We introduce the Conditional Self-Attention Imputation (CSAI) model, a novel recurrent neural network architecture designed to address imputation challenges in multivariate time series derived from hospital electronic health records (EHRs). CSAI introduces key novelties specific to EHR data: a) attention-based hidden state initialisation to capture both long- and short-range temporal dependencies, b) domain-informed temporal decay to mimic clinical recording patterns, and c) a non-uniform masking strategy that models non-random missingness. Comprehensive evaluation across four EHR benchmark datasets demonstrates CSAI's effectiveness compared to state-of-the-art architectures in data restoration and downstream tasks. CSAI is integrated into PyPOTS, an open-source Python toolbox for partially observed time series. This work significantly advances the state of neural network imputation applied to EHRs by more closely aligning algorithmic imputation with clinical realities.

Cardiac Magnetic Resonance (CMR) imaging is widely used to personalize heart models for cardiac digital twin analysis because of its ability to visualize soft tissues and capture dynamic functions. However, CMR images have an anisotropic nature, characterized by large inter-slice distances and misalignments from cardiac motion. These limitations result in data loss and measurement inaccuracies, hindering the capture of detailed anatomical structures. In this work, we introduce MorphiNet, a novel network that reproduces heart anatomy learned from high-resolution Computed Tomography (CT) images, unpaired with CMR images. MorphiNet encodes the anatomical structure as gradient fields, deforming template meshes into patient-specific geometries. A multilayer graph subdivision network refines these geometries while maintaining dense point correspondence, suitable for downstream computational analysis. MorphiNet achieved the strongest overall trade-off in bi-ventricular myocardium reconstruction on CMR patients with tetralogy of Fallot, with 0.3 higher Dice score and 2.6 lower Hausdorff distance compared to the best existing template-based methods, while achieving comparable geometric accuracy to neural implicit function methods on CT data at $50\times $ faster inference. Cross-dataset validation on the Automated Cardiac Diagnosis Challenge confirmed robust generalization, achieving a 0.7 Dice score with 30% improvement over previous template-based approaches. We validate our anatomical learning approach through the successful restoration of missing cardiac structures and demonstrate significant improvement over standard Loop subdivision. Motion tracking experiments further confirm MorphiNet's capability for cardiac function analysis, including ejection-fraction estimates that correctly identify myocardial dysfunction in tetralogy of Fallot patients. Code and checkpoints are available at https://github.com/MalikTeng/MorphiNetV2.

Missing values are ubiquitous in multivariate time series (MTS) data, posing significant challenges for accurate analysis and downstream applications. In recent years, deep learning-based methods have successfully handled missing data by leveraging complex temporal dependencies and learned data distributions. In this survey, we provide a comprehensive summary of deep learning approaches for multivariate time series imputation (MTSI) tasks. We propose a novel taxonomy that categorizes existing methods based on two key perspectives: imputation uncertainty and neural network architecture. Furthermore, we summarize existing MTSI toolkits with a particular emphasis on the PyPOTS Ecosystem, which provides an integrated and standardized foundation for MTSI research. Finally, we discuss key challenges and future research directions, which give insight for further MTSI research. This survey aims to serve as a valuable resource for researchers and practitioners in the field of time series analysis and missing data imputation tasks. A well-maintained MTSI paper and tool list is available at https://github.com/WenjieDu/Awesome_Imputation.

We present a comprehensive analysis of deep learning approaches for Electronic Health Record (EHR) time-series imputation, examining how the interplay between architectural and framework design decisions gives rise to higher-level properties of a given deep imputer model and distinct biases towards complex data characteristics. Our investigation reveals the varying capabilities of deep imputers in capturing complex spatio-temporal dependencies within EHRs, and that the effectiveness of the model depends on how its combined biases align with the characteristics of the medical time series. Our experimental evaluation challenges common assumptions about model complexity, demonstrating that larger models do not necessarily improve performance. Rather, carefully designed architectures can better capture the complex patterns inherent in clinical data. The study highlights the need for imputation approaches that prioritise clinically meaningful data reconstruction over statistical accuracy. Our experiments further reveal up to 20% in variations of imputation performance based on preprocessing and implementation choices, emphasising the need for standardised benchmarking methodologies. Finally, we identify critical gaps between current deep imputation methods and medical requirements, highlighting the importance of integrating clinical insights to achieve more reliable imputation approaches for healthcare applications.

OBJECTIVES: Question answering (QA) systems have the potential to improve the quality of clinical care by providing health professionals with the latest and most relevant evidence. However, QA systems have not been widely adopted. This systematic review aims to characterize current medical QA systems, assess their suitability for healthcare, and identify areas of improvement. MATERIALS AND METHODS: We searched PubMed, IEEE Xplore, ACM Digital Library, ACL Anthology, and forward and backward citations on February 7, 2023. We included peer-reviewed journal and conference papers describing the design and evaluation of biomedical QA systems. Two reviewers screened titles, abstracts, and full-text articles. We conducted a narrative synthesis and risk of bias assessment for each study. We assessed the utility of biomedical QA systems. RESULTS: We included 79 studies and identified themes, including question realism, answer reliability, answer utility, clinical specialism, systems, usability, and evaluation methods. Clinicians' questions used to train and evaluate QA systems were restricted to certain sources, types and complexity levels. No system communicated confidence levels in the answers or sources. Many studies suffered from high risks of bias and applicability concerns. Only 8 studies completely satisfied any criterion for clinical utility, and only 7 reported user evaluations. Most systems were built with limited input from clinicians. DISCUSSION: While machine learning methods have led to increased accuracy, most studies imperfectly reflected real-world healthcare information needs. Key research priorities include developing more realistic healthcare QA datasets and considering the reliability of answer sources, rather than merely focusing on accuracy.

The ability to perform accurate prognosis is crucial for proactive clinical decision making, informed resource management and personalised care. Existing outcome prediction models suffer from a low recall of infrequent positive outcomes. We present a highly-scalable and robust machine learning framework to automatically predict adversity represented by mortality and ICU admission and readmission from time-series of vital signs and laboratory results obtained within the first 24 hours of hospital admission. The stacked ensemble platform comprises two components: a) an unsupervised LSTM Autoencoder that learns an optimal representation of the time-series, using it to differentiate the less frequent patterns which conclude with an adverse event from the majority patterns that do not, and b) a gradient boosting model, which relies on the constructed representation to refine prediction by incorporating static features. The model is used to assess a patient's risk of adversity and provides visual justifications of its prediction. Results of three case studies show that the model outperforms existing platforms in ICU and general ward settings, achieving average Precision-Recall Areas Under the Curve (PR-AUCs) of 0.891 (95% CI: 0.878-0.939) for mortality and 0.908 (95% CI: 0.870-0.935) in predicting ICU admission and readmission.