Objective: Temporal electronic health records (EHRs) can be a wealth of information for secondary uses, such as clinical events prediction or chronic disease management. However, challenges exist for temporal data representation. We therefore sought to identify these challenges and evaluate novel methodologies for addressing them through a systematic examination of deep learning solutions. Methods: We searched five databases (PubMed, EMBASE, the Institute of Electrical and Electronics Engineers [IEEE] Xplore Digital Library, the Association for Computing Machinery [ACM] digital library, and Web of Science) complemented with hand-searching in several prestigious computer science conference proceedings. We sought articles that reported deep learning methodologies on temporal data representation in structured EHR data from January 1, 2010, to August 30, 2020. We summarized and analyzed the selected articles from three perspectives: nature of time series, methodology, and model implementation. Results: We included 98 articles related to temporal data representation using deep learning. Four major challenges were identified, including data irregularity, data heterogeneity, data sparsity, and model opacity. We then studied how deep learning techniques were applied to address these challenges. Finally, we discuss some open challenges arising from deep learning. Conclusion: Temporal EHR data present several major challenges for clinical prediction modeling and data utilization. To some extent, current deep learning solutions can address these challenges. Future studies can consider designing comprehensive and integrated solutions. Moreover, researchers should incorporate additional clinical domain knowledge into study designs and enhance the interpretability of the model to facilitate its implementation in clinical practice.
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