Electronic Health Records often suffer from missing data, which poses a major problem in clinical practice and clinical studies. A novel approach for dealing with missing data are Generative Adversarial Nets (GANs), which have been generating huge research interest in image generation and transformation. Recently, researchers have attempted to apply GANs to missing data generation and imputation for EHR data: a major challenge here is the categorical nature of the data. State-of-the-art solutions to the GAN-based generation of categorical data involve either reinforcement learning, or learning a bidirectional mapping between the categorical and the real latent feature space, so that the GANs only need to generate real-valued features. However, these methods are designed to generate complete feature vectors instead of imputing only the subsets of missing features. In this paper we propose a simple and yet effective approach that is based on previous work on GANs for data imputation. We first motivate our solution by discussing the reason why adversarial training often fails in case of categorical features. Then we derive a novel way to re-code the categorical features to stabilize the adversarial training. Based on experiments on two real-world EHR data with multiple settings, we show that our imputation approach largely improves the prediction accuracy, compared to more traditional data imputation approaches.
Many studies have attempted to solve the problem of missing data using various approaches. Among them, Generative Adversarial Imputation Nets (GAIN) was first used to impute data with Generative Adversarial Nets (GAN) and good results were obtained. Subsequent studies have attempted to combine various approaches to address some of its limitations. ClueGAIN is first proposed in this study, which introduces transfer learning into GAIN to solve the problem of poor imputation performance in high missing rate data sets. ClueGAIN can also be used to measure the similarity between data sets to explor…
Learnable Prompt as Pseudo-Imputation: Rethinking the Necessity of Traditional EHR Data Imputation in Downstream Clinical Prediction
Peking University（北京大学）；School of Computer Science（计算机学院）；School of Software and Microelectronics（软件与微电子学院）；Center on Frontiers of Computing Studies（计算前沿研究中心）；National Engineering Research Center for Software Engineering（国家软件工程工程研究中心）；Peking University Information Technology Institute (Tianjin Binhai)（北京大学信息技术学院（天津滨海））
本文提出可学习提示作为伪插补（PAI）的新训练协议，以可学习提示建模下游模型对缺失值的隐式偏好，替代传统 EHR 插补模型，在多个临床预测任务和数据集上显著提升现有模型性能并具有更强鲁棒性。
Modern scientific research and applications very often encounter "fragmentary data" which brings big challenges to imputation and prediction. By leveraging the structure of response patterns, we propose a unified and flexible framework based on Generative Adversarial Nets (GAN) to deal with fragmentary data imputation and label prediction at the same time. Unlike most of the other generative model based imputation methods that either have no theoretical guarantee or only consider Missing Completed At Random (MCAR), the proposed FragmGAN has theoretical guarantees for imputation with data Missi…
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 …
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；University of Oxford（牛津大学）；Alan Turing Institute（艾伦·图灵研究所）
We propose a novel method for imputing missing data by adapting the well-known Generative Adversarial Nets (GAN) framework. Accordingly, we call our method Generative Adversarial Imputation Nets (GAIN). The generator (G) observes some components of a real data vector, imputes the missing components conditioned on what is actually observed, and outputs a completed vector. The discriminator (D) then takes a completed vector and attempts to determine which components were actually observed and which were imputed. To ensure that D forces G to learn the desired distribution, we provide D with some …
North Carolina State University（北卡罗来纳州立大学）；Intuit Inc.（财捷公司）
Real-world Electronic Health Records (EHRs) are often plagued by a high rate of missing data. In our EHRs, for example, the missing rates can be as high as 90% for some features, with an average missing rate of around 70% across all features. We propose a Time-Aware Dual-Cross-Visit missing value imputation method, named TA-DualCV, which spontaneously leverages multivariate dependencies across features and longitudinal dependencies both within- and cross-visit to maximize the information extracted from limited observable records in EHRs. Specifically, TA-DualCV captures the latent structure of…
Missing data is a common problem faced with real-world datasets. Imputation is a widely used technique to estimate the missing data. State-of-the-art imputation approaches, such as Generative Adversarial Imputation Nets (GAIN), model the distribution of observed data to approximate the missing values. Such an approach usually models a single distribution for the entire dataset, which overlooks the class-specific characteristics of the data. Class-specific characteristics are especially useful when there is a class imbalance. We propose a new method for imputing missing data based on its class-…
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…
Electronic health records (EHR) consist of longitudinal clinical observations portrayed with sparsity, irregularity, and high-dimensionality, which become major obstacles in drawing reliable downstream clinical outcomes. Although there exist great numbers of imputation methods to tackle these issues, most of them ignore correlated features, temporal dynamics and entirely set aside the uncertainty. Since the missing value estimates involve the risk of being inaccurate, it is appropriate for the method to handle the less certain information differently than the reliable data. In that regard, we …
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…
University of Notre Dame（圣母大学）；Lawrence Livermore National Laboratories（劳伦斯利弗莫尔国家实验室）
Imputation of missing data is a task that plays a vital role in a number of engineering and science applications. Often such missing data arise in experimental observations from limitations of sensors or post-processing transformation errors. Other times they arise from numerical and algorithmic constraints in computer simulations. One such instance and the application emphasis of this paper are numerical simulations of storm surge. The simulation data corresponds to time-series surge predictions over a number of save points within the geographic domain of interest, creating a spatio-temporal …
Cardiovascular disease (CVD) is a class of diseases that involve the heart or blood vessels and according to World Health Organization is the leading cause of death worldwide. EHR data regarding this case, as well as medical cases in general, contain missing values very frequently. The percentage of missingness may vary and is linked with instrument errors, manual data entry procedures, etc. Even though the missing rate is usually significant, in many cases the missing value imputation part is handled poorly either with case-deletion or with simple statistical approaches such as mode and media…
Stanford Center for Biomedical Informatics Research, Stanford University（斯坦福大学生物医学信息学研究中心）；USC Information Sciences Institute, University of Southern California（南加州大学信息科学研究所）
Electronic phenotyping is the task of ascertaining whether an individual has a medical condition of interest by analyzing their medical record and is foundational in clinical informatics. Increasingly, electronic phenotyping is performed via supervised learning. We investigate the effectiveness of multitask learning for phenotyping using electronic health records (EHR) data. Multitask learning aims to improve model performance on a target task by jointly learning additional auxiliary tasks and has been used in disparate areas of machine learning. However, its utility when applied to EHR data h…
Sloan School of Management and Operations Research Center（斯隆管理学院与运筹学研究中心）；Massachusetts Institute of Technology（麻省理工学院）
Missing data is a common problem in real-world settings and particularly relevant in healthcare applications where researchers use Electronic Health Records (EHR) and results of observational studies to apply analytics methods. This issue becomes even more prominent for longitudinal data sets, where multiple instances of the same individual correspond to different observations in time. Standard imputation methods do not take into account patient specific information incorporated in multivariate panel data. We introduce the novel imputation algorithm MedImpute that addresses this problem, exten…
University of California, Santa Barbara（加州大学圣巴巴拉分校）；UC, Davis Health（加州大学戴维斯分校医疗中心）
Multiple organ failure (MOF) is a severe syndrome with a high mortality rate among Intensive Care Unit (ICU) patients. Early and precise detection is critical for clinicians to make timely decisions. An essential challenge in applying machine learning models to electronic health records (EHRs) is the pervasiveness of missing values. Most existing imputation methods are involved in the data preprocessing phase, failing to capture the relationship between data and outcome for downstream predictions. In this paper, we propose classifier-guided generative adversarial imputation networks Classifier…
Sepsis Prediction Using Graph Convolutional Networks over Patient-Feature-Value Triplets
College of Computer and Information Science（计算机与信息科学学院）；State Key Laboratory of Public Big Data（公共大数据国家重点实验室）；Department of Anesthesiology（麻醉科）；Key Laboratory of Perioperative Multi-organ Protection（围术期多器官保护关键实验室）
ETH Zurich（苏黎世联邦理工学院）；SIB Swiss Institute of Bioinformatics（SIB瑞士生物信息学研究所）
The signature transform is a 'universal nonlinearity' on the space of continuous vector-valued paths, and has received attention for use in machine learning on time series. However, real-world temporal data is typically observed at discrete points in time, and must first be transformed into a continuous path before signature techniques can be applied. We make this step explicit by characterising it as an imputation problem, and empirically assess the impact of various imputation strategies when applying signature-based neural nets to irregular time series data. For one of these strategies, Gau…
The rapid growth of electronic health record (EHR) datasets opens up promising opportunities to understand human diseases in a systematic way. However, effective extraction of clinical knowledge from the EHR data has been hindered by its sparsity and noisy information. We present KG-ETM, an end-to-end knowledge graph-based multimodal embedded topic model. KG-ETM distills latent disease topics from EHR data by learning the embedding from the medical knowledge graphs. We applied KG-ETM to a large-scale EHR dataset consisting of over 1 million patients. We evaluated its performance based on EHR r…
Korea University（高丽大学）；Electronics and Telecommunications Research Institute（电子与电信研究院）
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…
University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）
Deep Learning (DL) methods have dramatically increased in popularity in recent years. While its initial success was demonstrated in the classification and manipulation of image data, there has been significant growth in the application of DL methods to problems in the biomedical sciences. However, the greater prevalence and complexity of missing data in biomedical datasets present significant challenges for DL methods. Here, we provide a formal treatment of missing data in the context of Variational Autoencoders (VAEs), a popular unsupervised DL architecture commonly utilized for dimension red…
SMART: Towards Pre-trained Missing-Aware Model for Patient Health Status Prediction
School of Computer Science, Peking University（北京大学计算机学院）；National Research and Engineering Center of Software Engineering, Peking University（北京大学国家软件工程研究与工程中心）；Center on Frontiers of Computing Studies, Peking University（北京大学计算前沿研究中心）
Representation Learning of Lab Values via Masked AutoEncoders
Massachusetts Institute of Technology (MIT)（麻省理工学院）；Université Paris-Saclay（巴黎-萨克雷大学）；University of Michigan（密歇根大学）；Northeastern University（东北大学）；Harvard Medical School（哈佛医学院）；Brigham and Women’s Hospital/Dana-Farber Cancer Institute（哈佛医学院-布里特医院/达纳-法伯癌症研究所）；Beth Israel Deaconess Medical Center（贝斯以色列医疗中心）
Technical University Munich（慕尼黑工业大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Pre-training has shown success in different areas of machine learning, such as Computer Vision (CV), Natural Language Processing (NLP) and medical imaging. However, it has not been fully explored for clinical data analysis. Even though an immense amount of Electronic Health Record (EHR) data is recorded, data and labels can be scarce if the data is collected in small hospitals or deals with rare diseases. In such scenarios, pre-training on a larger set of EHR data could improve the model performance. In this paper, we apply unsupervised pre-training to heterogeneous, multi-modal EHR data for p…
University of Toronto（多伦多大学）；Harvard University（哈佛大学）；Stanford University（斯坦福大学）
In many contemporary applications, large amounts of unlabeled data are readily available while labeled examples are limited. There has been substantial interest in semi-supervised learning (SSL) which aims to leverage unlabeled data to improve estimation or prediction. However, current SSL literature focuses primarily on settings where labeled data is selected randomly from the population of interest. Non-random sampling, while posing additional analytical challenges, is highly applicable to many real world problems. Moreover, no SSL methods currently exist for estimating the prediction perfor…
University of Kentucky（肯塔基大学）；Shanghai Jiaotong University（上海交通大学）；Affiliated 6th People’s Hospital（附属第六人民医院）
Many real-world Electronic Health Record (EHR) data contains a large proportion of missing values. Leaving substantial portion of missing information unaddressed usually causes significant bias, which leads to invalid conclusion to be drawn. On the other hand, training a machine learning model with a much smaller nearly-complete subset can drastically impact the reliability and accuracy of model inference. Data imputation algorithms that attempt to replace missing data with meaningful values inevitably increase the variability of effect estimates with increased missingness, making it unreliabl…
Seoul National University（首尔国立大学）；Samsung Electronics Co. Ltd.（三星电子有限公司）；Seoul National University College of Medicine（首尔国立大学医学院）
Electronic health records (EHRs) have contributed to the computerization of patient records and can thus be used not only for efficient and systematic medical services, but also for research on biomedical data science. However, there are many missing values in EHRs when provided in matrix form, which is an important issue in many biomedical EHR applications. In this paper, we propose a two-stage framework that includes missing data imputation and disease prediction to address the missing data problem in EHRs. We compared the disease prediction performance of generative adversarial networks (GA…
Seoul National University（首尔大学）；Institute of Engineering Research, Seoul National University（首尔大学工程研究所）
Most deep learning classification studies assume clean data. However, when dealing with the real world data, we encounter three problems such as 1) missing data, 2) class imbalance, and 3) missing label problems. These problems undermine the performance of a classifier. Various preprocessing techniques have been proposed to mitigate one of these problems, but an algorithm that assumes and resolves all three problems together has not been proposed yet. In this paper, we propose HexaGAN, a generative adversarial network framework that shows promising classification performance for all three prob…
