Electronic health records (EHR) are characterized as non-stationary, heterogeneous, noisy, and sparse data; therefore, it is challenging to learn the regularities or patterns inherent within them. In particular, sparseness caused mostly by many missing values has attracted the attention of researchers, who have attempted to find a better use of all available samples for determining the solution of a primary target task through the defining a secondary imputation problem. Methodologically, existing methods, either deterministic or stochastic, have applied different assumptions to impute missing values. However, once the missing values are imputed, most existing methods do not consider the fidelity or confidence of the imputed values in the modeling of downstream tasks. Undoubtedly, an erroneous or improper imputation of missing variables can cause difficulties in modeling as well as a degraded performance. In this study, we present a novel variational recurrent network that (i) estimates the distribution of missing variables allowing to represent uncertainty in the imputed values, (ii) updates hidden states by explicitly applying fidelity based on a variance of the imputed values during a recurrence (i.e., uncertainty propagation over time), and (iii) predicts the possibility of in-hospital mortality. It is noteworthy that our model can conduct these procedures in a single stream and learn all network parameters jointly in an end-to-end manner. We validated the effectiveness of our method using the public datasets of MIMIC-III and PhysioNet challenge 2012 by comparing with and outperforming other state-of-the-art methods for mortality prediction considered in our experiments. In addition, we identified the behavior of the model that well represented the uncertainties for the imputed estimates, which indicated a high correlation between the calculated MAE and the uncertainty.
Mortality prediction of diverse rare diseases using electronic health record (EHR) data is a crucial task for intelligent healthcare. However, data insufficiency and the clinical diversity of rare diseases make it hard for directly training deep learning models on individual disease data or all the data from different diseases. Mortality prediction for these patients with different diseases can be viewed as a multi-task learning problem with insufficient data and large task number. But the tasks with little training data also make it hard to train task-specific modules in multi-task learning m…
Electronic Health Record (EHR) systems provide critical, rich and valuable information at high frequency. One of the most exciting applications of EHR data is in developing a real-time mortality warning system with tools from survival analysis. However, most of the survival analysis methods used recently are based on (semi)parametric models using static covariates. These models do not take advantage of the information conveyed by the time-varying EHR data. In this work, we present an application of a highly scalable survival analysis method, BoXHED 2.0 to develop a real-time in-ICU mortality w…
College of Information and Computer Sciences（信息与计算机科学学院）；University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）
Intensive Care Unit Electronic Health Records (ICU EHRs) store multimodal data about patients including clinical notes, sparse and irregularly sampled physiological time series, lab results, and more. To date, most methods designed to learn predictive models from ICU EHR data have focused on a single modality. In this paper, we leverage the recently proposed interpolation-prediction deep learning architecture(Shukla and Marlin 2019) as a basis for exploring how physiological time series data and clinical notes can be integrated into a unified mortality prediction model. We study both early and…
Time series data are prevalent in electronic health records, mostly in the form of physiological parameters such as vital signs and lab tests. The patterns of these values may be significant indicators of patients' clinical states and there might be patterns that are unknown to clinicians but are highly predictive of some outcomes. Many of these values are also missing which makes it difficult to apply existing methods like decision trees. We propose a recurrent neural network model that reduces overfitting to noisy observations by limiting interactions between features. We analyze its perform…
Northwestern University Feinberg School of Medicine（西北大学范伯格医学院）
Background: The increasing adoption of electronic health records (EHR) across the US has created troves of computable data, to which machine learning methods have been applied to extract useful insights. EHR data, represented as a three-dimensional analogue of a matrix (tensor), is decomposed into two-dimensional factors that can be interpreted as computational phenotypes. Methods: We apply constrained tensor factorization to derive computational phenotypes and predict mortality in cohorts of patients with breast, prostate, colorectal, or lung cancer in the Northwestern Medicine Enterprise Dat…
The intensive care units (ICUs) are responsible for generating a wealth of useful data in the form of Electronic Health Record (EHR). This data allows for the development of a prediction tool with perfect knowledge backing. We aimed to build a mortality prediction model on 2012 Physionet Challenge mortality prediction database of 4000 patients admitted in ICU. The challenges in the dataset, such as high dimensionality, imbalanced distribution, and missing values were tackled with analytical methods and tools via feature engineering and new variable construction. The objective of the research i…
Electronic health records (EHR) are rich heterogeneous collection of patient health information, whose broad adoption provides great opportunities for systematic health data mining. However, heterogeneous EHR data types and biased ascertainment impose computational challenges. Here, we present mixEHR, an unsupervised generative model integrating collaborative filtering and latent topic models, which jointly models the discrete distributions of data observation bias and actual data using latent disease-topic distributions. We apply mixEHR on 12.8 million phenotypic observations from the MIMIC d…
Rolling Day-Wise Mortality Prediction in Critically Ill Patients With AKI on CRRT Utilizing Machine Pressure Waveforms
University of Alabama at Birmingham（阿拉巴马大学伯明翰分校）；University of Cincinnati（辛辛那提大学）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）；UT Southwestern Medical Center（德克萨斯大学西南医学中心）
Florida State University（佛罗里达州立大学）；University of Florida（佛罗里达大学）
Predicting the risk of mortality for patients with acute myocardial infarction (AMI) using electronic health records (EHRs) data can help identify risky patients who might need more tailored care. In our previous work, we built computational models to predict one-year mortality of patients admitted to an intensive care unit (ICU) with AMI or post myocardial infarction syndrome. Our prior work only used the structured clinical data from MIMIC-III, a publicly available ICU clinical database. In this study, we enhanced our work by adding the word embedding features from free-text discharge summar…
Dynamic assessment of patient status (e.g. by an automated, continuously updated assessment of outcome) in the Intensive Care Unit (ICU) is of paramount importance for early alerting, decision support and resource allocation. Extraction and cleaning of expert-selected clinical variables discards information and protracts collaborative efforts to introduce machine learning in medicine. We present improved aggregation methods for a flexible deep learning architecture which learns a joint representation of patient chart, lab and output events. Our models outperform recent deep learning models for…
Geisinger（盖辛格医疗中心）；University of Kentucky（肯塔基大学）；University of New Mexico（新墨西哥大学）
Predicting future clinical events helps physicians guide appropriate intervention. Machine learning has tremendous promise to assist physicians with predictions based on the discovery of complex patterns from historical data, such as large, longitudinal electronic health records (EHR). This study is a first attempt to demonstrate such capabilities using raw echocardiographic videos of the heart. We show that a large dataset of 723,754 clinically-acquired echocardiographic videos (~45 million images) linked to longitudinal follow-up data in 27,028 patients can be used to train a deep neural net…
University of Pittsburgh（匹兹堡大学）；Beijing Information Science & Technology University（北京信息科技大学）；University of Pittsburgh Medical Center（匹兹堡大学医学中心）；Astrata Solutions（阿斯特拉塔解决方案公司）
Heart failure (HF) is a major cause of mortality. Accurately monitoring HF progress and adjust therapies are critical for improving patient outcomes. An experienced cardiologist can make accurate HF stage diagnoses based on combination of symptoms, signs, and lab results from the electronic health records (EHR) of a patient, without directly measuring heart function. We examined whether machine learning models, more specifically the XGBoost model, can accurately predict patient stage based on EHR, and we further applied the SHapley Additive exPlanations (SHAP) framework to identify informative…
Hasso Plattner Institute for Digital Health at Mount Sinai（西奈山哈索·普拉特纳数字健康研究所）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）；School of Informatics, Computing, and Engineering, Indiana University（印第安纳大学信息学、计算与工程学院）；Dell Medical School, University of Texas at Austin（德克萨斯大学奥斯汀分校戴尔医学院）；School of Informatics, University of Texas at Austin（德克萨斯大学奥斯汀分校信息学院）
Computational prediction of in-hospital mortality in the setting of an intensive care unit can help clinical practitioners to guide care and make early decisions for interventions. As clinical data are complex and varied in their structure and components, continued innovation of modeling strategies is required to identify architectures that can best model outcomes. In this work, we train a Heterogeneous Graph Model (HGM) on Electronic Health Record data and use the resulting embedding vector as additional information added to a Convolutional Neural Network (CNN) model for predicting in-hospita…
In this work, we propose a multi-task recurrent neural network with attention mechanism for predicting cardiovascular events from electronic health records (EHRs) at different time horizons. The proposed approach is compared to a standard clinical risk predictor (QRISK) and machine learning alternatives using 5-year data from a NHS Foundation Trust. The proposed model outperforms standard clinical risk scores in predicting stroke (AUC=0.85) and myocardial infarction (AUC=0.89), considering the largest time horizon. Benefit of using an \gls{mt} setting becomes visible for very short time horizo…
College of Information and Computer Sciences（信息与计算机科学学院）；University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）
While the volume of electronic health records (EHR) data continues to grow, it remains rare for hospital systems to capture dense physiological data streams, even in the data-rich intensive care unit setting. Instead, typical EHR records consist of sparse and irregularly observed multivariate time series, which are well understood to present particularly challenging problems for machine learning methods. In this paper, we present a new deep learning architecture for addressing this problem based on the use of a semi-parametric interpolation network followed by the application of a prediction n…
Cornell University（康奈尔大学）；Michigan State University（密歇根州立大学）；University of Michigan（密歇根大学）；Oregon Health & Science University（俄勒冈健康与科学大学）
In recent years, increasingly augmentation of health data, such as patient Electronic Health Records (EHR), are becoming readily available. This provides an unprecedented opportunity for knowledge discovery and data mining algorithms to dig insights from them, which can, later on, be helpful to the improvement of the quality of care delivery. Predictive modeling of clinical risk, including in-hospital mortality, hospital readmission, chronic disease onset, condition exacerbation, etc., from patient EHR, is one of the health data analytic problems that attract most of the interests. The reason …
ICU Mortality Prediction Using Long Short-Term Memory Networks
Faculty of Medicine, University of Monastir（莫纳斯提尔大学医学院）；Higher Institute of Computer Sciences and Mathematics, University of Monastir（莫纳斯提尔大学高等计算机科学与数学学院）
TOBB University of Economics and Technology（TOBB经济与技术大学）
Drug representations have played an important role in cheminformatics. However, in the healthcare domain, drug representations have been underused relative to the rest of Electronic Health Record (EHR) data, due to the complexity of high dimensional drug representations and the lack of proper pipeline that will allow to convert clinical drugs to their representations. Time-varying vital signs, laboratory measurements, and related time-series signals are commonly used to predict clinical outcomes. In this work, we demonstrated that using clinical drug representations in addition to other clinic…
A Comprehensive Benchmark for COVID-19 Predictive Modeling Using Electronic Health Records in Intensive Care
University of Edinburgh（爱丁堡大学）；Health Data Research UK（英国健康数据研究中心）；Peking University（北京大学）；Peking University Third Hospital（北京大学第三医院）；Kaihong Digital（凯宏数字）
Beijing University of Technology（北京工业大学）；University College Dublin（都柏林大学学院）；ADAPT SFI Research Centre（ADAPT SFI研究中心）
Stroke is widely considered as the second most common cause of mortality. The adverse consequences of stroke have led to global interest and work for improving the management and diagnosis of stroke. Various techniques for data mining have been used globally for accurate prediction of occurrence of stroke based on the risk factors that are associated with the electronic health care records (EHRs) of the patients. In particular, EHRs routinely contain several thousands of features and most of them are redundant and irrelevant that need to be discarded to enhance the prediction accuracy. The cho…
Heinz College of Information Systems and Public Policy（海因茨信息系统与公共政策学院）；Carnegie Mellon University（卡内基梅隆大学）
In healthcare, the highest risk individuals for morbidity and mortality are rarely those with the greatest modifiable risk. By contrast, many machine learning formulations implicitly attend to the highest risk individuals. We focus on this problem in point processes, a popular modeling technique for the analysis of the temporal event sequences in electronic health records (EHR) data with applications in risk stratification and risk score systems. We show that optimization of the log-likelihood function also gives disproportionate attention to high risk individuals and leads to poor prediction …
Think as a Doctor: An Interpretable AI Approach for ICU Mortality Prediction
School of Information Management & Engineering, Shanghai University of Finance and Economics（上海金融学院信息管理与工程学院）；Key Laboratory of Data Intelligence and Management (Beihang University), Ministry of Industry and Information Technology, School of Economics and Management, Beihang University（北京航空航天大学数据智能与管理重点实验室）
CT-HEG: A Bidirectional, Timestamp-Attributed Event Graph for ICU In-Hospital Mortality Prediction - An Architectural Ablation Study
Westcliff University（韦斯特克利夫大学）；Northern University Bangladesh（孟加拉国北方大学）；Stanton University（斯坦顿大学）；Washington University of Science and Technology（华盛顿科技大学）
Robô Laura；University of São Paulo（圣保罗大学）；Pontifical Catholic University of Parana（巴拉那天主教大学）；Federal University of Parana（巴拉那联邦大学）
Early recognition of clinical deterioration (CD) has vital importance in patients' survival from exacerbation or death. Electronic health records (EHRs) data have been widely employed in Early Warning Scores (EWS) to measure CD risk in hospitalized patients. Recently, EHRs data have been utilized in Machine Learning (ML) models to predict mortality and CD. The ML models have shown superior performance in CD prediction compared to EWS. Since EHRs data are structured and tabular, conventional ML models are generally applied to them, and less effort is put into evaluating the artificial neural ne…
Self-explaining Neural Network with Concept-based Explanations for ICU Mortality Prediction
Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA（计算机科学与工程系，华盛顿大学圣路易斯分校）；Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA（信息学院，华盛顿大学医学学院）；Department of Anaesthesiology, Washington University School of Medicine, St. Louis, MO, USA（麻醉学系，华盛顿大学医学学院）；Department of Pulmonary Critical Care and Medicine, Washington University School of Medicine, St. Louis, MO, USA（呼吸科重症医学系，华盛顿大学医学学院）
School of Biomedical Informatics, University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心生物医学信息学院）；School of Public Health, University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心公共卫生学院）；School of Computer Science and Technology, Dalian University of Technology（大连理工大学计算机科学与技术学院）；Computer Science Department, School of Engineering, Rice University（莱斯大学工程学院计算机科学系）
Recently, there is great interest to investigate the application of deep learning models for the prediction of clinical events using electronic health records (EHR) data. In EHR data, a patient's history is often represented as a sequence of visits, and each visit contains multiple events. As a result, deep learning models developed for sequence modeling, like recurrent neural networks (RNNs) are common architecture for EHR-based clinical events predictive models. While a large variety of RNN models were proposed in the literature, it is unclear if complex architecture innovations will offer s…
F. Hoffmann-La Roche Ltd（罗氏制药公司）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；ETH Zurich（苏黎世联邦理工学院）；John A. Paulson School of Engineering and Applied Sciences, Harvard University（哈佛大学约翰·A·保尔森工程与应用科学学院）；Beth Israel Deaconess Medical Center, Harvard Medical School（哈佛医学院贝斯以色列女执事医疗中心）；MIT Critical Data, Laboratory for Computational Physiology, Institute for Medical Engineering and Science, Harvard-MIT Health Sciences & Technology（哈佛-麻省理工健康科学与技术研究所医学工程与科学研究所计算生理学实验室MIT关键数据）；University Hospital of Tübingen（蒂宾根大学医院）；Kantonsspital Winterthur（温特图尔州立医院）
Coronavirus Disease 2019 (COVID-19) is an emerging respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with rapid human-to-human transmission and a high case fatality rate particularly in older patients. Due to the exponential growth of infections, many healthcare systems across the world are under pressure to care for increasing amounts of at-risk patients. Given the high number of infected patients, identifying patients with the highest mortality risk early is critical to enable effective intervention and optimal prioritisation of care. Here, we pre…
Improving Hospital Risk Prediction with Knowledge-Augmented Multimodal EHR Modeling
Department of Computer Science, University of Virginia（大学计算机科学系）；University of Virginia School of Medicine（弗吉尼亚大学医学院）；Virginia Polytechnic Institute and State University（弗吉尼亚理工学院和州立大学）；Biocomplexity Institute and Initiative, University of Virginia（大学生物复杂性研究所）；Division of Infectious Diseases & International Health, University of Virginia School of Medicine（大学感染性疾病与国际卫生分会）
TA-RNN-Medical-Hybrid: A Time-Aware and Interpretable Framework for Mortality Risk Prediction
Department of Computer Engineering, SRC.,Islamic Azad university（计算机工程系，伊斯兰教Azad大学）；School of Computer Engineering, Iran university of Science and technology（计算机工程学院，伊朗科学技术大学）
We present a machine learning pipeline and model that uses the entire uncurated EHR for prediction of in-hospital mortality at arbitrary time intervals, using all available chart, lab and output events, without the need for pre-processing or feature engineering. Data for more than 45,000 American ICU patients from the MIMIC-III database were used to develop an ICU mortality prediction model. All chart, lab and output events were treated by the model in the same manner inspired by Natural Language Processing (NLP). Patient events were discretized by percentile and mapped to learnt embeddings be…
CardioMeta: Calibrated Multi-Task Prediction of Diabetes, Hypertension, and Cardiovascular Disease Across Population and EHR Data
School of Computing, Wichita State University（威奇托州立大学计算学院）；Department of Computer Science and Engineering, American International University-Bangladesh（孟加拉国美国国际大学计算机科学与工程系）；School of Computer Science and Engineering, The University of Aizu（会津大学计算机科学与工程学院）
Electronic Health Records (EHRs) exhibit a high amount of missing data due to variations of patient conditions and treatment needs. Imputation of missing values has been considered an effective approach to deal with this challenge. Existing work separates imputation method and prediction model as two independent parts of an EHR-based machine learning system. We propose an integrated end-to-end approach by utilizing a Compound Density Network (CDNet) that allows the imputation method and prediction model to be tuned together within a single framework. CDNet consists of a Gated recurrent unit (G…
Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院西奈山哈索·普拉特纳数字健康研究所）；Indiana University（印第安纳大学）；Weill Cornell Medicine（威尔康奈尔医学院）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）；Harvard University（哈佛大学）；University of Texas at Austin（德克萨斯大学奥斯汀分校）
Machine Learning (ML) models typically require large-scale, balanced training data to be robust, generalizable, and effective in the context of healthcare. This has been a major issue for developing ML models for the coronavirus-disease 2019 (COVID-19) pandemic where data is highly imbalanced, particularly within electronic health records (EHR) research. Conventional approaches in ML use cross-entropy loss (CEL) that often suffers from poor margin classification. For the first time, we show that contrastive loss (CL) improves the performance of CEL especially for imbalanced EHR data and the re…
The School of Computer Science and Technology, Xi’an Jiaotong University（西安交通大学计算机科学与技术学院）；The School of Life Science and Technology, Xi’an Jiaotong University（西安交通大学生命科学与技术学院）；Lishui People’s Hospital（丽水市人民医院）
The incidence of Acute Kidney Injury (AKI) commonly happens in the Intensive Care Unit (ICU) patients, especially in the adults, which is an independent risk factor affecting short-term and long-term mortality. Though researchers in recent years highlight the early prediction of AKI, the performance of existing models are not precise enough. The objective of this research is to precisely predict AKI by means of Convolutional Neural Network on Electronic Health Record (EHR) data. The data sets used in this research are two public Electronic Health Record (EHR) databases: MIMIC-III and eICU data…
Prompting Large Language Models for Zero-Shot Clinical Prediction with Structured Longitudinal Electronic Health Record Data
Institute of Artificial Intelligence, Beihang University（北京航空航天大学人工智能研究院）；Centre for Medical Informatics, University of Edinburgh（爱丁堡大学医学信息学中心）；School of Computing, National University of Singapore（新加坡国立大学计算机学院）；National Engineering Research Center for Software Engineering, Peking University（北京大学国家软件工程研究中心）；Health Data Research UK（英国健康数据研究中心）
Inadequacy of common stochastic neural networks for reliable clinical decision support
Leipzig University（莱比锡大学）；Innovation Center Computer Assisted Surgery (ICCAS), Leipzig University（莱比锡大学计算机辅助手术创新中心）；Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University（莱比锡大学德累斯顿/莱比锡可扩展数据分析与人工智能中心）
