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Multivariate time-series data are frequently observed in critical care settings and are typically characterized by sparsity (missing information) and irregular time intervals. Existing approaches for learning representations in this domain handle these challenges by either aggregation or imputation of values, which in-turn suppresses the fine-grained information and adds undesirable noise/overhead into the machine learning model. To tackle this problem, we propose a S elf-supervised Tra nsformer for T ime- S eries (STraTS) model, which overcomes these pitfalls by treating time-series as a set of observation triplets instead of using the standard dense matrix representation. It employs a novel Continuous Value Embedding technique to encode continuous time and variable values without the need for discretization. It is composed of a Transformer component with multi-head attention layers, which enable it to learn contextual triplet embeddings while avoiding the problems of recurrence and vanishing gradients that occur in recurrent architectures. In addition, to tackle the problem of limited availability of labeled data (which is typically observed in many healthcare applications), STraTS utilizes self-supervision by leveraging unlabeled data to learn better representations by using time-series forecasting as an auxiliary proxy task. Experiments on real-world multivariate clinical time-series benchmark datasets demonstrate that STraTS has better prediction performance than state-of-the-art methods for mortality prediction, especially when labeled data is limited. Finally, we also present an interpretable version of STraTS, which can identify important measurements in the time-series data. Our data preprocessing and model implementation codes are available at https://github.com/sindhura97/STraTS . 

Abstract Medical images are difficult to comprehend for a person without expertise. The scarcity of medical practitioners across the globe often face the issue of physical and mental fatigue due to the high number of cases, inducing human errors during the diagnosis. In such scenarios, having an additional opinion can be helpful in boosting the confidence of the decision maker. Thus, it becomes crucial to have a reliable visual question answering (VQA) system to provide a ‘second opinion’ on medical cases. However, most of the VQA systems that work today cater to real-world problems and are not specifically tailored for handling medical images. Moreover, the VQA system for medical images needs to consider a limited amount of training data available in this domain. In this paper, we develop MedFuseNet , an attention-based multimodal deep learning model, for VQA on medical images taking the associated challenges into account. Our MedFuseNet aims at maximizing the learning with minimal complexity by breaking the problem statement into simpler tasks and predicting the answer. We tackle two types of answer prediction—categorization and generation. We conducted an extensive set of quantitative and qualitative analyses to evaluate the performance of MedFuseNet . Our experiments demonstrate that MedFuseNet outperforms the state-of-the-art VQA methods, and that visualization of the captured attentions showcases the intepretability of our model’s predicted results. 

Developing prediction models for emerging infectious diseases from relatively small numbers of cases is a critical need for improving pandemic preparedness. Using COVID-19 as an exemplar, we propose a transfer learning methodology for developing predictive models from multi-modal electronic healthcare records by leveraging information from more prevalent diseases with shared clinical characteristics. Our novel hierarchical, multi-modal model ($${\textsc {TransMED}}$$$TRANS\mathrm{MED}$) integrates baseline risk factors from the natural language processing of clinical notes at admission, time-series measurements of biomarkers obtained from laboratory tests, and discrete diagnostic, procedure and drug codes. We demonstrate the alignment of$${\textsc {TransMED}}$$$TRANS\mathrm{MED}$’s predictions with well-established clinical knowledge about COVID-19 through univariate and multivariate risk factor driven sub-cohort analysis.$${\textsc {TransMED}}$$$TRANS\mathrm{MED}$’s superior performance over state-of-the-art methods shows that leveraging patient data across modalities and transferring prior knowledge from similar disorders is critical for accurate prediction of patient outcomes, and this approach may serve as an important tool in the early response to future pandemics.

 

Electronic health records (EHRs) have been heavily used in modern healthcare systems for recording patients' admission information to health facilities. Many data-driven approaches employ temporal features in EHR for predicting specific diseases, readmission times, and diagnoses of patients. However, most existing predictive models cannot fully utilize EHR data, due to an inherent lack of labels in supervised training for some temporal events. Moreover, it is hard for the existing methods to simultaneously provide generic and personalized interpretability. To address these challenges, we propose Sherbet, a self-supervised graph learning framework with hyperbolic embeddings for temporal health event prediction. We first propose a hyperbolic embedding method with information flow to pretrain medical code representations in a hierarchical structure. We incorporate these pretrained representations into a graph neural network (GNN) to detect disease complications and design a multilevel attention method to compute the contributions of particular diseases and admissions, thus enhancing personalized interpretability. We present a new hierarchy-enhanced historical prediction proxy task in our self-supervised learning framework to fully utilize EHR data and exploit medical domain knowledge. We conduct a comprehensive set of experiments on widely used publicly available EHR datasets to verify the effectiveness of our model. Our results demonstrate the proposed model's strengths in both predictive tasks and interpretable abilities.