Optimization of Genomic Classifiers for Clinical Deployment: Evaluation of Bayesian Optimization to Select Predictive Models of Acute Infection and In-Hospital Mortality
Inflammatix, Inc.（英弗马特克斯公司）
Michael B. Mayhew, Elizabeth Tran, Kirindi Choi, Uros Midic, Roland Luethy, Nandita Damaraju, Ljubomir Buturovic
备注：
Preprint of an article published in Pacific Symposium on Biocomputing \c{opyright} [Year] World Scientific Publishing Co., Singapore, http://psb.stanford.edu/ (12 pages, 3 figures); Supplementary Material included (23 pages, 16 figures)
Acute infection, if not rapidly and accurately detected, can lead to sepsis, organ failure and even death. Current detection of acute infection as well as assessment of a patient's severity of illness are imperfect. Characterization of a patient's immune response by quantifying expression levels of specific genes from blood represents a potentially more timely and precise means of accomplishing both tasks. Machine learning methods provide a platform to leverage this 'host response' for development of deployment-ready classification models. Prioritization of promising classifiers is dependent, in part, on hyperparameter optimization for which a number of approaches including grid search, random sampling and Bayesian optimization have been shown to be effective. We compare HO approaches for the development of diagnostic classifiers of acute infection and in-hospital mortality from gene expression of 29 diagnostic markers. We take a deployment-centered approach to our comprehensive analysis, accounting for heterogeneity in our multi-study patient cohort with our choices of dataset partitioning and hyperparameter optimization objective as well as assessing selected classifiers in external (as well as internal) validation. We find that classifiers selected by Bayesian optimization for in-hospital mortality can outperform those selected by grid search or random sampling. However, in contrast to previous research: 1) Bayesian optimization is not more efficient in selecting classifiers in all instances compared to grid search or random sampling-based methods and 2) we note marginal gains in classifier performance in only specific circumstances when using a common variant of Bayesian optimization (i.e. automatic relevance determination). Our analysis highlights the need for further practical, deployment-centered benchmarking of HO approaches in the healthcare context.
Huma Therapeutics Limited（Huma Therapeutics有限公司）；Imperial College London（帝国理工学院）；University of Belgrade（贝尔格莱德大学）；University of Exeter（埃克塞特大学）；Johns Hopkins Bloomberg School Public Health（约翰斯·霍普金斯大学彭博公共卫生学院）
The COVID-19 pandemic has created an urgent need for robust, scalable monitoring tools supporting stratification of high-risk patients. This research aims to develop and validate prediction models, using the UK Biobank, to estimate COVID-19 mortality risk in confirmed cases. From the 11,245 participants testing positive for COVID-19, we develop a data-driven random forest classification model with excellent performance (AUC: 0.91), using baseline characteristics, pre-existing conditions, symptoms, and vital signs, such that the score could dynamically assess mortality risk with disease deterio…
Florida State University（佛罗里达州立大学）；University of Florida（佛罗里达大学）
Heart disease remains the leading cause of death in the United States. Compared with risk assessment guidelines that require manual calculation of scores, machine learning-based prediction for disease outcomes such as mortality can be utilized to save time and improve prediction accuracy. This study built and evaluated various machine learning models to predict one-year mortality in patients diagnosed with acute myocardial infarction or post myocardial infarction syndrome in the MIMIC-III database. The results of the best performing shallow prediction models were compared to a deep feedforward…
IMEDACS；Vivace Health Solutions Inc（Vivace健康解决方案公司）；Johns Hopkins University（约翰斯·霍普金斯大学）；Scripps Memorial Hospital - Encinitas（斯克里普斯恩西尼塔斯纪念医院）
Although timely sepsis diagnosis and prompt interventions in Intensive Care Unit (ICU) patients are associated with reduced mortality, early clinical recognition is frequently impeded by non-specific signs of infection and failure to detect signs of sepsis-induced organ dysfunction in a constellation of dynamically changing physiological data. The goal of this work is to identify patient at risk of life-threatening sepsis utilizing a data-centered and machine learning-driven approach. We derive a mortality risk predictive dynamic Bayesian network (DBN) guided by a customized sepsis knowledgeba…
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…
Bayesian models are increasing fit to large administrative data sets and then used to make individualized recommendations. For instance, Medicare's Hospital Compare webpage provides information to patients about specific hospital mortality rates for a heart attack or Acute Myocardial Infarction (AMI). Hospital Compare's current recommendations are based on a random effects logit model with a random hospital indicator and patient risk factors. By checking the out of sample calibration of their individualized predictions against general empirical advice, we are led to substantial revisions of th…
Bayesian ACCESS for Understanding Latent Epidemic Trajectories from Publicly Released Suppressed Data: Application to U.S. Opioid-related Overdose Mortality
The University of Texas Health Science Center at Houston（休斯顿德克萨斯大学健康科学中心）
Artificial Intelligence (AI) Based Prediction of Mortality, for COVID-19 Patients
Imam Abdulrahman Bin Faisal University（伊玛目阿卜杜勒拉赫曼·本·费萨尔大学）；Ahsanullah University of Science and Technology（阿赫萨努拉科技大学）；Health Cluster（卫生集群）；Ajman University（阿治曼大学）
Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas（应用数学与系统研究所）；Instituto Mexicano del Seguro Social（墨西哥社会保险研究所）；Hospital Clínico Quirúrgico Hermanos Ameijeiras（阿梅赫拉斯兄弟临床外科医院）
Background: Several studies have highlighted the importance of considering sex differences in the diagnosis and treatment of Acute Coronary Syndrome (ACS). However, the identification of sex-specific risk markers in ACS sub-populations has been scarcely studied. The present study aims to explore machine learning (ML) models to identify in-hospital mortality markers for women and men in ACS sub-populations collected from a public database of electronic health records (EHR). Methods: We extracted 1,299 patients with ST-elevation myocardial infarction (STEMI) and 2,820 patients with non-ST-elevat…
Machine Learning-Based Prediction of ICU Mortality in Sepsis-Associated Acute Kidney Injury Patients Using MIMIC-IV Database with Validation from eICU Database
University of Southern California（南加州大学）；Iran University of Medical Sciences（伊朗医学科学大学）；California State University（加利福尼亚州立大学）；California State Polytechnic University（加利福尼亚州_polytechnic大学）
Despite of the fast development of highly effective vaccines to control the current COVID$-$19 pandemic, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the continuous emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) variants of concern. It is likely that real-time genomic surveillance will be continuously needed as an unceasing monitoring tool, necessary to follow the spillover of the disease spread and the evolution of the virus. In this context, new genomic variants of SARS-CoV-2 that may e…
Acute kidney injury (AKI) in critically ill patients is associated with significant morbidity and mortality. Development of novel methods to identify patients with AKI earlier will allow for testing of novel strategies to prevent or reduce the complications of AKI. We developed data-driven prediction models to estimate the risk of new AKI onset. We generated models from clinical notes within the first 24 hours following intensive care unit (ICU) admission extracted from Medical Information Mart for Intensive Care III (MIMIC-III). From the clinical notes, we generated clinically meaningful word…
Machine learning predicts long-term mortality after acute myocardial infarction using systolic time intervals and routinely collected clinical data
École de technologie supérieure, Université du Québec（魁北克大学高等技术学院）；K. N. Toosi University of Technology（K. N. 图什理工大学）；Centre de recherche de l’Institut universitaire de gériatrie de Montréal（蒙特利尔大学老年学研究所）
Respiratory complications due to coronavirus disease COVID-19 have claimed tens of thousands of lives in 2020. Many cases of COVID-19 escalate from Severe Acute Respiratory Syndrome (SARS-CoV-2) to viral pneumonia to acute respiratory distress syndrome (ARDS) to death. Extracorporeal membranous oxygenation (ECMO) is a life-sustaining oxygenation and ventilation therapy that may be used for patients with severe ARDS when mechanical ventilation is insufficient to sustain life. While early planning and surgical cannulation for ECMO can increase survival, clinicians report the lack of a risk score…
The acute respiratory distress syndrome (ARDS) is a severe form of hypoxemic respiratory failure with in-hospital mortality of 35-46%. High mortality is thought to be related in part to challenges in making a prompt diagnosis, which may in turn delay implementation of evidence-based therapies. A deep neural network (DNN) algorithm utilizing unbiased ventilator waveform data (VWD) may help to improve screening for ARDS. We first show that a convolutional neural network-based ARDS detection model can outperform prior work with random forest models in AUC (0.95+/-0.019 vs. 0.88+/-0.064), accuracy…
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）
Identifying acute illness phenotypes via deep temporal interpolation and clustering network on physiologic signatures
University of Florida（佛罗里达大学）；Intelligent Critical Care Center（智能重症监护中心）；College of Pharmacy（药学院）；Center for Natural Products, Drug Discovery and Development（天然产物、药物发现与开发中心）；J. Crayton Pruitt Family Department of Biomedical Engineering（J.克雷顿·普鲁伊特家族生物医学工程系）
National Sun Yat-sen University（国立中山大学）；Kaohsiung Medical University（高雄医学大学）
Patients with Acute Kidney Injury (AKI) increase mortality, morbidity, and long-term adverse events. Therefore, early identification of AKI may improve renal function recovery, decrease comorbidities, and further improve patients' survival. To control certain risk factors and develop targeted prevention strategies are important to reduce the risk of AKI. Drug-drug interactions and drug-disease interactions are critical issues for AKI. Typical statistical approaches cannot handle the complexity of drug-drug and drug-disease interactions. In this paper, we propose a novel learning algorithm, Dee…
University of Florida（佛罗里达大学）；Emerging Pathogens Institute（新兴病原体研究所）
Bacterial infections are responsible for high mortality worldwide. Antimicrobial resistance underlying the infection, and multifaceted patient's clinical status can hamper the correct choice of antibiotic treatment. Randomized clinical trials provide average treatment effect estimates but are not ideal for risk stratification and optimization of therapeutic choice, i.e., individualized treatment effects (ITE). Here, we leverage large-scale electronic health record data, collected from Southern US academic clinics, to emulate a clinical trial, i.e., 'target trial', and develop a machine learnin…
In the United States, more than 5 million patients are admitted annually to ICUs, with ICU mortality of 10%-29% and costs over $82 billion. Acute brain dysfunction status, delirium, is often underdiagnosed or undervalued. This study's objective was to develop automated computable phenotypes for acute brain dysfunction states and describe transitions among brain dysfunction states to illustrate the clinical trajectories of ICU patients. We created two single-center, longitudinal EHR datasets for 48,817 adult patients admitted to an ICU at UFH Gainesville (GNV) and Jacksonville (JAX). We develop…
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…
Bangabandhu Sheikh Mujibur Rahman Science and Technology University（班加班杜谢赫穆吉布·拉赫曼科技大学）；Khulna University（库尔纳大学）；Jatiya Kabi Kazi Nazrul Islam University（贾蒂亚·卡比·卡齐·纳兹鲁尔·伊斯兰大学）；University of Canberra（堪培拉大学）；Nagasaki University（长崎大学）；The Garvan Institute of Medical Research（加尔文医学研究所）；Royal North Shore Hospital SERT Institute（皇家北岸医院SERT研究所）；University of New South Wales（新南威尔士大学）；World Health Organization (WHO) Centre on eHealth（世界卫生组织电子健康中心）
Background: Providing appropriate care for people suffering from COVID-19, the disease caused by the pandemic SARS-CoV-2 virus is a significant global challenge. Many individuals who become infected have pre-existing conditions that may interact with COVID-19 to increase symptom severity and mortality risk. COVID-19 patient comorbidities are likely to be informative about individual risk of severe illness and mortality. Accurately determining how comorbidities are associated with severe symptoms and mortality would thus greatly assist in COVID-19 care planning and provision. Methods: To assess…
University of Coimbra（科英布拉大学）；Polytechnic of Coimbra（科英布拉理工学院）
We intend to create a new risk assessment methodology that combines the best characteristics of both risk score and machine learning models. More specifically, we aim to develop a method that, besides having a good performance, offers a personalized model and outcome for each patient, presents high interpretability, and incorporates an estimation of the prediction reliability which is not usually available. By combining these features in the same approach we expect that it can boost the confidence of physicians to use such a tool in their daily activity. In order to achieve the mentioned goals…
Copula Based Fusion of Clinical and Genomic Machine Learning Risk Scores for Breast Cancer Risk Stratification
Department of Mathematics, University of Louisiana at Lafayette（路易斯安那州立大学拉斐特分校数学系）；Department of Physical Sciences & Mathematics, West Liberty University（韦斯特里布利大学物理科学与数学系）；Department of Mathematics and Statistics, Minnesota State University（明尼苏达州立大学数学与统计学系）
University of Rochester School of Medicine and Dentistry（罗切斯特大学医学与牙科学院）；University of Rochester Medical Center（罗切斯特大学医学中心）；Rochester Center for Health Informatics（罗切斯特健康信息学中心）；University of Rochester（罗切斯特大学）；University of Rochester Information Systems Division（罗切斯特大学信息系统部）
Acute Kidney Injury (AKI), the abrupt decline in kidney function due to temporary or permanent injury, is associated with increased mortality, morbidity, length of stay, and hospital cost. Sometimes, simple interventions such as medication review or hydration can prevent AKI. There is therefore interest in estimating risk of AKI at hospitalization. To gain insight into this task, we employ multilayer perceptron (MLP) and recurrent neural networks (RNNs) using serum creatinine (sCr) as a lone feature. We explore different feature input structures, including variable-length look-backs and a nest…
University of Rochester Medical Center（罗切斯特大学医学中心）；University of Rochester（罗切斯特大学）；Goergen Institute for Data Science（戈尔根数据科学研究所）
Acute Kidney Injury (AKI), a sudden decline in kidney function, is associated with increased mortality, morbidity, length of stay, and hospital cost. Since AKI is sometimes preventable, there is great interest in prediction. Most existing studies consider all patients and therefore restrict to features available in the first hours of hospitalization. Here, the focus is instead on rehospitalized patients, a cohort in which rich longitudinal features from prior hospitalizations can be analyzed. Our objective is to provide a risk score directly at hospital re-entry. Gradient boosting, penalized l…
University of Florida（佛罗里达大学）；Intelligent Critical Care Center (IC3)（智能重症监护中心）
Acute brain dysfunctions (ABD), which include coma and delirium, are prevalent in the ICU, especially among older patients. The current approach in manual assessment of ABD by care providers may be sporadic and subjective. Hence, there exists a need for a data-driven robust system automating the assessment and prediction of ABD. In this work, we develop a machine learning system for real-time prediction of ADB using Electronic Health Record (HER) data. Our data processing pipeline enables integration of static and temporal data, and extraction of features relevant to ABD. We train several stat…
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…
Acute kidney injury (AKI) is a common and serious complication after a surgery which is associated with morbidity and mortality. The majority of existing perioperative AKI risk score prediction models are limited in their generalizability and do not fully utilize the physiological intraoperative time-series data. Thus, there is a need for intelligent, accurate, and robust systems, able to leverage information from large-scale data to predict patient's risk of developing postoperative AKI. A retrospective single-center cohort of 2,911 adult patients who underwent surgery at the University of Fl…
University of Maryland, Baltimore County（马里兰大学巴尔的摩县分校）；Northeast Georgia Health System（东北乔治亚医疗系统）；Palos Health（帕洛斯医疗中心）；Penn State University（宾夕法尼亚州立大学）；Purdue University（普渡大学）
Recent advances in causal inference techniques, more specifically, in the theory of structural causal models, provide the framework for identification of causal effects from observational data in the cases where the causal graph is identifiable, i.e., the data generating mechanism can be recovered from the joint distribution. However, no such studies have been done to demonstrate this concept with a clinical example. We present a complete framework to estimate the causal effect from observational data by augmenting expert knowledge in the model development phase and with a practical clinical a…
Indian Institute of Technology, Delhi（印度理工学院德里分校）；AFMC（武装部队医学院）；All India Institute of Medical Sciences（全印度医学科学研究所）；Indian Institute of Science Education and Research, Bhopal（印度科学教育与研究院博帕尔分校）；Armed Forces Medical College（武装部队医学院）
Many countries are now experiencing the third wave of the COVID-19 pandemic straining the healthcare resources with an acute shortage of hospital beds and ventilators for the critically ill patients. This situation is especially worse in India with the second largest load of COVID-19 cases and a relatively resource-scarce medical infrastructure. Therefore, it becomes essential to triage the patients based on the severity of their disease and devote resources towards critically ill patients. Yan et al. 1 have published a very pertinent research that uses Machine learning (ML) methods to predict…
TabulaTime: A Novel Multimodal Deep Learning Framework for Advancing Acute Coronary Syndrome Prediction through Environmental and Clinical Data Integration
Department of Computing, and Mathematics, Manchester Metropolitan University（计算机与数学系，曼彻斯特 Metropolitan 大学）；Blackpool Teaching Hospitals NHS Foundation Trust（布莱克浦教学医院 NHS 基础信托）；Northern Care Alliance, NHS Foundation Trust（北方护理联盟，NHS 基础信托）；Department of Engineering, Manchester Metropolitan University（工程系，曼彻斯特 Metropolitan 大学）；Faculty of Business and Law, Manchester Metropolitan University（商业与法律学院，曼彻斯特 Metropolitan 大学）；Faculty of Medical Sciences, Newcastle University（医学科学学院，纽卡斯尔大学）
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）
University College London（伦敦大学学院）；National Hospital for Neurology & Neurosurgery（国立神经内外科医院）；National Hospital for Neurology and Neurosurgery（国立神经内外科医院）；St Georges Hospital（圣乔治医院）；The Alan Turing Institute（艾伦·图灵研究所）；Institute of Neurology, University College London（伦敦大学学院神经学研究所）
Background Information: Falls are associated with high direct and indirect costs, and significant morbidity and mortality for patients. Pathological falls are usually a result of a compromised motor system, and/or cognition. Very little research has been conducted on predicting falls based on this premise. Aims: To demonstrate that cognitive and motor tests can be used to create a robust predictive tool for falls. Methods: Three tests of attention and executive function (Stroop, Trail Making, and Semantic Fluency), a measure of physical function (Walk-12), a series of questions (concerning rec…
University of Minnesota（明尼苏达大学）；Nanyang Technological University（南洋理工大学）
Monitoring patients in ICU is a challenging and high-cost task. Hence, predicting the condition of patients during their ICU stay can help provide better acute care and plan the hospital's resources. There has been continuous progress in machine learning research for ICU management, and most of this work has focused on using time series signals recorded by ICU instruments. In our work, we show that adding clinical notes as another modality improves the performance of the model for three benchmark tasks: in-hospital mortality prediction, modeling decompensation, and length of stay forecasting t…
MANDARIN: Mixture-of-Experts Framework for Dynamic Delirium and Coma Prediction in ICU Patients: Development and Validation of an Acute Brain Dysfunction Prediction Model
University of Florida（佛罗里达大学）；Stanford University（斯坦福大学）
University of Michigan（密歇根大学）；Institute for Healthcare Policy & Innovation（医疗政策与创新研究所）
Recurrent neural networks (RNNs) are commonly applied to clinical time-series data with the goal of learning patient risk stratification models. Their effectiveness is due, in part, to their use of parameter sharing over time (i.e., cells are repeated hence the name recurrent). We hypothesize, however, that this trait also contributes to the increased difficulty such models have with learning relationships that change over time. Conditional shift, i.e., changes in the relationship between the input X and the output y, arises when risk factors associated with the event of interest change over t…
Predicting Breast Cancer Survival: A Survival Analysis Approach Using Log Odds and Clinical Variables
Federal College of Animal Health and Production Technology（联邦动物卫生与生产技术学院）；Universidad Mayor de San Andres（圣安德烈斯大学）；National University of Computer & Emerging Sciences-FAST（国立计算机与新兴科学大学（FAST大学））；University of Khartoum（喀土穆大学）；University of Jazan（贾赞大学）；New York Institute of Technology（纽约理工学院）；Khalifa Gull Nawaz Teaching Hospital（哈利法·古尔·纳瓦兹教学医院）
Explainable AI for Infection Prevention and Control: Modeling CPE Acquisition and Patient Outcomes in an Irish Hospital with Transformers
School of Computing（计算学院）；Dublin City University（都柏林城市大学）；ADAPT Centre（ADAPT中心）；University College Dublin（都柏林大学）；St James’s Hospital（圣詹姆斯医院）；Health Service Executive (HSE)（健康服务执行局）；Trinity College Dublin（三一学院）
