The surging availability of electronic medical records (EHR) leads to increased research interests in medical predictive modeling. Recently many deep learning based predicted models are also developed for EHR data and demonstrated impressive performance. However, a series of recent studies showed that these deep models are not safe: they suffer from certain vulnerabilities. In short, a well-trained deep network can be extremely sensitive to inputs with negligible changes. These inputs are referred to as adversarial examples. In the context of medical informatics, such attacks could alter the result of a high performance deep predictive model by slightly perturbing a patient's medical records. Such instability not only reflects the weakness of deep architectures, more importantly, it offers guide on detecting susceptible parts on the inputs. In this paper, we propose an efficient and effective framework that learns a time-preferential minimum attack targeting the LSTM model with EHR inputs, and we leverage this attack strategy to screen medical records of patients and identify susceptible events and measurements. The efficient screening procedure can assist decision makers to pay extra attentions to the locations that can cause severe consequence if not measured correctly. We conduct extensive empirical studies on a real-world urgent care cohort and demonstrate the effectiveness of the proposed screening approach.
Harvard Medical School（哈佛医学院）；MIT（麻省理工学院）；Massachusetts Institute of Technology（麻省理工学院）
The discovery of adversarial examples has raised concerns about the practical deployment of deep learning systems. In this paper, we demonstrate that adversarial examples are capable of manipulating deep learning systems across three clinical domains. For each of our representative medical deep learning classifiers, both white and black box attacks were highly successful. Our models are representative of the current state of the art in medical computer vision and, in some cases, directly reflect architectures already seeing deployment in real world clinical settings. In addition to the technic…
Takatsuki High School（高槻高中）；Shibaura Institute of Technology（芝浦工业大学）；Mie University（三重大学）；Osaka Medical and Pharmaceutical University（大阪医疗药科大学）
This paper reports our preliminary work on medical incident prediction in general, and fall risk prediction in specific, using machine learning. Data for the machine learning are generated only from the particular subset of the electronic medical records (EMR) at Osaka Medical and Pharmaceutical University Hospital. As a result of conducting three experiments such as (1) machine learning algorithm comparison, (2) handling imbalance, and (3) investigation of explanatory variable contribution to the fall incident prediction, we find the investigation of explanatory variables the most effective.
Medical Foundation Models are Susceptible to Targeted Misinformation Attacks
University Hospital Aachen（亚琛大学医院）；University Medical Center of the Johannes Gutenberg-University（约翰内斯·古腾堡大学医学中心）；University Medicine Essen（埃森大学医学部）；Ocumeda GmbH（Ocumeda有限公司）；Charité - Universitätsmedizin Berlin（柏林夏里特医学院）；Freie Universität Berlin（柏林自由大学）；Humboldt Universität zu Berlin（柏林洪堡大学）；Berlin Institute of Health at Charité - Universitätsmedizin Berlin（柏林夏里特医学院柏林健康研究所）；Technical University Dresden（德累斯顿工业大学）；University Hospital Dresden（德累斯顿大学医院）；University Hospital Heidelberg（海德堡大学医院）
Medical Applications of Graph Convolutional Networks Using Electronic Health Records: A Survey
Lehigh University（利哈伊大学）；Plaksha University（普拉卡莎大学）；Hackensack Meridian School of Medicine（哈肯萨克子午线医学院）；New York College of Podiatric Medicine at Touro University（托罗大学附属纽约足医学院）
University of Pittsburgh（匹兹堡大学）；Carnegie Mellon University（卡内基梅隆大学）
During an infectious disease pandemic, it is critical to share electronic medical records or models (learned from these records) across regions. Applying one region's data/model to another region often have distribution shift issues that violate the assumptions of traditional machine learning techniques. Transfer learning can be a solution. To explore the potential of deep transfer learning algorithms, we applied two data-based algorithms (domain adversarial neural networks and maximum classifier discrepancy) and model-based transfer learning algorithms to infectious disease detection tasks. W…
Feature engineering remains a major bottleneck when creating predictive systems from electronic medical records. At present, an important missing element is detecting predictive regular clinical motifs from irregular episodic records. We present Deepr (short for Deep record), a new end-to-end deep learning system that learns to extract features from medical records and predicts future risk automatically. Deepr transforms a record into a sequence of discrete elements separated by coded time gaps and hospital transfers. On top of the sequence is a convolutional neural net that detects and combin…
Medical knowledge graphs (KGs) constructed from Electronic Medical Records (EMR) contain abundant information about patients and medical entities. The utilization of KG embedding models on these data has proven to be efficient for different medical tasks. However, existing models do not properly incorporate patient demographics and most of them ignore the probabilistic features of the medical KG. In this paper, we propose DARLING (Demographic Aware pRobabiListic medIcal kNowledge embeddinG), a demographic-aware medical KG embedding framework that explicitly incorporates demographics in the med…
The treatment effects of medications play a key role in guiding medical prescriptions. They are usually assessed with randomized controlled trials (RCTs), which are expensive. Recently, large-scale electronic health records (EHRs) have become available, opening up new opportunities for more cost-effective assessments. However, assessing a treatment effect from EHRs is challenging: it is biased by unobserved confounders, unmeasured variables that affect both patients' medical prescription and their outcome, e.g. the patients' social economic status. To adjust for unobserved confounders, we deve…
Viterbi School of Engineering, University of Southern California（南加州大学维特比工程学院）；The Hong Kong Polytechnic University（香港理工大学）；Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）；Beijing Jiaotong University（北京交通大学）；The Broad institute of MIT and Harvard（麻省理工学院与哈佛大学博德研究所）；Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology（麻省理工学院计算机科学与人工智能实验室）
Sometimes electrical medical records are restricted and difficult to centralize for machine learning, which could only be trained in distributed manner that involved many institutions in the process. However, sometimes some institutions are likely to figure out the private data used for training certain models based on the parameters they obtained, which is a violation of privacy and certain regulations. Under those circumstances, we develop an algorithm, called 'federated machine learning with anonymous random hybridization'(abbreviated as 'FeARH'), using mainly hybridization algorithm to eli…
Tsinghua University（清华大学）；Tsinghua National Laboratory of Information Science and Technology（清华信息科学与技术国家实验室）；Beijing University of Posts and Telecommunications（北京邮电大学）；Huangshi Central Hospital of Edong Healthcare Group, Hubei Polytechnic University（湖北理工学院鄂东医疗集团黄石市中心医院）
Automatically extracting useful information from electronic medical records along with conducting disease diagnoses is a promising task for both clinical decision support(CDS) and neural language processing(NLP). Most of the existing systems are based on artificially constructed knowledge bases, and then auxiliary diagnosis is done by rule matching. In this study, we present a clinical intelligent decision approach based on Convolutional Neural Networks(CNN), which can automatically extract high-level semantic information of electronic medical records and then perform automatic diagnosis witho…
GradValley Translational Data Science Research Lab（GradValley转化数据科学研究实验室）
De-identification of clinical records is an extremely important process which enables the use of the wealth of information present in them. There are a lot of techniques available for this but none of the method implementation has evaluated the scalability, which is an important benchmark. We evaluated numerous deep learning techniques such as BiLSTM-CNN, IDCNN, CRF, BiLSTM-CRF, SpaCy, etc. on both the performance and efficiency. We propose that the SpaCy model implementation for scrubbing sensitive PHI data from medical records is both well performing and extremely efficient compared to other…
Electronic medical record (EMR) data contains historical sequences of visits of patients, and each visit contains rich information, such as patient demographics, hospital utilisation and medical codes, including diagnosis, procedure and medication codes. Most existing EMR embedding methods capture visit-code associations by constructing input visit representations as binary vectors with a static vocabulary of medical codes. With this limited representation, they fail in encapsulating rich attribute information of visits (demographics and utilisation information) and/or codes (e.g., medical cod…
University of Massachusetts（马萨诸塞大学）；Bedford VAMC and CHOIR（贝德福德退伍军人医疗中心与CHOIR）
Sequence labeling for extraction of medical events and their attributes from unstructured text in Electronic Health Record (EHR) notes is a key step towards semantic understanding of EHRs. It has important applications in health informatics including pharmacovigilance and drug surveillance. The state of the art supervised machine learning models in this domain are based on Conditional Random Fields (CRFs) with features calculated from fixed context windows. In this application, we explored various recurrent neural network frameworks and show that they significantly outperformed the CRF models.
Stanford（斯坦福大学）；Stanford Children’s Health（斯坦福儿童医院）；Stanford Health Care（斯坦福医疗保健中心）；Center for Biomedical Informatics Research, Stanford（斯坦福生物医学信息学研究中心）
Machine learning (ML) applications in healthcare are extensively researched, but successful translations to the bedside are scant. Healthcare institutions are establishing frameworks to govern and promote the implementation of accurate, actionable and reliable models that integrate with clinical workflow. Such governance frameworks require an accompanying technical framework to deploy models in a resource efficient manner. Here we present DEPLOYR, a technical framework for enabling real-time deployment and monitoring of researcher created clinical ML models into a widely used electronic medica…
University of Warsaw（华沙大学）；Institute of Computer Science Polish Academy of Sciences（波兰科学院计算机科学研究所）
Is it true that patients with similar conditions get similar diagnoses? In this paper we show NLP methods and a unique corpus of documents to validate this claim. We (1) introduce a method for representation of medical visits based on free-text descriptions recorded by doctors, (2) introduce a new method for clustering of patients' visits and (3) present an~application of the proposed method on a corpus of 100,000 visits. With the proposed method we obtained stable and separated segments of visits which were positively validated against final medical diagnoses. We show how the presented algori…
Stability in clinical prediction models is crucial for transferability between studies, yet has received little attention. The problem is paramount in high dimensional data which invites sparse models with feature selection capability. We introduce an effective method to stabilize sparse Cox model of time-to-events using clinical structures inherent in Electronic Medical Records. Model estimation is stabilized using a feature graph derived from two types of EMR structures: temporal structure of disease and intervention recurrences, and hierarchical structure of medical knowledge and practices.…
Georgia Institute of Technology（佐治亚理工学院）；Sutter Health（萨特健康）
Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such conc…
Boston Medical Center（波士顿医学中心）；Boston University（波士顿大学）
Urban living in modern large cities has significant adverse effects on health, increasing the risk of several chronic diseases. We focus on the two leading clusters of chronic disease, heart disease and diabetes, and develop data-driven methods to predict hospitalizations due to these conditions. We base these predictions on the patients' medical history, recent and more distant, as described in their Electronic Health Records (EHR). We formulate the prediction problem as a binary classification problem and consider a variety of machine learning methods, including kernelized and sparse Support…
Japan Advanced Institute of Science and Technology（日本北陆先端科学技术大学院大学）
Appropriate treatment regimens play a vital role in improving patient health status. Although some achievements have been made, few of the recent studies of learning treatment regimens have exploited different kinds of patient information due to the difficulty in adopting heterogeneous data to many data mining methods. Moreover, current studies seem too rigid with fixed intervals of treatment periods corresponding to the varying lengths of hospital stay. To this end, this work proposes a generic data-driven framework which can derive group-treatment regimens from electronic medical records by …
Centre for Pattern Recognition and Data Analytics（模式识别与数据分析中心）；Deakin University（迪肯大学）
Understanding the latent processes from Electronic Medical Records could be a game changer in modern healthcare. However, the processes are complex due to the interaction between at least three dynamic components: the illness, the care and the recording practice. Existing methods are inadequate in capturing the dynamic structure of care. We propose an end-to-end model that reads medical record and predicts future risk. The model adopts the algebraic view in that discrete medical objects are embedded into continuous vectors lying in the same space. The bag of disease and comorbidities recorded …
ASAPP（ASAPP公司）；Massachusetts Institute of Technology（麻省理工学院）
Both electronic health records and personal health records are typically organized by data type, with medical problems, medications, procedures, and laboratory results chronologically sorted in separate areas of the chart. As a result, it can be difficult to find all of the relevant information for answering a clinical question about a given medical problem. A promising alternative is to instead organize by problems, with related medications, procedures, and other pertinent information all grouped together. A recent effort by Buchanan (2017) manually defined, through expert consensus, 11 medic…
Machine learning (ML) and Natural Language Processing (NLP) have achieved remarkable success in many fields and have brought new opportunities and high expectation in the analyses of medical data. The most common type of medical data is the massive free-text electronic medical records (EMR). It is widely regarded that mining such massive data can bring up important information for improving medical practices as well as for possible new discoveries on complex diseases. However, the free EMR texts are lacking consistent standards, rich of private information, and limited in availability. Also, a…
Clova AI Research, NAVER Corp.（NAVER公司Clova AI研究院）；Seoul National University Bundang Hospital（首尔大学盆唐医院）
Predicting highrisk vascular diseases is a significant issue in the medical domain. Most predicting methods predict the prognosis of patients from pathological and radiological measurements, which are expensive and require much time to be analyzed. Here we propose deep attention models that predict the onset of the high risky vascular disease from symbolic medical histories sequence of hypertension patients such as ICD-10 and pharmacy codes only, Medical History-based Prediction using Attention Network (MeHPAN). We demonstrate two types of attention models based on 1) bidirectional gated recur…
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…
Electronic health records represent a holistic overview of patients' trajectories. Their increasing availability has fueled new hopes to leverage them and develop accurate risk prediction models for a wide range of diseases. Given the complex interrelationships of medical records and patient outcomes, deep learning models have shown clear merits in achieving this goal. However, a key limitation of these models remains their capacity in processing long sequences. Capturing the whole history of medical encounters is expected to lead to more accurate predictions, but the inclusion of records coll…
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…
The broad adoption of Electronic Health Records (EHR) has led to vast amounts of data being accumulated on a patient's history, diagnosis, prescriptions, and lab tests. Advances in recommender technologies have the potential to utilize this information to help doctors personalize the prescribed medications. In this work, we design a two-stage attention-based personalized medication recommender system called PREMIER which incorporates information from the EHR to suggest a set of medications. Our system takes into account the interactions among drugs in order to minimize the adverse effects for …
Isfahan University of Technology（伊斯法罕理工大学）；Medical University of Vienna（维也纳医科大学）；University of Isfahan（伊斯法罕大学）
Patient similarity assessment, which identifies patients similar to a given patient, can help improve medical care. The assessment can be performed using Electronic Medical Records (EMRs). Patient similarity measurement requires converting heterogeneous EMRs into comparable formats to calculate their distance. While versatile document representation learning methods have been developed in recent years, it is still unclear how complex EMR data should be processed to create the most useful patient representations. This study presents a new data representation method for EMRs that takes the infor…
Georgia Institute of Technology（佐治亚理工学院）；Google Brain（谷歌大脑）；IBM Research（IBM研究院）；Sutter Health（萨特医疗）；HINT Consultants（HINT咨询公司）
Deep learning models exhibit state-of-the-art performance for many predictive healthcare tasks using electronic health records (EHR) data, but these models typically require training data volume that exceeds the capacity of most healthcare systems. External resources such as medical ontologies are used to bridge the data volume constraint, but this approach is often not directly applicable or useful because of inconsistencies with terminology. To solve the data insufficiency challenge, we leverage the inherent multilevel structure of EHR data and, in particular, the encoded relationships among…
An unsupervised clustering analysis of breast cancer data derived from electronic health records enhanced through UMAP dimensionality reduction
Dipartimento di Informatica Sistemistica e Comunicazione, Università di Milano-Bicocca（信息系统与通信系，米兰比可卡大学）；Institute of Health Policy Management and Evaluation, University of Toronto（卫生政策管理与评估研究所，多伦多大学）
Georgia Institute of Technology（佐治亚理工学院）；Vanderbilt University（范德堡大学）；Sutter Health（萨特健康）
Access to electronic health record (EHR) data has motivated computational advances in medical research. However, various concerns, particularly over privacy, can limit access to and collaborative use of EHR data. Sharing synthetic EHR data could mitigate risk. In this paper, we propose a new approach, medical Generative Adversarial Network (medGAN), to generate realistic synthetic patient records. Based on input real patient records, medGAN can generate high-dimensional discrete variables (e.g., binary and count features) via a combination of an autoencoder and generative adversarial networks.…
Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph ne…
Beihang University（北京航空航天大学）；University of California, Davis（加利福尼亚大学戴维斯分校）
Machine learning for data-driven diagnosis has been actively studied in medicine to provide better healthcare. Supporting analysis of a patient cohort similar to a patient under treatment is a key task for clinicians to make decisions with high confidence. However, such analysis is not straightforward due to the characteristics of medical records: high dimensionality, irregularity in time, and sparsity. To address this challenge, we introduce a method for similarity calculation of medical records. Our method employs event and sequence embeddings. While we use an autoencoder for the event embed…
Stanford University（斯坦福大学）；Veterans Affairs Palo Alto Health Care System（退伍军人事务部帕洛阿尔托医疗保健系统）
Post-market medical device surveillance is a challenge facing manufacturers, regulatory agencies, and health care providers. Electronic health records are valuable sources of real world evidence to assess device safety and track device-related patient outcomes over time. However, distilling this evidence remains challenging, as information is fractured across clinical notes and structured records. Modern machine learning methods for machine reading promise to unlock increasingly complex information from text, but face barriers due to their reliance on large and expensive hand-labeled training …
Electronic medical records (EMR) contain longitudinal information about patients that can be used to analyze outcomes. Typically, studies on EMR data have worked with established variables that have already been acknowledged to be associated with certain outcomes. However, EMR data may also contain hitherto unrecognized factors for risk association and prediction of outcomes for a disease. In this paper, we present a scalable data-driven framework to analyze EMR data corpus in a disease agnostic way that systematically uncovers important factors influencing outcomes in patients, as supported b…
Dartmouth College（达特茅斯学院）；Dartmouth-Hitchcock Medical Center（达特茅斯-希区柯克医学中心）
Identifying patient characteristics that influence the rate of colorectal polyp recurrence can provide important insights into which patients are at higher risk for recurrence. We used natural language processing to extract polyp morphological characteristics from 953 polyp-presenting patients' electronic medical records. We used subsequent colonoscopy reports to examine how the time to polyp recurrence (731 patients experienced recurrence) is influenced by these characteristics as well as anthropometric features using Kaplan-Meier curves, Cox proportional hazards modeling, and random survival…
Delirium is a common acute onset brain dysfunction in the emergency setting and is associated with higher mortality. It is difficult to detect and monitor since its presentations and risk factors can be different depending on the underlying medical condition of patients. In our study, we aimed to identify subtypes within the delirium population and build subgroup-specific predictive models to detect delirium using Medical Information Mart for Intensive Care IV (MIMIC-IV) data. We showed that clusters exist within the delirium population. Differences in feature importance were also observed for…
Improving Colorectal Cancer Screening and Risk Assessment through Predictive Modeling on Medical Images and Records
Geisel School of Medicine at Dartmouth（达特茅斯盖泽尔医学院）；Dartmouth-Hitchcock Medical Center（达特茅斯-希区柯克医学中心）；New Hampshire Colonoscopy Registry（新罕布什尔结肠镜检查登记处）；White River Junction VA Medical Center（怀特河交界处退伍军人事务医疗中心）；Dartmouth College（达特茅斯学院）
IQVIA Inc.（艾昆纬公司）；University of Minnesota Twin Cities（明尼苏达大学双城分校）
Automatic representation learning of key entities in electronic health record (EHR) data is a critical step for healthcare informatics that turns heterogeneous medical records into structured and actionable information. Here we propose ME2Vec, an algorithmic framework for learning low-dimensional vectors of the most common entities in EHR: medical services, doctors, and patients. ME2Vec leverages diverse graph embedding techniques to cater for the unique characteristic of each medical entity. Using real-world clinical data, we demonstrate the efficacy of ME2Vec over competitive baselines on di…
Personalized predictive medicine necessitates the modeling of patient illness and care processes, which inherently have long-term temporal dependencies. Healthcare observations, recorded in electronic medical records, are episodic and irregular in time. We introduce DeepCare, an end-to-end deep dynamic neural network that reads medical records, stores previous illness history, infers current illness states and predicts future medical outcomes. At the data level, DeepCare represents care episodes as vectors in space, models patient health state trajectories through explicit memory of historical…
Convolutional neural network-based medical image classifiers have been shown to be especially susceptible to adversarial examples. Such instabilities are likely to be unacceptable in the future of automated diagnoses. Though statistical adversarial example detection methods have proven to be effective defense mechanisms, additional research is necessary that investigates the fundamental vulnerabilities of deep-learning-based systems and how best to build models that jointly maximize traditional and robust accuracy. This paper presents the inclusion of attention mechanisms in CNN-based medical …
University of Delaware（特拉华大学）；Delaware Biotechnology Institute（特拉华生物技术研究所）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；Christiana Care Health System（克里斯蒂安娜护理卫生系统）；Queen's University（女王大学）
Obesity is one of the leading health concerns in the United States. Researchers and health care providers are interested in understanding factors affecting obesity and detecting the likelihood of obesity as early as possible. In this paper, we set out to recognize children who have higher risk of obesity by identifying distinct growth patterns in them. This is done by using clustering methods, which group together children who share similar body measurements over a period of time. The measurements characterizing children within the same cluster are plotted as a function of age. We refer to the…
University of Wisconsin-Milwaukee（威斯康星大学密尔沃基分校）；AZH Wound and Vascular Center（AZH伤口与血管中心）
Wound prognostic models not only provide an estimate of wound healing time to motivate patients to follow up their treatments but also can help clinicians to decide whether to use a standard care or adjuvant therapies and to assist them with designing clinical trials. However, collecting prognosis factors from Electronic Medical Records (EMR) of patients is challenging due to privacy, sensitivity, and confidentiality. In this study, we developed time series medical generative adversarial networks (GANs) to generate synthetic wound prognosis factors using very limited information collected duri…
