Objective: Patient notes in electronic health records (EHRs) may contain critical information for medical investigations. However, the vast majority of medical investigators can only access de-identified notes, in order to protect the confidentiality of patients. In the United States, the Health Insurance Portability and Accountability Act (HIPAA) defines 18 types of protected health information (PHI) that needs to be removed to de-identify patient notes. Manual de-identification is impractical given the size of EHR databases, the limited number of researchers with access to the non-de-identified notes, and the frequent mistakes of human annotators. A reliable automated de-identification system would consequently be of high value.
Materials and Methods: We introduce the first de-identification system based on artificial neural networks (ANNs), which requires no handcrafted features or rules, unlike existing systems. We compare the performance of the system with state-of-the-art systems on two datasets: the i2b2 2014 de-identification challenge dataset, which is the largest publicly available de-identification dataset, and the MIMIC de-identification dataset, which we assembled and is twice as large as the i2b2 2014 dataset.
Results: Our ANN model outperforms the state-of-the-art systems. It yields an F1-score of 97.85 on the i2b2 2014 dataset, with a recall 97.38 and a precision of 97.32, and an F1-score of 99.23 on the MIMIC de-identification dataset, with a recall 99.25 and a precision of 99.06.
Conclusion: Our findings support the use of ANNs for de-identification of patient notes, as they show better performance than previously published systems while requiring no feature engineering.
Deep learning has demonstrated success in many applications; however, their use in healthcare has been limited due to the lack of transparency into how they generate predictions. Algorithms such as Recurrent Neural Networks (RNNs) when applied to Electronic Medical Records (EMR) introduce additional barriers to transparency because of the sequential processing of the RNN and the multi-modal nature of EMR data. This work seeks to improve transparency by: 1) introducing Learned Binary Masks (LBM) as a method for identifying which EMR variables contributed to an RNN model's risk of mortality (ROM…
Siemens AG（西门子股份公司）；Ludwig Maximilian University of Munich（慕尼黑路德维希-马克西米利安大学）
In clinical data sets we often find static information (e.g. patient gender, blood type, etc.) combined with sequences of data that are recorded during multiple hospital visits (e.g. medications prescribed, tests performed, etc.). Recurrent Neural Networks (RNNs) have proven to be very successful for modelling sequences of data in many areas of Machine Learning. In this work we present an approach based on RNNs, specifically designed for the clinical domain, that combines static and dynamic information in order to predict future events. We work with a database collected in the Charité Hospital…
Patient notes contain a wealth of information of potentially great interest to medical investigators. However, to protect patients' privacy, Protected Health Information (PHI) must be removed from the patient notes before they can be legally released, a process known as patient note de-identification. The main objective for a de-identification system is to have the highest possible recall. Recently, the first neural-network-based de-identification system has been proposed, yielding state-of-the-art results. Unlike other systems, it does not rely on human-engineered features, which allows it to…
In the context of the Electronic Health Record, automated diagnosis coding of patient notes is a useful task, but a challenging one due to the large number of codes and the length of patient notes. We investigate four models for assigning multiple ICD codes to discharge summaries taken from both MIMIC II and III. We present Hierarchical Attention-GRU (HA-GRU), a hierarchical approach to tag a document by identifying the sentences relevant for each label. HA-GRU achieves state-of-the art results. Furthermore, the learned sentence-level attention layer highlights the model decision process, allo…
Following each patient visit, physicians draft long semi-structured clinical summaries called SOAP notes. While invaluable to clinicians and researchers, creating digital SOAP notes is burdensome, contributing to physician burnout. In this paper, we introduce the first complete pipelines to leverage deep summarization models to generate these notes based on transcripts of conversations between physicians and patients. After exploring a spectrum of methods across the extractive-abstractive spectrum, we propose Cluster2Sent, an algorithm that (i) extracts important utterances relevant to each su…
NoteChat: A Dataset of Synthetic Doctor-Patient Conversations Conditioned on Clinical Notes
University of Massachusetts（马萨诸塞大学）；University of Minnesota（明尼苏达大学）；Microsoft（微软公司）；University of Edinburgh（爱丁堡大学）；University of Massachusetts, Lowell（马萨诸塞大学洛厄尔分校）
Impact of Large Language Model Assistance on Patients Reading Clinical Notes: A Mixed-Methods Study
Massachusetts Institute of Technology（麻省理工学院）；University of Michigan（密歇根大学）；Beth Israel Deaconess Medical Center（贝斯以色列女执事医疗中心）；Massachusetts General Hospital（麻省总医院）；Microsoft Research（微软研究院）；Mayo Clinic（梅奥诊所）
Comparing representations of long clinical texts for the task of patient note-identification
Inria（法国国家信息与自动化研究所）；Inserm（法国国家健康与医学研究院）；Data Science Platform, Imagine Institute（伊马金研究所数据科学平台）；Hôpital Universitaire Necker-Enfants Malades（内克尔-恩范茨-马拉德大学医院）；Assistance Publique - Hôpitaux de Paris (APHP)（巴黎公共医疗援助医院集团）；Université de Lorraine（洛林大学）；CNRS（法国国家科学研究中心）；LORIA（洛林计算机科学与应用实验室）；INESC-ID（里斯本大学学院计算机与系统工程研究中心）；Instituto Superior Técnico（里斯本高等技术学院）；Universidade de Lisboa（里斯本大学）
Massachusetts Institute of Technology（麻省理工学院）；University of Massachusetts（马萨诸塞大学）；Harvard T.H. Chan School of Public Health（哈佛大学陈曾熙公共卫生学院）；Massachusetts General Hospital（麻省总医院）；Tufts University School of Medicine（塔夫茨大学医学院）；Beth Israel Deaconess Medical Center（贝斯以色列女执事医疗中心）；Washington University School of Medicine（华盛顿大学医学院）；Philips Research North America（飞利浦北美研究院）；Harvard University（哈佛大学）；Adobe Research（Adobe研究院）
A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also ref…
University of Massachusetts Medical School（马萨诸塞大学医学院）；Bedford Veterans Affairs Medical Center（贝德福德退伍军人事务医疗中心）
Background: Electronic health record (EHR) notes contain abundant medical jargon that can be difficult for patients to comprehend. One way to help patients is to reduce information overload and help them focus on medical terms that matter most to them. Objective: The aim of this work was to develop FIT (Finding Important Terms for patients), an unsupervised natural language processing (NLP) system that ranks medical terms in EHR notes based on their importance to patients. Methods: We built FIT on a new unsupervised ensemble ranking model derived from the biased random walk algorithm to combin…
Clinical notes in electronic health records contain highly heterogeneous writing styles, including non-standard terminology or abbreviations. Using these notes in predictive modeling has traditionally required preprocessing (e.g. taking frequent terms or topic modeling) that removes much of the richness of the source data. We propose a pretrained hierarchical recurrent neural network model that parses minimally processed clinical notes in an intuitive fashion, and show that it improves performance for discharge diagnosis classification tasks on the Medical Information Mart for Intensive Care I…
WangLab at MEDIQA-Chat 2023: Clinical Note Generation from Doctor-Patient Conversations using Large Language Models
University of Toronto（多伦多大学）；Terrence Donnelly Centre for Cellular and Biomolecular Research（特伦斯·唐纳利细胞与生物分子研究中心）；Vector Institute for AI（向量人工智能研究院）；University Health Network（大学健康网络）；Sunnybrook Health Sciences Centre（桑尼布鲁克健康科学中心）
Antwerp University Hospital（安特卫普大学医院）；CLiPS Research Center, University of Antwerp（安特卫普大学 CLiPS 研究中心）
We have two main contributions in this work: 1. We explore the usage of a stacked denoising autoencoder, and a paragraph vector model to learn task-independent dense patient representations directly from clinical notes. We evaluate these representations by using them as features in multiple supervised setups, and compare their performance with those of sparse representations. 2. To understand and interpret the representations, we explore the best encoded features within the patient representations obtained from the autoencoder model. Further, we calculate the significance of the input features…
University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；School of Medicine and Public Health（医学与公共卫生学院）；Loyola University Chicago（芝加哥洛约拉大学）；Harvard Medical School（哈佛医学院）
Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance o…
CIMS, New York University（纽约大学库朗数学科学研究所）；CSAIL & IMES, Massachusetts Institute of Technology（麻省理工学院计算机科学与人工智能实验室及医学工程与科学研究所）
In this work, we present the Grounded Recurrent Neural Network (GRNN), a recurrent neural network architecture for multi-label prediction which explicitly ties labels to specific dimensions of the recurrent hidden state (we call this process "grounding"). The approach is particularly well-suited for extracting large numbers of concepts from text. We apply the new model to address an important problem in healthcare of understanding what medical concepts are discussed in clinical text. Using a publicly available dataset derived from Intensive Care Units, we learn to label a patient's diagnoses a…
St. John’s University（圣约翰大学）；Weill Cornell Medicine（威尔康奈尔医学院）
Clinical notes, which can be embedded into electronic medical records, document patient care delivery and summarize interactions between healthcare providers and patients. These clinical notes directly inform patient care and can also indirectly inform research and quality/safety metrics, among other indirect metrics. Recently, some states within the United States of America require patients to have open access to their clinical notes to improve the exchange of patient information for patient care. Thus, developing methods to assess the cyber risks of clinical notes before sharing and exchangi…
The University of Vermont（佛蒙特大学）；MassMutual Data Science（MassMutual数据科学公司）；VA Boston Healthcare System（波士顿VA医疗保健系统）
Medical systems in general, and patient treatment decisions and outcomes in particular, are affected by bias based on gender and other demographic elements. As language models are increasingly applied to medicine, there is a growing interest in building algorithmic fairness into processes impacting patient care. Much of the work addressing this question has focused on biases encoded in language models -- statistical estimates of the relationships between concepts derived from distant reading of corpora. Building on this work, we investigate how word choices made by healthcare practitioners and…
Clinical notes are an efficient way to record patient information but are notoriously hard to decipher for non-experts. Automatically simplifying medical text can empower patients with valuable information about their health, while saving clinicians time. We present a novel approach to automated simplification of medical text based on word frequencies and language modelling, grounded on medical ontologies enriched with layman terms. We release a new dataset of pairs of publicly available medical sentences and a version of them simplified by clinicians. Also, we define a novel text simplificati…
A Dataset and Resources for Identifying Patient Health Literacy Information from Clinical Notes
National Library of Medicine（国家医学图书馆）；Massachusetts Institute of Technology（麻省理工学院）；Yonsei University College of Medicine（延世大学医学院）；Beth Israel Deaconess Medical Center（贝斯以色列医疗中心）；NYC Health + Hospitals - Lincoln（纽约市卫生局-林肯医院）
Clinicians spend a significant amount of time inputting free-form textual notes into Electronic Health Records (EHR) systems. Much of this documentation work is seen as a burden, reducing time spent with patients and contributing to clinician burnout. With the aspiration of AI-assisted note-writing, we propose a new language modeling task predicting the content of notes conditioned on past data from a patient's medical record, including patient demographics, labs, medications, and past notes. We train generative models using the public, de-identified MIMIC-III dataset and compare generated not…
De-identification is the process of removing 18 protected health information (PHI) from clinical notes in order for the text to be considered not individually identifiable. Recent advances in natural language processing (NLP) has allowed for the use of deep learning techniques for the task of de-identification. In this paper, we present a deep learning architecture that builds on the latest NLP advances by incorporating deep contextualized word embeddings and variational drop out Bi-LSTMs. We test this architecture on two gold standard datasets and show that the architecture achieves state-of-…
Duke University（杜克大学）；Duke Clinical Research Institute（杜克临床研究所）
To identify patients who are hospitalized because of COVID-19 as opposed to those who were admitted for other indications, we compared the performance of different computable phenotype definitions for COVID-19 hospitalizations that use different types of data from the electronic health records (EHR), including structured EHR data elements, provider notes, or a combination of both data types. And conduct a retrospective data analysis utilizing chart review-based validation. Participants are 586 hospitalized individuals who tested positive for SARS-CoV-2 during January 2022. We used natural lang…
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…
Overview of the Problem List Summarization (ProbSum) 2023 Shared Task on Summarizing Patients' Active Diagnoses and Problems from Electronic Health Record Progress Notes
University of Wisconsin（威斯康星大学）；Loyola University Chicago（芝加哥洛约拉大学）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）
Isfahan University of Technology（伊斯法罕理工大学）；Medical University of Vienna（维也纳医科大学）
Identifying patient cohorts from clinical notes in secondary electronic health records is a fundamental task in clinical information management. However, with the growing number of clinical notes, it becomes challenging to analyze the data manually for phenotype detection. Automatic extraction of clinical concepts would helps to identify the patient phenotypes correctly. This paper proposes a novel hybrid model for automatically extracting patient phenotypes using natural language processing and deep learning models to determine the patient phenotypes without dictionaries and human interventio…
Antwerp University Hospital（安特卫普大学医院）；University of Antwerp（安特卫普大学）
We have three contributions in this work: 1. We explore the utility of a stacked denoising autoencoder and a paragraph vector model to learn task-independent dense patient representations directly from clinical notes. To analyze if these representations are transferable across tasks, we evaluate them in multiple supervised setups to predict patient mortality, primary diagnostic and procedural category, and gender. We compare their performance with sparse representations obtained from a bag-of-words model. We observe that the learned generalized representations significantly outperform the spar…
Natural language processing to automatically extract the presence and severity of esophagitis in notes of patients undergoing radiotherapy
Mass General Brigham（麻省总医院布里格姆医疗系统）；Harvard Medical School（哈佛医学院）；Brigham and Women’s Hospital（布莱根妇女医院）；Dana-Farber Cancer Institute（丹娜法伯癌症研究院）；Brown University（布朗大学）；Lifespan Cancer Institute（Lifespan癌症研究所）；Maastricht University（马斯特里赫特大学）；Boston Children’s Hospital（波士顿儿童医院）
University of Memphis（孟菲斯大学）；Adobe Research（奥多比研究院）；Johns Hopkins University（约翰斯·霍普金斯大学）
Clinical notes in Electronic Health Records (EHR) present rich documented information of patients to inference phenotype for disease diagnosis and study patient characteristics for cohort selection. Unsupervised user embedding aims to encode patients into fixed-length vectors without human supervisions. Medical concepts extracted from the clinical notes contain rich connections between patients and their clinical categories. However, existing unsupervised approaches of user embeddings from clinical notes do not explicitly incorporate medical concepts. In this study, we propose a concept-aware …
Effective representation learning of electronic health records is a challenging task and is becoming more important as the availability of such data is becoming pervasive. The data contained in these records are irregular and contain multiple modalities such as notes, and medical codes. They are preempted by medical conditions the patient may have, and are typically jotted down by medical staff. Accompanying codes are notes containing valuable information about patients beyond the structured information contained in electronic health records. We use transformer networks and the recently propos…
Imperial College London（帝国理工学院）；Pangaea Data Limited；Queen Mary University of London（伦敦玛丽女王大学）；Hong Kong Baptist University（香港浸会大学）
Objective: Clinical notes contain information not present elsewhere, including drug response and symptoms, all of which are highly important when predicting key outcomes in acute care patients. We propose the automatic annotation of phenotypes from clinical notes as a method to capture essential information, which is complementary to typically used vital signs and laboratory test results, to predict outcomes in the Intensive Care Unit (ICU). Methods: We develop a novel phenotype annotation model to annotate phenotypic features of patients which are then used as input features of predictive mod…
University of Massachusetts Medical School（马萨诸塞大学医学院）；University of Massachusetts（马萨诸塞大学）；Yale University（耶鲁大学）；Bedford Veterans Affairs Medical Center（贝德福德退伍军人事务医疗中心）
Objective: Allowing patients to access their own electronic health record (EHR) notes through online patient portals has the potential to improve patient-centered care. However, medical jargon, which abounds in EHR notes, has been shown to be a barrier for patient EHR comprehension. Existing knowledge bases that link medical jargon to lay terms or definitions play an important role in alleviating this problem but have low coverage of medical jargon in EHRs. We developed a data-driven approach that mines EHRs to identify and rank medical jargon based on its importance to patients, to support th…
National Institute of Technology Karnataka Surathkal（卡纳塔克苏拉特卡尔国家理工学院）
Existing Clinical Decision Support Systems (CDSSs) largely depend on the availability of structured patient data and Electronic Health Records (EHRs) to aid caregivers. However, in case of hospitals in developing countries, structured patient data formats are not widely adopted, where medical professionals still rely on clinical notes in the form of unstructured text. Such unstructured clinical notes recorded by medical personnel can also be a potential source of rich patient-specific information which can be leveraged to build CDSSs, even for hospitals in developing countries. If such unstruc…
HERMES: Contrast-Aware Knowledge Graph Reasoning from Clinical Notes for Patient Outcome Prediction
Business AI Lab, College of Technology, National Economics University（国民经济大学技术学院商业人工智能实验室）；Hanoi University of Science and Technology（河内理工大学）；A2I Lab, Phenikaa School of Computing, Phenikaa University（Phenikaa大学Phenikaa计算学院A2I实验室）；Department of Head and Neck Surgery, Vietnam National Cancer Hospital & Hanoi Medical University（越南国家癌症医院头颈外科与河内医科大学）；VNPT AI, VNPT Group（VNPT集团VNPT AI）
University of California（加利福尼亚大学）；Berkeley, CA（伯克利（加利福尼亚州）（注：此处仅保留原文机构相关部分，严格按要求处理））
We investigate the automatic classification of patient discharge notes into standard disease labels. We find that Convolutional Neural Networks with Attention outperform previous algorithms used in this task, and suggest further areas for improvement.
