Federated learning (FL) enables privacy-preserving model training across distributed Electronic Health Records (EHRs), but its deployment remains limited by data-view heterogeneity, where institutions maintain incompatible local schemas. Most existing methods address this by enforcing flat, aligned data views, which require extensive cross-site preprocessing and manual harmonisation that often discards client-specific features, or by projecting inputs into a shared latent space, which sacrifices interpretability. We propose a modelling shift from conventional FL with vectorised inputs to a symbolic, relation-centric framework, where each client organises its EHR data as a structured, type-aware relational graph. This enables client-specific inference without requiring schema alignment and supports FL across heterogeneous data views. To model over these symbolic structures, we introduce an architecture that combines relation-aware message passing with a learnable feature relevance mechanism, jointly enabling accurate local predictions and client-specific interpretability while supporting parameter sharing across clients. Beyond strong performance on three real-world EHR datasets exhibiting data-view heterogeneity, we further show that our framework supports multimodal FL under modality-level heterogeneity. Using MC-MED, a publicly available multimodal emergency department dataset, we demonstrate that our method accommodates clients with partially missing modalities, highlighting its robustness and scalability in real-world clinical settings.

Federated Learning (FL) enables collaborative clinical modelling across distributed electronic health records (EHRs) without sharing sensitive patient data. However, variations in medical practice, documentation standards, and data collection across institutions create data-view heterogeneity, where clients possess different or only partially overlapping clinical feature sets. This misalignment hinders the use of standard FL methods. Existing approaches rely on complex preprocessing and manual harmonisation, which can cause information loss, reduce data utility, limit scalability, and restrict client-specific personalisation. To address these limitations, we propose Personalised Attention-based Federated Graph Network (PAFNet), a scalable FL framework that enables meaningful parameter exchange across heterogeneous clients by mapping their distinct data-views into a shared latent space through client-specific projection layers. It then applies a personalised adaptation mechanism using trainable parameter masks, allowing each client to selectively incorporate global model parameters relevant to its own feature set. This design preserves local specificity, improves generalisation, and removes the need for heavy manual preprocessing common in existing approaches. Across CURIAL, eICU, and MIMIC-III datasets, PAFNet consistently outperformed state-of-the-art data-view heterogeneity FL baselines, demonstrating strong generalisation under substantial differences in client feature sets. By enabling effective personalisation and cross-institutional knowledge sharing without extensive harmonisation, PAFNet offers a robust and scalable solution for the federated training of clinical models in data-view heterogeneous environments.

This paper presents Adaptive Parameter Optimisation (APO), a novel framework for optimising shared models across multiple clinical tasks, addressing the challenges of balancing strict parameter sharing—often leading to task conflicts—and soft parameter sharing, which may limit effective cross-task information exchange. The proposed APO framework leverages insights from the lazy behaviour observed in over-parameterised neural networks, where only a small subset of parameters undergo any substantial updates during training. APO dynamically identifies and updates task-specific parameters while treating parameters associated with other tasks as protected, limiting their modification to prevent interference. The remaining unassigned parameters remain unchanged, embodying the lazy training phenomenon. This dynamic management of task-specific, protected, and unclaimed parameters across tasks enables effective information sharing, preserves task-specific adaptability, and mitigates gradient conflicts without enforcing a uniform representation. Experimental results across diverse healthcare datasets demonstrate that APO surpasses traditional information-sharing approaches, such as multi-task learning and model-agnostic meta-learning, in improving task performance.

Federated Learning (FL) involves a server aggregating local models from clients to compute a global model. However, this process can struggle to position the global model in low-loss regions of the parameter space for all clients, resulting in subpar convergence and inequitable performance across clients. This issue is particularly pronounced in non-IID settings, common in clinical contexts, where variations in data distribution, class imbalance, and training sample sizes result in client heterogeneity. To address this issue, we propose a mode connectivity-based FL framework that ensures the global model resides within the overlapping low-loss regions of all clients in the parameter space. This framework models the low-loss regions as non-linear mode connections between the current global and local models, and optimises to identify an intersection among these mode connections to define the new global model. This approach enhances training stability and convergence, yielding better and more equitable performance compared to standard FL frameworks like federated averaging. Empirical evaluations across multiple healthcare datasets demonstrate the benefits of the proposed framework.

Targeted and uniform interventions to a system are crucial for unveiling causal relationships. While several methods have been developed to leverage interventional data for causal structure learning, their practical application in real-world scenarios often remains challenging. Recent benchmark studies have highlighted these difficulties, even when large numbers of single-variable intervention samples are available. In this work, we demonstrate, both theoretically and empirically, that such datasets contain a wealth of causal information that can be effectively extracted under realistic assumptions about the data distribution. More specifically, we introduce a novel variant of interventional faithfulness, which relies on comparisons between the marginal distributions of each variable across observational and interventional settings, and we introduce a score on causal orders. Under this assumption, we are able to prove strong theoretical guarantees on the optimum of our score that also hold for large-scale settings. To empirically verify our theory, we introduce Intersort, an algorithm designed to infer the causal order from datasets containing large numbers of single-variable interventions by approximately optimizing our score. Intersort outperforms baselines (GIES, DCDI, PC and EASE) on almost all simulated data settings replicating common benchmarks in the field. Our proposed novel approach to modeling interventional datasets thus offers a promising avenue for advancing causal inference, highlighting significant potential for further enhancements under realistic assumptions.

While machine learning algorithms hold promise for personalised medicine, their clinical adoption remains limited, partly due to biases that can compromise the reliability of predictions. In this article, we focus on sample selection bias (SSB), a specific type of bias where the study population is less representative of the target population, leading to biased and potentially harmful decisions. Despite being well-known in the literature, SSB remains scarcely studied in machine learning for healthcare. Moreover, the existing machine learning techniques try to correct the bias mostly by balancing distributions between the study and the target populations, which may result in a loss of predictive performance. To address these problems, our study illustrates the potential risks associated with SSB by examining SSB’s impact on the performance of machine learning algorithms. Most importantly, we propose a new research direction for addressing SSB, based on the target population identification rather than the bias correction. Specifically, we propose two independent networks (T-Net) and a multitasking network (MT-Net) for addressing SSB, where one network/task identifies the target subpopulation which is representative of the study population and the second makes predictions for the identified subpopulation. Our empirical results with synthetic and semi-synthetic datasets highlight that SSB can lead to a large drop in the performance of an algorithm for the target population as compared with the study population, as well as a substantial difference in the performance for the target subpopulations that are representative of the selected and the non-selected patients from the study population. Furthermore, our proposed techniques demonstrate robustness across various settings, including different dataset sizes, event rates and selection rates, outperforming the existing bias correction techniques.

Given radiology images, automatic radiology report generation aims to produce informative text that reports diseases. It can benefit current clinical practice in diagnostic radiology. Existing methods typically rely on large-scale medical datasets annotated by clinicians to train desirable models. However, for novel diseases, sufficient training data are typically not available. We propose a prompt-based deep learning framework, i.e., PromptLLM, to align, autoencode, and prompt the (large) language model to generate reports for novel diseases accurately and efficiently. Our method includes three major steps: 1) aligning visual images and textual reports to learn general knowledge across modalities from diseases where labeled data are sufficient, 2) autoencoding the LLM using unlabeled data of novel diseases to learn the specific knowledge and writing styles of the novel disease, and 3) prompting the LLM with learned knowledge and writing styles to report the novel diseases contained in the radiology images. Through the above three steps, with limited labels on novel diseases, we show that PromptLLM can rapidly learn the corresponding knowledge for accurate novel disease reporting. The experiments on COVID-19 and diverse thorax diseases show that our approach, utilizing 1% of the training data, achieves desirable performance compared to previous methods. It shows that our approach allows us to relax the reliance on labeled data that is common to existing methods. It could have a real-world impact on data analysis during the early stages of novel diseases.

The discovery of therapeutics to treat genetically-driven pathologies relies on identifying genes involved in the underlying disease mechanism. Existing approaches search over the billions of potential interventions to maximize the expected influence on the target phenotype. However, to reduce the risk of failure in future stages of trials, practical experiment design aims to find a set of interventions that maximally change a target phenotype via diverse mechanisms. We propose DiscoBAX - a sample-efficient method for maximizing the rate of significant discoveries per experiment while simultaneously probing for a wide range of diverse mechanisms during a genomic experiment campaign. We provide theoretical guarantees of optimality under standard assumptions, and conduct a comprehensive experimental evaluation covering both synthetic as well as real-world experimental design tasks. DiscoBAX outperforms existing state-of-the-art methods for experimental design, selecting effective and diverse perturbations in biological systems.

Multiple sclerosis (MS) affects the central nervous system with a wide range of symptoms. MS can, for example, cause pain, changes in mood and fatigue, and may impair a person's movement, speech and visual functions. Diagnosis of MS typically involves a combination of complex clinical assessments and tests to rule out other diseases with similar symptoms. New technologies, such as smartphone monitoring in free-living conditions, could potentially aid in objectively assessing the symptoms of MS by quantifying symptom presence and intensity over long periods of time. Here, we present a deep-learning approach to diagnosing MS from smartphone-derived digital biomarkers that uses a novel combination of a multilayer perceptron with neural soft attention to improve learning of patterns in long-term smartphone monitoring data. Using data from a cohort of 774 participants, we demonstrate that our deep-learning models are able to distinguish between people with and without MS with an area under the receiver operating characteristic curve of 0.88 (95% CI: 0.70, 0.88). Our experimental results indicate that digital biomarkers derived from smartphone data could in the future be used as additional diagnostic criteria for MS.

Estimating what would be an individual's potential response to varying levels of exposure to a treatment is of high practical relevance for several important fields, such as healthcare, economics and public policy. However, existing methods for learning to estimate counterfactual outcomes from observational data are either focused on estimating average dose-response curves, or limited to settings with only two treatments that do not have an associated dosage parameter. Here, we present a novel machine-learning approach towards learning counterfactual representations for estimating individual dose-response curves for any number of treatments with continuous dosage parameters with neural networks. Building on the established potential outcomes framework, we introduce performance metrics, model selection criteria, model architectures, and open benchmarks for estimating individual dose-response curves. Our experiments show that the methods developed in this work set a new state-of-the-art in estimating individual dose-response.

Parkinson’s disease is a neurodegenerative disease that can affect a person’s movement, speech, dexterity, and cognition. Clinicians primarily diagnose Parkinson’s disease by performing a clinical assessment of symptoms. However, misdiagnoses are common. One factor that contributes to misdiagnoses is that the symptoms of Parkinson’s disease may not be prominent at the time the clinical assessment is performed. Here, we present a machine-learning approach towards distinguishing between people with and without Parkinson’s disease using long-term data from smartphone-based walking, voice, tapping and memory tests. We demonstrate that our attentive deep-learning models achieve significant improvements in predictive performance over strong baselines (area under the receiver operating characteristic curve = 0.85) in data from a cohort of 1853 participants. We also show that our models identify meaningful features in the input data. Our results confirm that smartphone data collected over extended periods of time could in the future potentially be used as a digital biomarker for the diagnosis of Parkinson’s disease.

Knowledge of the importance of input features towards decisions made by machine-learning models is essential to increase our understanding of both the models and the underlying data. Here, we present a new approach to estimating feature importance with neural networks based on the idea of distributing the features of interest among experts in an attentive mixture of experts (AME). AMEs use attentive gating networks trained with a Granger-causal objective to learn to jointly produce accurate predictions as well as estimates of feature importance in a single model. Our experiments show (i) that the feature importance estimates provided by AMEs compare favourably to those provided by state-of-theart methods, (ii) that AMEs are significantly faster at estimating feature importance than existing methods, and (iii) that the associations discovered by AMEs are consistent with those reported by domain experts.

Feature importance estimates that inform users about the degree to which given inputs influence the output of a predictive model are crucial for understanding, validating, and interpreting machine-learning models. However, providing fast and accurate estimates of feature importance for high-dimensional data, and quantifying the uncertainty of such estimates remain open challenges. Here, we frame the task of providing explanations for the decisions of machine-learning models as a causal learning task, and train causal explanation (CXPlain) models that learn to estimate to what degree certain inputs cause outputs in another machine-learning model. CXPlain can, once trained, be used to explain the target model in little time, and enables the quantification of the uncertainty associated with its feature importance estimates via bootstrap ensembling. We present experiments that demonstrate that CXPlain is significantly more accurate and faster than existing model-agnostic methods for estimating feature importance. In addition, we confirm that the uncertainty estimates provided by CXPlain ensembles are strongly correlated with their ability to accurately estimate feature importance on held-out data.

Patients in the intensive care unit (ICU) require constant and close supervision. To assist clinical staff in this task, hospitals use monitoring systems that trigger audiovisual alarms if their algorithms indicate that a patient’s condition may be worsening. However, current monitoring systems are extremely sensitive to movement artefacts and technical errors. As a result, they typically trigger hundreds to thousands of false alarms per patient per day - drowning the important alarms in noise and adding to the exhaustion of clinical staff. In this setting, data is abundantly available, but obtaining trustworthy annotations by experts is laborious and expensive. We frame the problem of false alarm reduction from multivariate time series as a machine-learning task and address it with a novel multitask network architecture that utilises distant supervision through multiple related auxiliary tasks in order to reduce the number of expensive labels required for training. We show that our approach leads to significant improvements over several state-of-the-art baselines on real-world ICU data and provide new insights on the importance of task selection and architectural choices in distantly supervised multitask learning.