In this study, we introduce a sophisticated generative conditional strategy designed to impute missing values within datasets, an area of considerable importance in statistical analysis. Specifically, we initially elucidate the theoretical underpinnings of the Generative Conditional Missing Imputation Networks (GCMI), demonstrating its robust properties in the context of the Missing Completely at Random (MCAR) and the Missing at Random (MAR) mechanisms. Subsequently, we enhance the robustness and accuracy of GCMI by integrating a multiple imputation framework using a chained equations approach. This innovation serves to bolster model stability and improve imputation performance significantly. Finally, through a series of meticulous simulations and empirical assessments utilizing benchmark datasets, we establish the superior efficacy of our proposed methods when juxtaposed with other leading imputation techniques currently available. This comprehensive evaluation not only underscores the practicality of GCMI but also affirms its potential as a leading-edge tool in the field of statistical data analysis.

Masked autoencoders (MAEs) are increasingly applied to electronic health records (EHR) for learning general-purpose representations that support diverse clinical tasks. However, existing approaches typically rely on uniform random masking, implicitly assuming all features are equally predictable. In reality, laboratory tests exhibit substantial heterogeneity in volatility: some biomarkers (e.g., sodium) remain stable, while others (e.g., lactate) fluctuate considerably and are more difficult to model. Clinically, volatile biomarkers often signal acute pathophysiology and require more sophisticated modeling to capture their complex temporal patterns. We propose a volatility-aware pretraining strategy, Coefficient of Variation Masking (CV-Masking), that adaptively adjusts masking probabilities according to the intrinsic variability of each feature. Combined with a value-only masking objective aligned with clinical workflows, CV-Masking yields systematic improvements over random and variance-based strategies. Experiments on a large panel of laboratory tests show that CV-Masking enhances reconstruction, improves downstream predictive performance, and accelerates convergence, producing more robust and clinically meaningful EHR representations.

Abstract-- Clinical risk prediction using electronic health records (EHRs) is vital to facilitate timely interventions and clinical decision support. However, modeling heterogeneous and irregular temporal EHR data presents significant challenges. We propose KAT -GNN (Knowledge-Augmented Temporal Graph Neural Network), a graph-based framework that integrates clinical knowledge and temporal dynamics for risk prediction. These graphs are then augmented using two knowledge sources: (1) ontology-driven edges derived from SNOMED CT and (2) co-occurrence priors extracted from EHRs. Subsequently, a time-aware transformer is employed to capture longitudinal dynamics from the graph-encoded patient representations. KAT -GNN is evaluated on three distinct datasets and tasks: coronary artery disease (CAD) prediction using the Chang Gung Research Database (CGRD) and in-hospital mortality prediction using the MIMIC-III and MIMIC-IV datasets. KAT - GNN achieves state-of-the-art performance in CAD prediction (AUROC: 0.9269 0.0029) and demonstrated strong results in mortality prediction in MIMIC-III (AUROC: 0.9230 0.0070) and MIMIC-IV (AUROC: 0.8849 0.0089), consistently outperforming established baselines such as GRASP and RETAIN. Ablation studies confirm that both knowledge-based augmentation and the temporal modeling component are significant contributors to performance gains. These findings demonstrate that the integration of clinical knowledge into graph representations, coupled with a time-aware attention mechanism, provides an effective and generalizable approach for risk prediction across diverse clinical tasks and datasets. NTRODUCTION This study was supported by grants from the National Science and T echnology Council, T aiwan (NSTC 114-2221-E-A49-061), the Higher Education Sprout Project of the National Y ang Ming Chiao T ung University and MOE, T aiwan (CGMH-NYCU-114-CORPG2P0072), and Chang Gung Memorial Hospital (CMRPG2P0342).

Electronic health records arise from the complex interaction between patients and the healthcare system. This observation process of interactions, referred to as clinical presence, often impacts observed outcomes. When using electronic health records to develop clinical prediction models, it is standard practice to overlook clinical presence, impacting performance and limiting the transportability of models when this interaction evolves. We propose a multi-task recurrent neural network that jointly models the inter-observation time and the missingness processes characterising this interaction in parallel to the survival outcome of interest. Our work formalises the concept of clinical presence shift when the prediction model is deployed in new settings (e.g. different hospitals, regions or countries), and we theoretically justify why the proposed joint modelling can improve transportability under changes in clinical presence. We demonstrate, in a real-world mortality prediction task in the MIMIC-III dataset, how the proposed strategy improves performance and transportability compared to state-of-the-art prediction models that do not incorporate the observation process. These results emphasise the importance of leveraging clinical presence to improve performance and create more transportable clinical prediction models.

In the emergency department (ED), patients undergo triage and multiple laboratory tests before diagnosis. This time-consuming process causes ED crowding which impacts patient mortality, medical errors, staff burnout, etc. This work proposes (time) cost-effective diagnostic assistance that leverages artificial intelligence systems to help ED clinicians make efficient and accurate diagnoses. In collaboration with ED clinicians, we use public patient data to curate MIMIC-ED-Assist, a benchmark for AI systems to suggest laboratory tests that minimize wait time while accurately predicting critical outcomes such as death. With MIMIC-ED-Assist, we develop ED-Copilot which sequentially suggests patient-specific laboratory tests and makes diagnostic predictions. ED-Copilot employs a pre-trained bio-medical language model to encode patient information and uses reinforcement learning to minimize ED wait time and maximize prediction accuracy. On MIMIC-ED-Assist, ED-Copilot improves prediction accuracy over baselines while halving average wait time from four hours to two hours. ED-Copilot can also effectively personalize treatment recommendations based on patient severity, further highlighting its potential as a diagnostic assistant. Since MIMIC-ED-Assist is a retrospective benchmark, ED-Copilot is restricted to recommend only observed tests. We show ED-Copilot achieves competitive performance without this restriction as the maximum allowed time increases. Our code is available at https://github.com/cxcscmu/ED-Copilot.

In the dynamic hospital setting, decision support can be a valuable tool for improving patient outcomes. Data-driven inference of future outcomes is challenging in this dynamic setting, where long sequences such as laboratory tests and medications are updated frequently. This is due in part to heterogeneity of data types and mixed-sequence types contained in variable length sequences. In this work we design a probabilistic unsupervised model for multiple arbitrary-length sequences contained in hospitalization Electronic Health Record (EHR) data. The model uses a latent variable structure and captures complex relationships between medications, diagnoses, laboratory tests, neurological assessments, and medications. It can be trained on original data, without requiring any lossy transformations or time binning. Inference algorithms are derived that use partial data to infer properties of the complete sequences, including their length and presence of specific values. We train this model on data from subjects receiving medical care in the Kaiser Permanente Northern California integrated healthcare delivery system. The results are evaluated against held-out data for predicting the length of sequences and presence of Intensive Care Unit (ICU) in hospitalization bed sequences. Our method outperforms a baseline approach, showing that in these experiments the trained model captures information in the sequences that is informative of their future values.

With the advent of generative audio features, there is an increasing need for rapid evaluation of their impact on speech intelligibility. Beyond the existing laboratory measures, which are expensive and do not scale well, there has been comparatively little work on crowdsourced assessment of intelligibility. Standards and recommendations are yet to be defined, and publicly available multilingual test materials are lacking. In response to this challenge, we propose an approach for a crowdsourced intelligibility assessment. We detail the test design, the collection and public release of the multilingual speech data, and the results of our early experiments.

Scheduling laboratory tests for ICU patients presents a significant challenge. Studies show that 20-40% of lab tests ordered in the ICU are redundant and could be eliminated without compromising patient safety. Prior work has leveraged offline reinforcement learning (Offline-RL) to find optimal policies for ordering lab tests based on patient information. However, new ICU patient datasets have since been released, and various advancements have been made in Offline-RL methods. In this study, we first introduce a preprocessing pipeline for the newly-released MIMIC-IV dataset geared toward time-series tasks. We then explore the efficacy of state-of-the-art Offline-RL methods in identifying better policies for ICU patient lab test scheduling. Besides assessing methodological performance, we also discuss the overall suitability and practicality of using Offline-RL frameworks for scheduling laboratory tests in ICU settings.

Irregular sampling of time series in electronic health records (EHRs) is one of the main challenges for developing machine learning models. Additionally, the pattern of missing data in certain clinical variables is not at random but depends on the decisions of clinicians and the state of the patient. Point process is a mathematical framework for analyzing event sequence data that is consistent with irregular sampling patterns. Our model, TEE4EHR, is a transformer event encoder (TEE) with point process loss that encodes the pattern of laboratory tests in EHRs. The utility of our TEE has been investigated in a variety of benchmark event sequence datasets. Additionally, we conduct experiments on two real-world EHR databases to provide a more comprehensive evaluation of our model. Firstly, in a self-supervised learning approach, the TEE is jointly learned with an existing attention-based deep neural network which gives superior performance in negative log-likelihood and future event prediction. Besides, we propose an algorithm for aggregating attention weights that can reveal the interaction between the events. Secondly, we transfer and freeze the learned TEE to the downstream task for the outcome prediction, where it outperforms state-of-the-art models for handling irregularly sampled time series. Furthermore, our results demonstrate that our approach can improve representation learning in EHRs and can be useful for clinical prediction tasks.

Multiple Sclerosis (MS) is a chronic disease developed in human brain and spinal cord, which can cause permanent damage or deterioration of the nerves. The severity of MS disease is monitored by the Expanded Disability Status Scale (EDSS), composed of several functional sub-scores. Early and accurate classification of MS disease severity is critical for slowing down or preventing disease progression via applying early therapeutic intervention strategies. Recent advances in deep learning and the wide use of Electronic Health Records (EHR) creates opportunities to apply data-driven and predictive modeling tools for this goal. Previous studies focusing on using single-modal machine learning and deep learning algorithms were limited in terms of prediction accuracy due to the data insufficiency or model simplicity. In this paper, we proposed an idea of using patients' multimodal longitudinal and longitudinal EHR data to predict multiple sclerosis disease severity at the hospital visit. This work has two important contributions. First, we describe a pilot effort to leverage structured EHR data, neuroimaging data and clinical notes to build a multi-modal deep learning framework to predict patient's MS disease severity. The proposed pipeline demonstrates up to 25% increase in terms of the area under the Area Under the Receiver Operating Characteristic curve (AUROC) compared to models using single-modal data. Second, the study also provides insights regarding the amount useful signal embedded in each data modality with respect to MS disease prediction, which may improve data collection processes.