Deep Learning with Heterogeneous Graph Embeddings for Mortality Prediction from Electronic Health Records
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）
Tingyi Wanyan, Hossein Honarvar, Ariful Azad, Ying Ding, Benjamin S. Glicksberg
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-hospital mortality. We show that the additional information provided by including time as a vector in the embedding captures the relationships between medical concepts, lab tests, and diagnoses, which enhances predictive performance. We find that adding HGM to a CNN model increases the mortality prediction accuracy up to 4\%. This framework serves as a foundation for future experiments involving different EHR data types on important healthcare prediction tasks.
The COVID-19 pandemic has caused ~ 2 million fatalities. Significant progress has been made in advancing our understanding of the disease process, one of the unanswered questions, however, is the anomaly in the case/mortality ratio with Mexico as a clear example. Herein, this anomaly is explored by spatial analysis and whether mortality varies locally according to local factors. To address this, hexagonal cartogram maps (hexbin) used to spatially map COVID-19 mortality and visualise association with patient-level data on demographics and pre-existing health conditions. This was further interro…
Social Determinants of Health and Fentanyl Overdose Mortality Across US Counties: An XGBoost and SHAP Analysis Identifying Silent Risk Counties and Treatment Deserts
Disadvantaged groups around the world have suffered and endured higher mortality during the current COVID-19 pandemic. This contrast disparity suggests that socioeconomic and health-related factors may drive inequality in disease outcome. To identify these factors correlated with COVID-19 outcome, country aggregate data provided by the Lancet COVID-19 Commission subjected to correlation analysis. Socioeconomic and health-related variables were used to predict mortality in the top 5 most affected countries using ridge regression and extreme gradient boosting (XGBoost) models. Our data reveal th…
Statistical vs. Deep Learning Models for Estimating Substance Overdose Excess Mortality in the US
Harvard University（哈佛大学）；Boston Children's Hospital（波士顿儿童医院）；Broad Institute of MIT and Harvard（MIT和哈佛联合研究所）；Massachusetts Institute of Technology（麻省理工学院）；Harvard Medical School（哈佛医学院）
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…
Stockholm University（斯德哥尔摩大学）；Getinge（洁定）；QRIOS IT
Although Machine Learning (ML) can be seen as a promising tool to improve clinical decision-making for supporting the improvement of medication plans, clinical procedures, diagnoses, or medication prescriptions, it remains limited by access to healthcare data. Healthcare data is sensitive, requiring strict privacy practices, and typically stored in data silos, making traditional machine learning challenging. Federated learning can counteract those limitations by training machine learning models over data silos while keeping the sensitive data localized. This study proposes a federated learning…
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…
Population stratification for prediction of mortality in post-AKI patients
Institute of Applied Health Sciences, University of Aberdeen（阿伯丁大学应用卫生科学学院）；Institute of Mathematics and Statistics, University of Sao Paulo（圣保罗大学数学与统计学院）
Massachusetts Institute of Technology（麻省理工学院）；Harvard University（哈佛大学）；National Bureau of Economic Research（美国国家经济研究局）；Harvard Medical School（哈佛医学院）
Risk prediction is central to both clinical medicine and public health. While many machine learning models have been developed to predict mortality, they are rarely applied in the clinical literature, where classification tasks typically rely on logistic regression. One reason for this is that existing machine learning models often seek to optimize predictions by incorporating features that are not present in the databases readily available to providers and policy makers, limiting generalizability and implementation. Here we tested a number of machine learning classifiers for prediction of six…
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）
Canadian VIGOUR Centre, University of Alberta（阿尔伯塔大学加拿大VIGOUR中心）；University of Alberta（阿尔伯塔大学）；Alberta Health Services（阿尔伯塔卫生服务局）；Alberta Machine Intelligence Institute（阿尔伯塔机器智能研究所）
Pandemic outbreaks such as COVID-19 occur unexpectedly, and need immediate action due to their potential devastating consequences on global health. Point-of-care routine assessments such as electrocardiogram (ECG), can be used to develop prediction models for identifying individuals at risk. However, there is often too little clinically-annotated medical data, especially in early phases of a pandemic, to develop accurate prediction models. In such situations, historical pre-pandemic health records can be utilized to estimate a preliminary model, which can then be fine-tuned based on limited av…
University of Athens（雅典大学）；Brandeis University（布兰迪斯大学）
The Infant Mortality Rate (IMR) is the number of infants per 1000 that do not survive until their first birthday. It is an important metric providing information about infant health but it also measures the society's general health status. Despite the high level of prosperity in the U.S.A., the country's IMR is higher than that of many other developed countries. Additionally, the U.S.A. exhibits persistent inequalities in the IMR across different racial and ethnic groups. In this paper, we study the infant mortality prediction using features extracted from birth certificates. We are interested…
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…
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…
Mortality prediction in intensive care units is considered one of the critical steps for efficiently treating patients in serious condition. As a result, various prediction models have been developed to address this problem based on modern electronic healthcare records. However, it becomes increasingly challenging to model such tasks as time series variables because some laboratory test results such as heart rate and blood pressure are sampled with inconsistent time frequencies. In this paper, we propose several deep learning models using the same features as the SAPS II score. To derive insig…
Academy of Arts and Design, Tsinghua University（清华大学美术学院）；Massachusetts Institute of Technology（麻省理工学院）
Electronic medical records (EMRs) supports the development of machine learning algorithms for predicting disease incidence, patient response to treatment, and other healthcare events. But insofar most algorithms have been centralized, taking little account of the decentralized, non-identically independently distributed (non-IID), and privacy-sensitive characteristics of EMRs that can complicate data collection, sharing and learning. To address this challenge, we introduced a community-based federated machine learning (CBFL) algorithm and evaluated it on non-IID ICU EMRs. Our algorithm clustere…
Temporal Validation Changes the Apparent Public-Health Utility of Under-Five Mortality Prediction in Bangladesh: A Four-Round DHS Machine-Learning Study
Data Science Research Lab, Department of Statistics, University of Rajshahi（数据科学研究实验室，统计学系，拉贾沙希大学）；Department of Statistics, University of Rajshahi（统计学系，拉贾沙希大学）
Geisel School of Medicine at Dartmouth（达特茅斯盖泽尔医学院）；Dartmouth Hitchcock Medical Center（达特茅斯-希区柯克医疗中心）；The Dartmouth Institute for Health Policy and Clinical Practice（达特茅斯健康政策与临床实践研究所）
Importance: Following a century of increase, life expectancy in the United States has stagnated and begun to decline in recent decades. Using satellite images and street view images prior work has demonstrated associations of the built environment with income, education, access to care and health factors such as obesity. However, assessment of learned image feature relationships with variation in crude mortality rate across the United States has been lacking. Objective: Investigate prediction of county-level mortality rates in the U.S. using satellite images. Design: Satellite images were extr…
The recent release of large-scale healthcare datasets has greatly propelled the research of data-driven deep learning models for healthcare applications. However, due to the nature of such deep black-boxed models, concerns about interpretability, fairness, and biases in healthcare scenarios where human lives are at stake call for a careful and thorough examinations of both datasets and models. In this work, we focus on MIMIC-IV (Medical Information Mart for Intensive Care, version IV), the largest publicly available healthcare dataset, and conduct comprehensive analyses of dataset representati…
Northeastern University（东北大学）；New York University School of Medicine（纽约大学医学院）
Patients with severe Coronavirus disease 19 (COVID-19) typically require supplemental oxygen as an essential treatment. We developed a machine learning algorithm, based on a deep Reinforcement Learning (RL), for continuous management of oxygen flow rate for critical ill patients under intensive care, which can identify the optimal personalized oxygen flow rate with strong potentials to reduce mortality rate relative to the current clinical practice. Basically, we modeled the oxygen flow trajectory of COVID-19 patients and their health outcomes as a Markov decision process. Based on individual …
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…
Predicting Patient Recovery or Mortality Using Deep Neural Decision Tree and Forest
University of Tehran（德黑兰大学）；Tehran University of Medical Sciences（德黑兰医科大学）；Isfahan University of Medical Sciences（伊斯法罕医科大学）；Mashhad University of Medical Sciences（马什哈德医科大学）
University of Illinois at Chicago（伊利诺伊大学芝加哥分校）；Amazon（亚马逊）；Northwestern University（西北大学）
Predicting patient mortality is an important and challenging problem in the healthcare domain, especially for intensive care unit (ICU) patients. Electronic health notes serve as a rich source for learning patient representations, that can facilitate effective risk assessment. However, a large portion of clinical notes are unstructured and also contain domain specific terminologies, from which we need to extract structured information. In this paper, we introduce an embedding framework to learn semantically-plausible distributed representations of clinical notes that exploits the semantic corr…
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）
Brac University（布拉克大学）；Islamic University of Technology（伊斯兰科技大学）；Khulna University of Engineering and Technology（库尔纳工程技术大学）；University of Toronto（多伦多大学）
COVID-19 pandemic is an ongoing global pandemic which has caused unprecedented disruptions in the public health sector and global economy. The virus, SARS-CoV-2 is responsible for the rapid transmission of coronavirus disease. Due to its contagious nature, the virus can easily infect an unprotected and exposed individual from mild to severe symptoms. The study of the virus effects on pregnant mothers and neonatal is now a concerning issue globally among civilians and public health workers considering how the virus will affect the mother and the neonates health. This paper aims to develop a pre…
Data on hundreds of variables related to individual consumer finance behavior (such as credit card and loan activity) is routinely collected in many countries and plays an important role in lending decisions. We postulate that the detailed nature of this data may be used to predict outcomes in seemingly unrelated domains such as individual health. We build a series of machine learning models to demonstrate that credit report data can be used to predict individual mortality. Variable groups related to credit cards and various loans, mostly unsecured loans, are shown to carry significant predict…
Electronic Health Records (EHRs) provide a wealth of information for machine learning algorithms to predict the patient outcome from the data including diagnostic information, vital signals, lab tests, drug administration, and demographic information. Machine learning models can be built, for example, to evaluate patients based on their predicted mortality or morbidity and to predict required resources for efficient resource management in hospitals. In this paper, we demonstrate that an attacker can manipulate the machine learning predictions with EHRs easily and selectively at test time by ba…
Peking University（北京大学）；Health Data Research（健康数据研究所）；University of Edinburgh（爱丁堡大学）；Peking University Third Hospital（北京大学第三医院）；Peking University People’s Hospital（北京大学人民医院）；University of Exeter（埃克塞特大学）
Objective: Peritoneal Dialysis (PD) is one of the most widely used life-supporting therapies for patients with End-Stage Renal Disease (ESRD). Predicting mortality risk and identifying modifiable risk factors based on the Electronic Medical Records (EMR) collected along with the follow-up visits are of great importance for personalized medicine and early intervention. Here, our objective is to develop a deep learning model for a real-time, individualized, and interpretable mortality prediction model - AICare. Method and Materials: Our proposed model consists of a multi-channel feature extracti…
King’s College London（伦敦国王学院）；University College London（伦敦大学学院）
The ability to perform accurate prognosis of patients is crucial for proactive clinical decision making, informed resource management and personalised care. Existing outcome prediction models suffer from a low recall of infrequent positive outcomes. We present a highly-scalable and robust machine learning framework to automatically predict adversity represented by mortality and ICU admission from time-series vital signs and laboratory results obtained within the first 24 hours of hospital admission. The stacked platform comprises two components: a) an unsupervised LSTM Autoencoder that learns …
Mila（米拉研究所）；Université de Montréal（蒙特利尔大学）；University of Tennessee, Knoxville（田纳西大学诺克斯维尔分校）
Healthcare data continues to flourish yet a relatively small portion, mostly structured, is being utilized effectively for predicting clinical outcomes. The rich subjective information available in unstructured clinical notes can possibly facilitate higher discrimination but tends to be under-utilized in mortality prediction. This work attempts to assess the gain in performance when multiple notes that have been minimally preprocessed are used as an input for prediction. A hierarchical architecture consisting of both convolutional and recurrent layers is used to concurrently model the differen…
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…
Wright State University（莱特州立大学）；Kno.e.sis Research Center（Kno.e.sis研究中心）
Early hospital mortality prediction is critical as intensivists strive to make efficient medical decisions about the severely ill patients staying in intensive care units. As a result, various methods have been developed to address this problem based on clinical records. However, some of the laboratory test results are time-consuming and need to be processed. In this paper, we propose a novel method to predict mortality using features extracted from the heart signals of patients within the first hour of ICU admission. In order to predict the risk, quantitative features have been computed based…
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…
Florida State University（佛罗里达州立大学）；Tallahassee Memorial Hospital（塔拉哈西纪念医院）
Deep neural networks have achieved remarkable success in various challenging tasks. However, the black-box nature of such networks is not acceptable to critical applications, such as healthcare. In particular, the existence of adversarial examples and their overgeneralization to irrelevant, out-of-distribution inputs with high confidence makes it difficult, if not impossible, to explain decisions by such networks. In this paper, we analyze the underlying mechanism of generalization of deep neural networks and propose an ($n$, $k$) consensus algorithm which is insensitive to adversarial example…
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…
NAVER Cloud AI Lab（NAVER云人工智能实验室）；Seoul National University Hospital Healthcare System Gangnam Center（首尔国立大学医院医疗系统江南中心）；Seoul National University Hospital（首尔国立大学医院）；Korea University Anam Hospital（高丽大学安岩医院）；Korea University College of Medicine（高丽大学医学院）；DaNaA Data（DaNaA数据公司）；Seoul National University College of Medicine（首尔国立大学医学院）；Institute on Aging, Seoul National University（首尔国立大学衰老研究所）
Background: While deep learning technology, which has the capability of obtaining latent representations based on large-scale data, can be a potential solution for the discovery of a novel aging biomarker, existing deep learning methods for biological age estimation usually depend on chronological ages and lack of consideration of mortality and morbidity that are the most significant outcomes of aging. Methods: This paper proposes a novel deep learning model to learn latent representations of biological aging in regard to subjects' morbidity and mortality. The model utilizes health check-up da…
