DynaGraph: Interpretable Multi-Label Prediction from EHRs via Dynamic Graph Learning and Contrastive Augmentation

Learning from longitudinal electronic health records is limited if it does not capture the temporal trajectories of the patient's state in a clinical setting. Graph models allow us to capture the hidden dependencies of the multivariate time-series when the graphs are constructed in a similar dynamic manner. Previous dynamic graph models require a pre-defined and/or static graph structure, which is unknown in most cases, or they only capture the spatial relations between the features. Furthermore in healthcare, the interpretability of the model is an essential requirement to build trust with clinicians. In addition to previously proposed attention mechanisms, there has not been an interpretable dynamic graph framework for data from multivariate electronic health records (EHRs). Here, we propose DynaGraph, an end-to-end interpretable contrastive graph model that learns the dynamics of multivariate time-series EHRs as part of optimisation. We validate our model in four real-world clinical datasets, ranging from primary care to secondary care settings with broad demographics, in challenging settings where tasks are imbalanced and multi-labelled. Compared to state-of-the-art models, DynaGraph achieves significant improvements in balanced accuracy and sensitivity over the nearest complex competitors in time-series or dynamic graph modelling across three ICU and one primary care datasets. Through a pseudo-attention approach to graph construction, our model also indicates the importance of clinical covariates over time, providing means for clinical validation.

AnchorInv: Few-Shot Class-Incremental Learning of Physiological Signals via Representation Space Guided Inversion

Deep learning models have demonstrated exceptional performance in a variety of real-world applications. These successes are often attributed to strong base models that can generalize to novel tasks with limited supporting data while keeping prior knowledge intact. However, these impressive results are based on the availability of a large amount of high-quality data, which is often lacking in specialized biomedical applications. In such fields, models are usually developed with limited data that arrive incrementally with novel categories. This requires the model to adapt to new information while preserving existing knowledge. Few-Shot Class-Incremental Learning (FSCIL) methods offer a promising approach to addressing these challenges, but they also depend on strong base models that face the same aforementioned limitations. To overcome these constraints, we propose AnchorInv following the straightforward and efficient buffer-replay strategy. Instead of selecting and storing raw data, AnchorInv generates synthetic samples guided by anchor points in the feature space. This approach protects privacy and regularizes the model for adaptation. When evaluated on three public physiological time series datasets, AnchorInv exhibits efficient knowledge forgetting prevention and improved adaptation to novel classes, surpassing state-of-the-art baselines.

DTR-Bench: An in silico Environment and Benchmark Platform for Reinforcement Learning Based Dynamic Treatment Regime

Reinforcement learning (RL) has garnered increasing recognition for its potential to optimise dynamic treatment regimes (DTRs) in personalised medicine, particularly for drug dosage prescriptions and medication recommendations. However, a significant challenge persists: the absence of a unified framework for simulating diverse healthcare scenarios and a comprehensive analysis to benchmark the effectiveness of RL algorithms within these contexts. To address this gap, we introduce \textit{DTR-Bench}, a benchmarking platform comprising four distinct simulation environments tailored to common DTR applications, including cancer chemotherapy, radiotherapy, glucose management in diabetes, and sepsis treatment. We evaluate various state-of-the-art RL algorithms across these settings, particularly highlighting their performance amidst real-world challenges such as pharmacokinetic/pharmacodynamic (PK/PD) variability, noise, and missing data. Our experiments reveal varying degrees of performance degradation among RL algorithms in the presence of noise and patient variability, with some algorithms failing to converge. Additionally, we observe that using temporal observation representations does not consistently lead to improved performance in DTR settings. Our findings underscore the necessity of developing robust, adaptive RL algorithms capable of effectively managing these complexities to enhance patient-specific healthcare. We have open-sourced our benchmark and code at https://github.com/GilesLuo/DTR-Bench.

Reinforcement Learning in Dynamic Treatment Regimes Needs Critical Reexamination

In the rapidly changing healthcare landscape, the implementation of offline reinforcement learning (RL) in dynamic treatment regimes (DTRs) presents a mix of unprecedented opportunities and challenges. This position paper offers a critical examination of the current status of offline RL in the context of DTRs. We argue for a reassessment of applying RL in DTRs, citing concerns such as inconsistent and potentially inconclusive evaluation metrics, the absence of naive and supervised learning baselines, and the diverse choice of RL formulation in existing research. Through a case study with more than 17,000 evaluation experiments using a publicly available Sepsis dataset, we demonstrate that the performance of RL algorithms can significantly vary with changes in evaluation metrics and Markov Decision Process (MDP) formulations. Surprisingly, it is observed that in some instances, RL algorithms can be surpassed by random baselines subjected to policy evaluation methods and reward design. This calls for more careful policy evaluation and algorithm development in future DTR works. Additionally, we discussed potential enhancements toward more reliable development of RL-based dynamic treatment regimes and invited further discussion within the community. Code is available at https://github.com/GilesLuo/ReassessDTR.

A Survey of Few-Shot Learning for Biomedical Time Series

Advancements in wearable sensor technologies and the digitization of medical records have contributed to the unprecedented ubiquity of biomedical time series data. Data-driven models have tremendous potential to assist clinical diagnosis and improve patient care by improving long-term monitoring capabilities, facilitating early disease detection and intervention, as well as promoting personalized healthcare delivery. However, accessing extensively labeled datasets to train data-hungry deep learning models encounters many barriers, such as long-tail distribution of rare diseases, cost of annotation, privacy and security concerns, data-sharing regulations, and ethical considerations. An emerging approach to overcome the scarcity of labeled data is to augment AI methods with human-like capabilities to leverage past experiences to learn new tasks with limited examples, called few-shot learning. This survey provides a comprehensive review and comparison of few-shot learning methods for biomedical time series applications. The clinical benefits and limitations of such methods are discussed in relation to traditional data-driven approaches. This paper aims to provide insights into the current landscape of few-shot learning for biomedical time series and its implications for future research and applications.

Understanding Missingness in Time-series Electronic Health Records for Individualized Representation

With the widespread of machine learning models for healthcare applications, there is increased interest in building applications for personalized medicine. Despite the plethora of proposed research for personalized medicine, very few focus on representing missingness and learning from the missingness patterns in time-series Electronic Health Records (EHR) data. The lack of focus on missingness representation in an individualized way limits the full utilization of machine learning applications towards true personalization. In this brief communication, we highlight new insights into patterns of missingness with real-world examples and implications of missingness in EHRs. The insights in this work aim to bridge the gap between theoretical assumptions and practical observations in real-world EHRs. We hope this work will open new doors for exploring directions for better representation in predictive modelling for true personalization.

A Perspective on Individualized Treatment Effects Estimation from Time-series Health Data

The burden of diseases is rising worldwide, with unequal treatment efficacy for patient populations that are underrepresented in clinical trials. Healthcare, however, is driven by the average population effect of medical treatments and, therefore, operates in a "one-size-fits-all" approach, not necessarily what best fits each patient. These facts suggest a pressing need for methodologies to study individualized treatment effects (ITE) to drive personalized treatment. Despite the increased interest in machine-learning-driven ITE estimation models, the vast majority focus on tabular data with limited review and understanding of methodologies proposed for time-series electronic health records (EHRs). To this end, this work provides an overview of ITE works for time-series data and insights into future research. The work summarizes the latest work in the literature and reviews it in light of theoretical assumptions, types of treatment settings, and computational frameworks. Furthermore, this work discusses challenges and future research directions for ITEs in a time-series setting. We hope this work opens new directions and serves as a resource for understanding one of the exciting yet under-studied research areas.

IGNITE: Individualized GeNeration of Imputations in Time-series Electronic health records

Electronic Health Records present a valuable modality for driving personalized medicine, where treatment is tailored to fit individual-level differences. For this purpose, many data-driven machine learning and statistical models rely on the wealth of longitudinal EHRs to study patients' physiological and treatment effects. However, longitudinal EHRs tend to be sparse and highly missing, where missingness could also be informative and reflect the underlying patient's health status. Therefore, the success of data-driven models for personalized medicine highly depends on how the EHR data is represented from physiological data, treatments, and the missing values in the data. To this end, we propose a novel deep-learning model that learns the underlying patient dynamics over time across multivariate data to generate personalized realistic values conditioning on an individual's demographic characteristics and treatments. Our proposed model, IGNITE (Individualized GeNeration of Imputations in Time-series Electronic health records), utilises a conditional dual-variational autoencoder augmented with dual-stage attention to generate missing values for an individual. In IGNITE, we further propose a novel individualized missingness mask (IMM), which helps our model generate values based on the individual's observed data and missingness patterns. We further extend the use of IGNITE from imputing missingness to a personalized data synthesizer, where it generates missing EHRs that were never observed prior or even generates new patients for various applications. We validate our model on three large publicly available datasets and show that IGNITE outperforms state-of-the-art approaches in missing data reconstruction and task prediction.

DySurv: Dynamic Deep Learning Model for Survival Prediction in the ICU

Survival analysis helps approximate underlying distributions of time-to-events which in the case of critical care like in the ICU can be a powerful tool for dynamic mortality risk prediction. Extending beyond the classical Cox model, deep learning techniques have been leveraged over the last years relaxing the many constraints of their counterparts from statistical methods. In this work, we propose a novel conditional variational autoencoder-based method called DySurv which uses a combination of static and time-series measurements from patient electronic health records in estimating risk of death dynamically in the ICU. DySurv has been tested on standard benchmarks where it outperforms most existing methods including other deep learning methods and we evaluate it on a real-world patient database from MIMIC-IV. The predictive capacity of DySurv is consistent and the survival estimates remain disentangled across different datasets supporting the idea that dynamic deep learning models based on conditional variational inference in multi-task cases can be robust models for survival analysis.

How to Evaluate Semantic Communications for Images with ViTScore Metric?

Semantic communications (SC) have been expected to be a new paradigm shifting to catalyze the next generation communication, whose main concerns shift from accurate bit transmission to effective semantic information exchange in communications. However, the previous and widely-used metrics for images are not applicable to evaluate the image semantic similarity in SC. Classical metrics to measure the similarity between two images usually rely on the pixel level or the structural level, such as the PSNR and the MS-SSIM. Straightforwardly using some tailored metrics based on deep-learning methods in CV community, such as the LPIPS, is infeasible for SC. To tackle this, inspired by BERTScore in NLP community, we propose a novel metric for evaluating image semantic similarity, named Vision Transformer Score (ViTScore). We prove theoretically that ViTScore has 3 important properties, including symmetry, boundedness, and normalization, which make ViTScore convenient and intuitive for image measurement. To evaluate the performance of ViTScore, we compare ViTScore with 3 typical metrics (PSNR, MS-SSIM, and LPIPS) through 5 classes of experiments. Experimental results demonstrate that ViTScore can better evaluate the image semantic similarity than the other 3 typical metrics, which indicates that ViTScore is an effective performance metric when deployed in SC scenarios.