In many domains such as medicine, training data is in short supply. In such cases, external knowledge is often helpful in building predictive models. We propose a novel method to incorporate publicly available domain expertise to build accurate models. Specifically, we use word2vec models trained on a domain-specific corpus to estimate the relevance of each feature's text description to the prediction problem. We use these relevance estimates to rescale the features, causing more important features to experience weaker regularization.
We apply our method to predict the onset of five chronic diseases in the next five years in two genders and two age groups. Our rescaling approach improves the accuracy of the model, particularly when there are few positive examples. Furthermore, our method selects 60% fewer features, easing interpretation by physicians. Our method is applicable to other domains where feature and outcome descriptions are available.
Courant Institute of Mathematical Sciences, New York University（纽约大学库朗数学科学研究所）
Disparate areas of machine learning have benefited from models that can take raw data with little preprocessing as input and learn rich representations of that raw data in order to perform well on a given prediction task. We evaluate this approach in healthcare by using longitudinal measurements of lab tests, one of the more raw signals of a patient's health state widely available in clinical data, to predict disease onsets. In particular, we train a Long Short-Term Memory (LSTM) recurrent neural network and two novel convolutional neural networks for multi-task prediction of disease onset for…
Kyoto University（京都大学）；Kyowa Hakko Bio Co., Ltd.（协和发酵生物株式会社）；Yokohama City University（横滨市立大学）；Hirosaki University（弘前大学）
Early disease detection and prevention methods based on effective interventions are gaining attention. Machine learning technology has enabled precise disease prediction by capturing individual differences in multivariate data. Progress in precision medicine has revealed that substantial heterogeneity exists in health data at the individual level and that complex health factors are involved in the development of chronic diseases. However, it remains a challenge to identify individual physiological state changes in cross-disease onset processes because of the complex relationships among multipl…
TransFair: Transferring Fairness from Ocular Disease Classification to Progression Prediction
School of Computing and Informatics, University of Louisiana at Lafayette（路易斯安那大学拉斐特分校计算与信息学院）；Informatics Research Institute, University of Louisiana at Lafayette（路易斯安那大学拉斐特分校信息学研究所）；College of Engineering and Computer Science, Florida Atlantic University（佛罗里达大西洋大学工程与计算机科学学院）；Harvard Medical School（哈佛医学院）
Chronic kidney disease (CKD) has a poor prognosis due to excessive risk factors and comorbidities associated with it. The early detection of CKD faces challenges of insufficient medical histories of positive patients and complicated risk factors. In this paper, we propose the TRACE (Transformer-RNN Autoencoder-enhanced CKD Detector) framework, an end-to-end prediction model using patients' medical history data, to deal with these challenges. TRACE presents a comprehensive medical history representation with a novel key component: a Transformer-RNN autoencoder. The autoencoder jointly learns a …
Amazon Web Services Inc（亚马逊网络服务公司）；Cerner Corporation（塞纳公司）
Chronic disease progression is emerging as an important area of investment for healthcare providers. As the quantity and richness of available clinical data continue to increase along with advances in machine learning, there is great potential to advance our approaches to caring for patients. An ideal approach to this problem should generate good performance on at least three axes namely, a) perform across many clinical conditions without requiring deep clinical expertise or extensive data scientist effort, b) generalization across populations, and c) be explainable (model interpretability). W…
Inferring Chronic Treatment Onset from ePrescription Data: A Renewal Process Approach
Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia（计算机与信息科学学院，卢布尔雅那大学，斯洛文尼亚）；Faculty of Public Administration, University of Ljubljana, SI-1000 Ljubljana, Slovenia（公共行政学院，卢布尔雅那大学，斯洛文尼亚）
Comparison of deep learning and conventional methods for disease onset prediction
Erasmus University Medical Center（伊拉斯姆斯大学医学中心）；Yale School of Medicine（耶鲁医学院）；Ajou University Graduate School of Medicine（亚洲大学医学院研究生院）；Stanford School of Medicine（斯坦福医学院）；Stanford Health Care（斯坦福医疗保健）；Columbia University Irving Medical Center（哥伦比亚大学欧文医学中心）；Janssen Research and Development（杨森研发）
Chronic kidney disease (CKD) represents a slowly progressive disorder that can eventually require renal replacement therapy (RRT) including dialysis or renal transplantation. Early identification of patients who will require RRT (as much as 1 year in advance) improves patient outcomes, for example by allowing higher-quality vascular access for dialysis. Therefore, early recognition of the need for RRT by care teams is key to successfully managing the disease. Unfortunately, there is currently no commonly used predictive tool for RRT initiation. In this work, we present a machine learning model…
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…
University College London（伦敦大学学院）；University of Côte d’Azur（蔚蓝海岸大学）；Inria Sophia Antipolis（法国国家信息与自动化研究所索菲亚·安提波利斯中心）
We introduce Disease Knowledge Transfer (DKT), a novel technique for transferring biomarker information between related neurodegenerative diseases. DKT infers robust multimodal biomarker trajectories in rare neurodegenerative diseases even when only limited, unimodal data is available, by transferring information from larger multimodal datasets from common neurodegenerative diseases. DKT is a joint-disease generative model of biomarker progressions, which exploits biomarker relationships that are shared across diseases. Our proposed method allows, for the first time, the estimation of plausibl…
Out-of-distribution Reject Option Method for Dataset Shift Problem in Early Disease Onset Prediction
Graduate School of Medicine, Kyoto University（京都大学医学研究科）；Graduate School of Health and Nursing Science, Wakayama Medical University（和歌山医科大学健康与护理科学研究科）；Research Center for Health-Medical Data Science, Graduate School of Medicine, Hirosaki University（弘前大学医学研究科健康医疗数据科学研究中心）；Innovation Center for Health Promotion, Graduate School of Medicine, Hirosaki University（弘前大学医学研究科健康促进创新中心）；Center of Innovation Research Initiatives Organization, Hirosaki University（弘前大学创新研究倡议组织中心）
Augmented Risk Prediction for the Onset of Alzheimer's Disease from Electronic Health Records with Large Language Models
Michigan State University（密歇根州立大学）；Weill Cornell Medicine, Cornell University（康奈尔大学威尔医学院）；Massachusetts General Hospital, Harvard Medical School（哈佛医学院麻省总医院）
National Taiwan University（台湾大学）；King Abdullah University of Science and Technology（沙特阿拉伯国王阿卜杜拉科技大学）；Georgia Institute of Technology（佐治亚理工学院）；Bern University Hospital（伯尔尼大学医院）；Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology（沙特阿拉伯国王阿卜杜拉科技大学生物与环境科学与工程部门、计算机、电气与数学科学与工程部门）；Department of Ophthalmology, Bern University Hospital（伯尔尼大学医院眼科）
Age-Related Macular Degeneration (AMD) is an asymptomatic retinal disease which may result in loss of vision. There is limited access to high-quality relevant retinal images and poor understanding of the features defining sub-classes of this disease. Motivated by recent advances in machine learning we specifically explore the potential of generative modeling, using Generative Adversarial Networks (GANs) and style transferring, to facilitate clinical diagnosis and disease understanding by feature extraction. We design an analytic pipeline which first generates synthetic retinal images from clin…
Deep Learning in Early Alzheimer's disease's Detection: A Comprehensive Survey of Classification, Segmentation, and Feature Extraction Methods
University of Wah（瓦赫大学）；NUST（国家科技大学）；Washington University of Science and Technology Virginia（弗吉尼亚华盛顿科技大学）；Kansas State University（堪萨斯州立大学）；University of Alaska Anchorage（阿拉斯加安克雷奇大学）；State University of New York Polytechnic Institute（纽约州立大学理工学院）
Early detection of preventable diseases is important for better disease management, improved inter-ventions, and more efficient health-care resource allocation. Various machine learning approacheshave been developed to utilize information in Electronic Health Record (EHR) for this task. Majorityof previous attempts, however, focus on structured fields and lose the vast amount of information inthe unstructured notes. In this work we propose a general multi-task framework for disease onsetprediction that combines both free-text medical notes and structured information. We compareperformance of d…
Neoplasms (NPs) and neurological diseases and disorders (NDDs) are amongst the major classes of diseases underlying deaths of a disproportionate number of people worldwide. To determine if there exist some distinctive features in the local wiring patterns of protein interactions emerging at the onset of a disease belonging to either of these two classes, we examined 112 and 175 protein interaction networks belonging to NPs and NDDs, respectively. Orbit usage profiles (OUPs) for each of these networks were enumerated by investigating the networks' local topology. 56 non-redundant OUPs (nrOUPs) …
The proliferation of medical monitoring devices makes it possible to track health vitals at high frequency, enabling the development of dynamic health risk scores that change with the underlying readings. Survival analysis, in particular hazard estimation, is well-suited to analyzing this stream of data to predict disease onset as a function of the time-varying vitals. This paper introduces the software package BoXHED (pronounced 'box-head') for nonparametrically estimating hazard functions via gradient boosting. BoXHED 1.0 is a novel tree-based implementation of the generic estimator proposed…
Peking University（北京大学）；Lancaster University（兰卡斯特大学）；Peking University Third Hospital（北京大学第三医院）
Due to the characteristics of COVID-19, the epidemic develops rapidly and overwhelms health service systems worldwide. Many patients suffer from systemic life-threatening problems and need to be carefully monitored in ICUs. Thus the intelligent prognosis is in an urgent need to assist physicians to take an early intervention, prevent the adverse outcome, and optimize the medical resource allocation. However, in the early stage of the epidemic outbreak, the data available for analysis is limited due to the lack of effective diagnostic mechanisms, rarity of the cases, and privacy concerns. In th…
University of Tennessee Health Science Center（田纳西大学健康科学中心）
Fever can provide valuable information for diagnosis and prognosis of various diseases such as pneumonia, dengue, sepsis, etc., therefore, predicting fever early can help in the effectiveness of treatment options and expediting the treatment process. This study aims to develop novel algorithms that can accurately predict fever onset in critically ill patients by applying machine learning technique on continuous physiological data. We analyzed continuous physiological data collected every 5-minute from a cohort of over 200,000 critically ill patients admitted to an Intensive Care Unit (ICU) ove…
BITS Pilani K K Birla Goa Campus（BITS Pilani K K Birla 果阿校区）
Alzheimer's disease (AD) is a neurodegenerative disease that affects nearly 50 million individuals across the globe and is one of the leading causes of deaths globally. It is projected that by 2050, the number of people affected by the disease would more than double. Consequently, the growing advancements in technology beg the question, can technology be used to predict Alzheimer's for a better and early diagnosis? In this paper, we focus on this very problem. Specifically, we have trained both ML models and neural networks to predict and classify participants based on their speech patterns. W…
With the global population aging rapidly, Alzheimer's disease (AD) is particularly prominent in older adults, which has an insidious onset and leads to a gradual, irreversible deterioration in cognitive domains (memory, communication, etc.). Speech-based AD detection opens up the possibility of widespread screening and timely disease intervention. Recent advances in pre-trained models motivate AD detection modeling to shift from low-level features to high-level representations. This paper presents several efficient methods to extract better AD-related cues from high-level acoustic and linguist…
Amazon Web Services, Inc.（亚马逊云科技公司）；Cerner Corporation（塞纳公司）
In this paper we present a Recurrent neural networks (RNN) based architecture that achieves an AUCROC of 0.9147 for predicting the onset of Congestive Heart Failure (CHF) 15 months in advance using a 12-month observation window on a large cohort of 216,394 patients. We believe this to be the largest study in CHF onset prediction with respect to the number of CHF case patients in the cohort and the test set (3,332 CHF patients) on which the AUC metrics are reported. We explore the extent to which LSTM (Long Short Term Memory) based model, a variant of RNNs, can accurately predict the onset of C…
An Explainable Transformer Model for Alzheimer's Disease Detection Using Retinal Imaging
Nanotechnology, Biotechnology, Information Technology and Cognitive Science Laboratory, University of Tehran（特拉布宗大学纳米技术、生物技术、信息技术和认知科学实验室）；Department of Mechatronics, School of Intelligent Systems, College of Interdisciplinary Science and Technology, University of Tehran（特拉布宗大学机电系，智能系统学院，跨学科科学与技术学院）；School of Science and Technology, Faculty of Science, Agriculture, Business and Law, University of New England（新英格兰大学科学与技术学院，科学、农业、商业与法律学院）；Graduate School of Health, University of Technology Sydney（悉尼技术大学健康研究生院）；School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle（新castle大学医学与公共卫生学院，健康、医学与福祉学院）
