healthcare data analysts

Abstract: Computing local-level variable importance (VI) is critical for understanding machine learning models. Local permutation-based VI metrics offer a simple yet powerful approach, measuring how much a model's output changes when perturbing its inputs. However, existing perturbation strategies often ignore feature dependence or account for it only through restricted approximations. Perturbing a feature without fully respecting this dependence can generate unrealistic counterfactuals, thereby evaluating the model in regions unsupported by the observed data distribution. We address this gap by introducing a new model-agnostic local VI metric and estimator, Local Understanding of Covariate Importance with conditional Density estimation (LUCID). LUCID perturbs features of interest using plausible values drawn from the full conditional distribution given the remaining observed features. We establish theoretical connections between LUCID and existing VI measures, and provide an estimator with convergence guarantees and uncertainty quantification. Finally, we demonstrate LUCID's stable performance and practical utility across simulated and real-world examples.

Abstract: Task transition detection aims to identify when a person shifts from one task to another, providing a foundation for continuous health monitoring and timely context-aware interventions. While statistical and deep feature representations have demonstrated strong classification performance, they often rely on aggregated or latent features that are difficult to interpret in behavioural terms. Event-based features provide a compact and interpretable alternative by encoding behavioural and physiological patterns as discrete tokens with explicit semantic meaning, making them well suited for behavioural analysis in health informatics. Self-attention offers a mechanism for modelling interactions among such tokens; however, conventional self-attention classifiers primarily rely on token order and do not explicitly incorporate timing or duration information. As a result, informative temporal cues in event representations may not be fully exploited for task transition detection. This study proposes an event-based time-aware self-attention framework that represents behavioural signals as sequences of discrete events augmented with onset timestamps and durations. Event timing is encoded using a parameter-efficient kernel-based representation, while a novel type-aware duration embedding modulates information propagation according to event persistence. Experiments on a semi-naturalistic wearable dataset show that the proposed model outperforms existing event-based approaches, achieves performance beyond or comparable with statistical and deep-learning models with a more compact input representation, and provides improved interpretability through integrated-gradient-based analysis. These results indicate that explicit modelling of event timing and duration enhances both classification performance and interpretability, supporting reliable deployment in biomedical and health informatics applications.

Abstract: Time series causal discovery --- the process of detecting causation between time series --- has its roots in signal processing research from over a half century ago. It has since received active and widespread interest, evolving into different forms across domains such as statistics, dynamical systems and machine learning. Entering this fragmented and constantly evolving research landscape can be daunting. This tutorial provides a unified overview of time series causal discovery across research communities. We introduce the key principles invoked by modern discovery methods, and we discuss their limitations and assumptions. We also discuss how discovery methods are evaluated, benchmarked and fine-tuned. We further discuss how causal discovery for time series is becoming crucial for downstream tasks in agriculture and Earth science, in healthcare, and in artificial intelligence systems. We believe that this tutorial will serve as a valuable resource in navigating the deluge of recent causality research, as well as an invitation to signal processing audiences to contribute to causal problems. To further help readers, we host a companion repository to link to useful code packages and resources at https://github.com/CHAI-UK/Awesome-Time-Series-Causal-Discovery.

Abstract: Longitudinal models forecast how a patient's imaging state evolves, but accuracy does not show whether the patient's observed trajectory drives the prediction. A population-average forecast may be useful but cannot establish a patient-specific world-model claim. We introduce Patient, Place, Prior (P$^3$), an audit asking whether a forecast benefits from the patient's longitudinal imaging history (Patient), benefits from patient-matched externally supplied spatial support (Place), and gains predictive value beyond a population-average prediction under matched support and context (Prior). We also propose Cancer JEPA, a one-step model that forecasts frozen representations of future breast dynamic contrast-enhanced MRI examinations during neoadjuvant therapy. It adds a lesion-constrained neural correction, trained with an occlusion-based latent objective, to a patient-conditioned low-complexity reduced-rank regression baseline. This factorization permits a post-hoc P$^3$ audit of the frozen model. In a validation cohort previously used in development, forecast error is lower when the neural correction receives the patient's history rather than another patient's and patient-matched lesion occupancy maps rather than substituted maps. However, the descriptive 95% interval comparing the correction computed from patient history with the population-average neural correction includes zero. P$^3$ thus separates input use from evidence of patient-specific predictive value beyond a population-level pattern.

Abstract: Augmenting small concurrent studies with external or historical cohorts is attractive in drug development, where enrollment is slow, follow-up is expensive, and closely related trial or real-world data are often already available. Bayesian dynamic borrowing (BDB) provides a principled framework for adaptively controlling the influence of external data, but classical implementations often depend on hand-specified priors and MCMC-based inference, which can be computationally expensive and not generalizable. In this work, we study amortized neural posterior estimation (NPE) as a flexible alternative. A single network is pretrained on simulated current/external dataset pairs spanning covariate shift, outcome drift, and joint non-exchangeability, and then returns an approximate posterior for a scalar current-study target in a single forward pass. Through simulation studies, we find that NPE is most useful under outcome drift and joint mismatch: in the harder outcome-drift regimes, it gives up to about five-fold lower absolute bias than the best classical baseline and keeps Type I error close to nominal. After pretraining, posterior summaries are obtained in about 8 ms per dataset, roughly $10^3\times$ faster than MCMC-based borrowing baselines in our timing experiment. We further analyze Alzheimer's Disease Neuroimaging Initiative (ADNI) data and show that, when mild cognitive impairment outcomes differ across cohorts, the NPE formulation recovers the later-cohort risk level in this example without claiming greater precision. Code is available at https://github.com/ChinHungScott/NPE-for-Bayesian-Dynamic-Borrowing-MLHC-.

Abstract: Wearable actigraphy offers a scalable, ecologically valid alternative to episodic clinical assessment. However, predicting continuous adolescent crystallized intelligence ($G_c$) from such traces remains challenging due to irregular device adherence and complex behavioral-environmental interactions. We address this using daily summary data derived from 21-day Fitbit records of 6,091 adolescents in the Adolescent Brain Cognitive Development Study (Release 5.1). We propose SATURN, a Sleep-Activity Temporal Unified Regression Network. It represents participants as 21-node temporal graphs encoding daily behaviors and temporal adjacency. To prevent imputation artifacts, invalid-day edges are dynamically pruned during forward passes. Node embeddings are refined via residual GATv2 layers, aggregated through masked attention pooling, and fused with sociodemographic covariates. Under family-controlled, age-sex-BMI-stratified cross-validation, SATURN achieves $R^2 = 0.2783 \pm 0.0127$, consistently improving upon flattened machine learning (Gradient Boosting, $R^2 = 0.2372$) and sequential deep learning (BiLSTM, $R^2 = 0.2688$) baselines. Explainability analyses identify light activity, metabolic equivalents, and sleep duration as dominant predictors, while Monte Carlo dropout and subgroup analyses confirm equitable performance across sociodemographic strata. Ultimately, SATURN establishes a rigorous computational framework for digital cognitive phenotyping, offering a scalable pathway to complement traditional assessments by highlighting macro-level behavioral anomalies.

Abstract: Disease severity classification for genetic conditions is subjective and labor-intensive, creating bottlenecks in genomic screening, where commercial panels vary widely in size and overlap. We developed an autonomous AI agent integrating Reasoning and Acting (ReAct) with Retrieval-Augmented Generation (RAG) to classify 10,211 Human Phenotype Ontology terms. It uses American College of Medical Genetics (ACMG)-endorsed severity guidelines and American College of Obstetricians and Gynecologists (ACOG) quality-of-life criteria to retrieve PubMed literature, generate interpretable reasoning chains, and independently verify claims. At the phenotype level, using expert-curated cohorts, the agent achieved 93.55% accuracy (MCC 0.9237) with 82.6% to 91.4% of claims supported by direct evidence or valid inferences. Gene-level severity was aggregated across 8,738 pairs, identifying 3,283 autosomal recessive pairs with severe or profound presentations. External validation showed 95.2% concordance with Mackenzie's Mission gene list. This system enables standardized panel design by providing reliable, automated classification supported by direct evidence.