Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review
The University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心）；Harvard Medical School（哈佛医学院）；Weill Cornell Medicine, Cornell University（康奈尔大学威尔康奈尔医学院）
Yuqi Si, Jingcheng Du, Zhao Li, Xiaoqian Jiang, Timothy Miller, Fei Wang, W. Jim Zheng, Kirk Roberts
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.
Durham University（杜伦大学）；Teesside University（提赛德大学）；Institute of Microelectronics, Chinese Academy of Sciences（中国科学院微电子研究所）；University of Chinese Academy of Sciences（中国科学院大学）
Disruptive technologies provides unparalleled opportunities to contribute to the identifications of many aspects in pervasive healthcare, from the adoption of the Internet of Things through to Machine Learning (ML) techniques. As a powerful tool, ML has been widely applied in patient-centric healthcare solutions. To further improve the quality of patient care, Electronic Health Records (EHRs) are commonly adopted in healthcare facilities for analysis. It is a crucial task to apply AI and ML to analyse those EHRs for prediction and diagnostics due to their highly unstructured, unbalanced, incom…
Electronic Health Records (EHR) have been heavily used in modern healthcare systems for recording patients' admission information to hospitals. Many data-driven approaches employ temporal features in EHR for predicting specific diseases, readmission times, or 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 existing works to simultaneously provide generic and personalized interpretability. To address these challenges, we first propose a hyper…
Indiana University Bloomington（印第安纳大学伯明顿分校）；Renmin University of China（中国人民大学）；University of Texas at Austin（德克萨斯大学奥斯汀分校）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）
Electronic Health Record (EHR) data has been of tremendous utility in Artificial Intelligence (AI) for healthcare such as predicting future clinical events. These tasks, however, often come with many challenges when using classical machine learning models due to a myriad of factors including class imbalance and data heterogeneity (i.e., the complex intra-class variances). To address some of these research gaps, this paper leverages the exciting contrastive learning framework and proposes a novel contrastive regularized clinical classification model. The contrastive loss is found to substantial…
Effective modeling of electronic health records (EHR) is rapidly becoming an important topic in both academia and industry. A recent study showed that using the graphical structure underlying EHR data (e.g. relationship between diagnoses and treatments) improves the performance of prediction tasks such as heart failure prediction. However, EHR data do not always contain complete structure information. Moreover, when it comes to claims data, structure information is completely unavailable to begin with. Under such circumstances, can we still do better than just treating EHR data as a flat-struc…
KAIST（韩国科学技术院）；MIT（麻省理工学院）；Asan Medical Center（峨山医学中心）；University of Ulsan College of Medicine（蔚山大学医学院）
Substantial increase in the use of Electronic Health Records (EHRs) has opened new frontiers for predictive healthcare. However, while EHR systems are nearly ubiquitous, they lack a unified code system for representing medical concepts. Heterogeneous formats of EHR present a substantial barrier for the training and deployment of state-of-the-art deep learning models at scale. To overcome this problem, we introduce Description-based Embedding, DescEmb, a code-agnostic description-based representation learning framework for predictive modeling on EHR. DescEmb takes advantage of the flexibility o…
Contrastive Learning on Multimodal Analysis of Electronic Health Records
Harvard T.H. Chan School of Public Health（哈佛T.H. 柏林公共卫生学院）；Harvard Medical School（哈佛医学院）；Rutgers University（罗格斯大学）；National University of Singapore（新加坡国立大学）
HyMaTE: A Hybrid Mamba and Transformer Model for EHR Representation Learning
University of Delaware Newark Delaware USA；Thomas Jefferson University \& Nemours Children's Health Wilmington Delaware USA；University of Delaware；Thomas Jefferson University \& Nemours Children's Health
Information in electronic health records (EHR), such as clinical narratives, examination reports, lab measurements, demographics, and other patient encounter entries, can be transformed into appropriate data representations that can be used for downstream clinical machine learning tasks using representation learning. Learning better representations is critical to improve the performance of downstream tasks. Due to the advances in machine learning, we now can learn better and meaningful representations from EHR through disentangling the underlying factors inside data and distilling large amount…
University of California Los Angeles（加利福尼亚大学洛杉矶分校）
Advancements in machine learning algorithms have had a beneficial impact on representation learning, classification, and prediction models built using electronic health record (EHR) data. Effort has been put both on increasing models' overall performance as well as improving their interpretability, particularly regarding the decision-making process. In this study, we present a temporal deep learning model to perform bidirectional representation learning on EHR sequences with a transformer architecture to predict future diagnosis of depression. This model is able to aggregate five heterogenous …
IQVIA Inc.（艾昆纬公司）；University of Minnesota Twin Cities（明尼苏达大学双城分校）
Automatic representation learning of key entities in electronic health record (EHR) data is a critical step for healthcare informatics that turns heterogeneous medical records into structured and actionable information. Here we propose ME2Vec, an algorithmic framework for learning low-dimensional vectors of the most common entities in EHR: medical services, doctors, and patients. ME2Vec leverages diverse graph embedding techniques to cater for the unique characteristic of each medical entity. Using real-world clinical data, we demonstrate the efficacy of ME2Vec over competitive baselines on di…
Shandong University（山东大学）；WeChat, Tencent（腾讯微信）；University of Amsterdam（阿姆斯特丹大学）
Electronic health record (EHR) coding is the task of assigning ICD codes to each EHR. Most previous studies either only focus on the frequent ICD codes or treat rare and frequent ICD codes in the same way. These methods perform well on frequent ICD codes but due to the extremely unbalanced distribution of ICD codes, the performance on rare ones is far from satisfactory. We seek to improve the performance for both frequent and rare ICD codes by using a contrastive graph-based EHR coding framework, CoGraph, which re-casts EHR coding as a few-shot learning task. First, we construct a heterogeneou…
Georgia Institute of Technology（佐治亚理工学院）；IBM Research（IBM研究院）；Vanderbilt University（范德堡大学）；Sutter Health（萨特健康）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Researchers require timely access to real-world longitudinal electronic health records (EHR) to develop, test, validate, and implement machine learning solutions that improve the quality and efficiency of healthcare. In contrast, health systems value deeply patient privacy and data security. De-identified EHRs do not adequately address the needs of health systems, as de-identified data are susceptible to re-identification and its volume is also limited. Synthetic EHRs offer a potential solution. In this paper, we propose EHR Variational Autoencoder (EVA) for synthesizing sequences of discrete …
IBM Research Europe（IBM欧洲研究院）；Monash University（莫纳什大学）；University of Oxford（牛津大学）
The wide adoption of Electronic Health Records (EHR) has resulted in large amounts of clinical data becoming available, which promises to support service delivery and advance clinical and informatics research. Deep learning techniques have demonstrated performance in predictive analytic tasks using EHRs yet they typically lack model result transparency or explainability functionalities and require cumbersome pre-processing tasks. Moreover, EHRs contain heterogeneous and multi-modal data points such as text, numbers and time series which further hinder visualisation and interpretability. This p…
Australian Artificial Intelligence Institute（澳大利亚人工智能研究所）；University of Technology Sydney（悉尼科技大学）；The Children’s Cancer Research Unit（儿童癌症研究组）；The Children’s Hospital at Westmead（韦斯特米德儿童医院）
A meaningful understanding of clinical protocols and patient pathways helps improve healthcare outcomes. Electronic health records (EHR) reflect real-world treatment behaviours that are used to enhance healthcare management but present challenges; protocols and pathways are often loosely defined and with elements frequently not recorded in EHRs, complicating the enhancement. To solve this challenge, healthcare objectives associated with healthcare management activities can be indirectly observed in EHRs as latent topics. Topic models, such as Latent Dirichlet Allocation (LDA), are used to iden…
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, …
Question Answering (QA) is a widely-used framework for developing and evaluating an intelligent machine. In this light, QA on Electronic Health Records (EHR), namely EHR QA, can work as a crucial milestone towards developing an intelligent agent in healthcare. EHR data are typically stored in a relational database, which can also be converted to a directed acyclic graph, allowing two approaches for EHR QA: Table-based QA and Knowledge Graph-based QA. We hypothesize that the graph-based approach is more suitable for EHR QA as graphs can represent relations between entities and values more natur…
CDMT-EHR: A Continuous-Time Diffusion Framework for Generating Mixed-Type Time-Series Electronic Health Records
Department of Core Informatics, Graduate School of Informatics, Osaka Metropolitan University（核心信息学系，信息学研究生学校，大阪 Metropolitan 大学）；Smart Data & Knowledge Services Department, German Research Center for Artificial Intelligence (DFKI GmbH)（智能数据与知识服务部，德国人工智能研究中心（DFKI GmbH））；Department of Hematology and Department of Laboratory Medicine and Medical Informatics, Graduate School of Medicine, Osaka Metropolitan University（血液科和实验室医学与医学信息学系，医学研究生学校，大阪 Metropolitan 大学）
Predict and Interpret Health Risk using EHR through Typical Patients
Peking University（北京大学）；Key Laboratory of High Confidence Software Technologies, Ministry of Education（高可信软件技术教育部重点实验室）；National Engineering Research Center of Software Engineering, Peking University（北京大学软件工程国家工程研究中心）；Peking University Third Hospital（北京大学第三医院）；Coventry University（考文垂大学）
University of Klagenfurt（克拉根福大学）；University of Innsbruck（因斯布鲁克大学）
The introduction of electronic personal health records (EHR) enables nationwide information exchange and curation among different health care systems. However, the current EHR systems do not provide transparent means for diagnosis support, medical research or can utilize the omnipresent data produced by the personal medical devices. Besides, the EHR systems are centrally orchestrated, which could potentially lead to a single point of failure. Therefore, in this article, we explore novel approaches for decentralizing machine learning over distributed ledgers to create intelligent EHR systems th…
University of Illinois at Chicago（伊利诺伊大学芝加哥分校）；Beihang University（北京航空航天大学）；Lehigh University（理海大学）
Mining Electronic Health Records (EHRs) becomes a promising topic because of the rich information they contain. By learning from EHRs, machine learning models can be built to help human experts to make medical decisions and thus improve healthcare quality. Recently, many models based on sequential or graph models are proposed to achieve this goal. EHRs contain multiple entities and relations and can be viewed as a heterogeneous graph. However, previous studies ignore the heterogeneity in EHRs. On the other hand, current heterogeneous graph neural networks cannot be simply used on an EHR graph …
Question Answering on Electronic Health Records (EHR-QA) has a significant impact on the healthcare domain, and it is being actively studied. Previous research on structured EHR-QA focuses on converting natural language queries into query language such as SQL or SPARQL (NLQ2Query), so the problem scope is limited to pre-defined data types by the specific query language. In order to expand the EHR-QA task beyond this limitation to handle multi-modal medical data and solve complex inference in the future, more primitive systemic language is needed. In this paper, we design the program-based mode…
CAAT-EHR: Cross-Attentional Autoregressive Transformer for Multimodal Electronic Health Record Embeddings
Department of Computer Science and Engineering, University of North Texas（计算机科学与工程系，北卡罗来纳大学达顿分校）；BioDiscovery Institute, University of North Texas（生物发现研究所，北卡罗来纳大学达顿分校）；Center for Computational Life Sciences, University of North Texas（计算生命科学中心，北卡罗来纳大学达顿分校）
Large Language Models are Powerful Electronic Health Record Encoders
Berlin Institute of Health at Charité – Universitätsmedizin Berlin（柏林夏里特医学院健康研究所）；BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program（BIH生物医学创新学院，BIH夏里特数字临床科学家计划）；Deutsches Herzzentrum der Charité – Medical Heart Center of Charité and German Heart Institute Berlin（夏里特德国心脏中心 – 夏里特医学院和德国心脏研究所柏林）；Layer Health, Inc.（Layer Health公司）
Predicting the health risks of patients using Electronic Health Records (EHR) has attracted considerable attention in recent years, especially with the development of deep learning techniques. Health risk refers to the probability of the occurrence of a specific health outcome for a specific patient. The predicted risks can be used to support decision-making by healthcare professionals. EHRs are structured patient journey data. Each patient journey contains a chronological set of clinical events, and within each clinical event, there is a set of clinical/medical activities. Due to variations o…
University of Michigan（密歇根大学）；University of Michigan Medical School（密歇根大学医学院）
Objective: When patients develop acute respiratory failure, accurately identifying the underlying etiology is essential for determining the best treatment. However, differentiating between common medical diagnoses can be challenging in clinical practice. Machine learning models could improve medical diagnosis by aiding in the diagnostic evaluation of these patients. Materials and Methods: Machine learning models were trained to predict the common causes of acute respiratory failure (pneumonia, heart failure, and/or COPD). Models were trained using chest radiographs and clinical data from the e…
Time-Aware Attention for Enhanced Electronic Health Records Modeling
Department of Statistics and Data Science, National University of Singapore（统计与数据科学系，新加坡国立大学）；School of Computing, National University of Singapore（计算学院，新加坡国立大学）；Department of Biostatistics, Harvard T.H. Chan School of Public Health, USA（生物统计学系，哈佛T.H. Chan公共卫生学院，美国）
An intelligent machine that can answer human questions based on electronic health records (EHR-QA) has a great practical value, such as supporting clinical decisions, managing hospital administration, and medical chatbots. Previous table-based QA studies focusing on translating natural questions into table queries (NLQ2SQL), however, suffer from the unique nature of EHR data due to complex and specialized medical terminology, hence increased decoding difficulty. In this paper, we design UniQA, a unified encoder-decoder architecture for EHR-QA where natural language questions are converted to q…
Due to patient privacy protection concerns, machine learning research in healthcare has been undeniably slower and limited than in other application domains. High-quality, realistic, synthetic electronic health records (EHRs) can be leveraged to accelerate methodological developments for research purposes while mitigating privacy concerns associated with data sharing. The current state-of-the-art model for synthetic EHR generation is generative adversarial networks, which are notoriously difficult to train and can suffer from mode collapse. Denoising Diffusion Probabilistic Models, a class of …
Stanford School of Medicine（斯坦福大学医学院）；Stanford University（斯坦福大学）
There is an emerging trend in the reinforcement learning for healthcare literature. In order to prepare longitudinal, irregularly sampled, clinical datasets for reinforcement learning algorithms, many researchers will resample the time series data to short, regular intervals and use last-observation-carried-forward (LOCF) imputation to fill in these gaps. Typically, they will not maintain any explicit information about which values were imputed. In this work, we (1) call attention to this practice and discuss its potential implications; (2) propose an alternative representation of the patient …
