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Register a new userDeep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review
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Yuqi Si
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Patient representation learning refers to learning a dense mathematical representation of a patient that encodes meaningful information from Electronic Health Records (EHRs). This is generally performed using advanced deep learning methods. This study presents a systematic review of this field and provides both qualitative and quantitative analyses from a methodological perspective. We identified studies developing patient representations from EHRs with deep learning methods from MEDLINE, EMBASE, Scopus, the Association for Computing Machinery (ACM) Digital Library, and Institute of Electrical and Electronics Engineers (IEEE) Xplore Digital Library. After screening 363 articles, 49 papers were included for a comprehensive data collection. We noticed a typical workflow starting with feeding raw data, applying deep learning models, and ending with clinical outcome predictions as evaluations of the learned representations. Specifically, learning representations from structured EHR data was dominant (37 out of 49 studies). Recurrent Neural Networks were widely applied as the deep learning architecture (LSTM: 13 studies, GRU: 11 studies). Disease prediction was the most common application and evaluation (31 studies). Benchmark datasets were mostly unavailable (28 studies) due to privacy concerns of EHR data, and code availability was assured in 20 studies. We show the importance and feasibility of learning comprehensive representations of patient EHR data through a systematic review. Advances in patient representation learning techniques will be essential for powering patient-level EHR analyses. Future work will still be devoted to leveraging the richness and potential of available EHR data. Knowledge distillation and advanced learning techniques will be exploited to assist the capability of learning patient representation further.
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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.
The past decade has seen an explosion in the amount of digital information stored in electronic health records (EHR). While primarily designed for archiving patient clinical information and administrative healthcare tasks, many researchers have found secondary use of these records for various clinical informatics tasks. Over the same period, the machine learning community has seen widespread advances in deep learning techniques, which also have been successfully applied to the vast amount of EHR data. In this paper, we review these deep EHR systems, examining architectures, technical aspects, and clinical applications. We also identify shortcomings of current techniques and discuss avenues of future research for EHR-based deep learning.
Increasing volume of Electronic Health Records (EHR) in recent years provides great opportunities for data scientists to collaborate on different aspects of healthcare research by applying advanced analytics to these EHR clinical data. A key requirement however is obtaining meaningful insights from high dimensional, sparse and complex clinical data. Data science approaches typically address this challenge by performing feature learning in order to build more reliable and informative feature representations from clinical data followed by supervised learning. In this paper, we propose a predictive modeling approach based on deep learning based feature representations and word embedding techniques. Our method uses different deep architectures (stacked sparse autoencoders, deep belief network, adversarial autoencoders and variational autoencoders) for feature representation in higher-level abstraction to obtain effective and robust features from EHRs, and then build prediction models on top of them. Our approach is particularly useful when the unlabeled data is abundant whereas labeled data is scarce. We investigate the performance of representation learning through a supervised learning approach. Our focus is to present a comparative study to evaluate the performance of different deep architectures through supervised learning and provide insights in the choice of deep feature representation techniques. Our experiments demonstrate that for small data sets, stacked sparse autoencoder demonstrates a superior generality performance in prediction due to sparsity regularization whereas variational autoencoders outperform the competing approaches for large data sets due to its capability of learning the representation distribution
Increasing volume of Electronic Health Records (EHR) in recent years provides great opportunities for data scientists to collaborate on different aspects of healthcare research by applying advanced analytics to these EHR clinical data. A key requirement however is obtaining meaningful insights from high dimensional, sparse and complex clinical data. Data science approaches typically address this challenge by performing feature learning in order to build more reliable and informative feature representations from clinical data followed by supervised learning. In this paper, we propose a predictive modeling approach based on deep learning based feature representations and word embedding techniques. Our method uses different deep architectures (stacked sparse autoencoders, deep belief network, adversarial autoencoders and variational autoencoders) for feature representation in higher-level abstraction to obtain effective and robust features from EHRs, and then build prediction models on top of them. Our approach is particularly useful when the unlabeled data is abundant whereas labeled data is scarce. We investigate the performance of representation learning through a supervised learning approach. Our focus is to present a comparative study to evaluate the performance of different deep architectures through supervised learning and provide insights in the choice of deep feature representation techniques. Our experiments demonstrate that for small data sets, stacked sparse autoencoder demonstrates a superior generality performance in prediction due to sparsity regularization whereas variational autoencoders outperform the competing approaches for large data sets due to its capability of learning the representation distribution.
In recent years, we have witnessed an increased interest in temporal modeling of patient records from large scale Electronic Health Records (EHR). While simpler RNN models have been used for such problems, memory networks, which in other domains were found to generalize well, are underutilized. Traditional memory networks involve diffused and non-linear operations where influence of past events on outputs are not readily quantifiable. We posit that this lack of interpretability makes such networks not applicable for EHR analysis. While networks with explicit memory have been proposed recently, the discontinuities imposed by the discrete operations make such networks harder to train and require more supervision. The problem is further exacerbated in the limited data setting of EHR studies. In this paper, we propose a novel memory architecture that is more interpretable than traditional memory networks while being easier to train than explicit memory banks. Inspired by well-known models of human cognition, we propose partitioning the external memory space into (a) a primary explicit memory block to store exact replicas of recent events to support interpretations, followed by (b) a secondary blurred memory block that accumulates salient aspects of past events dropped from the explicit block as higher level abstractions and allow training with less supervision by stabilize the gradients. We apply the model for 3 learning problems on ICU records from the MIMIC III database spanning millions of data points. Our model performs comparably to the state-of the art while also, crucially, enabling ready interpretation of the results.
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