID), with heterogeneity arising from distinct population differences rather than sampling artefacts. Runtime governance is enforced by FLA$^3$, a healthcare-oriented FL platform providing study-scoped execution, policy-based authorisation, and signed audit logging. Standard sample-size-weighted aggregation (FedAvg) reduced the area under the receiver operating characteristic curve (ROC-AUC) at both sites relative to local-only training, as the global update was biased towards the larger AUMC distribution. FedMAP, a personalised aggregation method, raised ROC-AUC from 0.9470 to 0.9594 at AUMC and from 0.8558 to 0.8671 at NHSBT relative to local-only training, achieving the highest macro ROC-AUC of 0.9133 and the best macro balanced accuracy overall. These results support personalised aggregation in clinical federations where client sample size and task relevance diverge substantially.

Recent Methodological Advances in Federated Learning for Healthcare

For healthcare datasets, it is often not possible to combine data samples from multiple sites due to ethical, privacy or logistical concerns. Federated learning allows for the utilisation of powerful machine learning algorithms without requiring the pooling of data. Healthcare data has many simultaneous challenges which require new methodologies to address, such as highly-siloed data, class imbalance, missing data, distribution shifts and non-standardised variables. Federated learning adds significant methodological complexity to conventional centralised machine learning, requiring distributed optimisation, communication between nodes, aggregation of models and redistribution of models. In this systematic review, we consider all papers on Scopus that were published between January 2015 and February 2023 and which describe new federated learning methodologies for addressing challenges with healthcare data. We performed a detailed review of the 89 papers which fulfilled these criteria. Significant systemic issues were identified throughout the literature which compromise the methodologies in many of the papers reviewed. We give detailed recommendations to help improve the quality of the methodology development for federated learning in healthcare.

Dis-AE: Multi-domain & Multi-task Generalisation on Real-World Clinical Data

Clinical data is often affected by clinically irrelevant factors such as discrepancies between measurement devices or differing processing methods between sites. In the field of machine learning (ML), these factors are known as domains and the distribution differences they cause in the data are known as domain shifts. ML models trained using data from one domain often perform poorly when applied to data from another domain, potentially leading to wrong predictions. As such, developing machine learning models that can generalise well across multiple domains is a challenging yet essential task in the successful application of ML in clinical practice. In this paper, we propose a novel disentangled autoencoder (Dis-AE) neural network architecture that can learn domain-invariant data representations for multi-label classification of medical measurements even when the data is influenced by multiple interacting domain shifts at once. The model utilises adversarial training to produce data representations from which the domain can no longer be determined. We evaluate the model's domain generalisation capabilities on synthetic datasets and full blood count (FBC) data from blood donors as well as primary and secondary care patients, showing that Dis-AE improves model generalisation on multiple domains simultaneously while preserving clinically relevant information.