Advancements in machine learning algorithms have had a beneficial impact on representation learning, classification, and prediction models built using electronic health record (EHR) data. Effort has been put both on increasing models' overall performance as well as improving their interpretability, particularly regarding the decision-making process. In this study, we present a temporal deep learning model to perform bidirectional representation learning on EHR sequences with a transformer architecture to predict future diagnosis of depression. This model is able to aggregate five heterogenous and high-dimensional data sources from the EHR and process them in a temporal manner for chronic disease prediction at various prediction windows. We applied the current trend of pretraining and fine-tuning on EHR data to outperform the current state-of-the-art in chronic disease prediction, and to demonstrate the underlying relation between EHR codes in the sequence. The model generated the highest increases of precision-recall area under the curve (PRAUC) from 0.70 to 0.76 in depression prediction compared to the best baseline model. Furthermore, the self-attention weights in each sequence quantitatively demonstrated the inner relationship between various codes, which improved the model's interpretability. These results demonstrate the model's ability to utilize heterogeneous EHR data to predict depression while achieving high accuracy and interpretability, which may facilitate constructing clinical decision support systems in the future for chronic disease screening and early detection.
EviDep: Uncertainty-Aware Multimodal Depression Estimation via Disentangled Evidential Learning
School of Computer Science and Technology, University of Science and Technology of China（中国科学技术大学计算机科学与技术学院）；School of Computer Science and Information Engineering, Hefei University of Technology（合肥工业大学计算机科学与信息工程学院）；Department of Psychiatry, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China（中国科学技术大学附属第一医院精神科，生命科学与医学学院）
Bidirectional Generative Pre-training for Improving Healthcare Time-series Representation Learning
School of Computer Science, McGill University（麦吉尔大学计算机学院）；School of Population and Global Health, McGill University（麦吉尔大学人口与全球健康学院）；Mila - Quebec AI Institute（米拉-魁北克人工智能研究所）
University of Alberta（阿尔伯塔大学）；The Affiliated Kangning Hospital of Wenzhou Medical University（温州医科大学附属康宁医院）；Wenzhou Medical University（温州医科大学）
Depression is increasingly impacting individuals both physically and psychologically worldwide. It has become a global major public health problem and attracts attention from various research fields. Traditionally, the diagnosis of depression is formulated through semi-structured interviews and supplementary questionnaires, which makes the diagnosis heavily relying on physicians experience and is subject to bias. Mental health monitoring and cloud-based remote diagnosis can be implemented through an automated depression diagnosis system. In this article, we propose an attention-based multimoda…
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.
MERID: Multimodal Exploration via Recursive Self-Improvement Agents for Major Depression Analysis
Yale University（耶鲁大学）；Zhejiang University（浙江大学）；Northwestern University（西北大学）；University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；Tsinghua University（清华大学）；Stevens Institute of Technology（史蒂文斯理工学院）
Depression is one of the most prevalent mental disorders, which seriously affects one's life. Traditional depression diagnostics commonly depends on rating with scales, which can be labor-intensive and subjective. In this context, Automatic Depression Detection (ADD) has been attracting more attention for its low cost and objectivity. ADD systems are able to detect depression automatically from some medical records, like video sequences. However, it remains challenging to effectively extract depression-specific information from long sequences, thereby hindering a satisfying accuracy. In this p…
Key features of mental illnesses are reflected in speech. Our research focuses on designing a multimodal deep learning structure that automatically extracts salient features from recorded speech samples for predicting various mental disorders including depression, bipolar, and schizophrenia. We adopt a variety of pre-trained models to extract embeddings from both audio and text segments. We use several state-of-the-art embedding techniques including BERT, FastText, and Doc2VecC for the text representation learning and WaveNet and VGG-ish models for audio encoding. We also leverage huge auxilia…
Université Paris-Est（巴黎东部大学）；INSAT Institut National des Sciences Appliquées et de Technologie（突尼斯应用科学与技术学院）；Yobitrust（优比特信托公司）；University of Sciences and Arts in Lebanon（黎巴嫩科学与艺术大学）；Université de Bourgogne Franche Comté（勃艮第-弗朗什-孔泰大学）
Clinical depression or Major Depressive Disorder (MDD) is a common and serious medical illness. In this paper, a deep recurrent neural network-based framework is presented to detect depression and to predict its severity level from speech. Low-level and high-level audio features are extracted from audio recordings to predict the 24 scores of the Patient Health Questionnaire and the binary class of depression diagnosis. To overcome the problem of the small size of Speech Depression Recognition (SDR) datasets, expanding training labels and transferred features are considered. The proposed approa…
Recording Brain Activity While Listening to Music Using Wearable EEG Devices Combined with Bidirectional Long Short-Term Memory Networks
School of Music, Jiangxi Normal University（江西师范大学音乐学院）；School of Electronic Information, HuZhou College（湖州学院电子信息学院）；San Francisco State University（旧金山州立大学）
University of Sydney（悉尼大学）；Capital Markets CRC（资本市场合作研究中心）；University of Technology Sydney（悉尼科技大学）
Automated extraction of concepts from patient clinical records is an essential facilitator of clinical research. For this reason, the 2010 i2b2/VA Natural Language Processing Challenges for Clinical Records introduced a concept extraction task aimed at identifying and classifying concepts into predefined categories (i.e., treatments, tests and problems). State-of-the-art concept extraction approaches heavily rely on handcrafted features and domain-specific resources which are hard to collect and define. For this reason, this paper proposes an alternative, streamlined approach: a recurrent neur…
University of Technology Sydney（悉尼科技大学）；The University of Queensland（昆士兰大学）
Electronic health records (EHRs) are longitudinal records of a patient's interactions with healthcare systems. A patient's EHR data is organized as a three-level hierarchy from top to bottom: patient journey - all the experiences of diagnoses and treatments over a period of time; individual visit - a set of medical codes in a particular visit; and medical code - a specific record in the form of medical codes. As EHRs begin to amass in millions, the potential benefits, which these data might hold for medical research and medical outcome prediction, are staggering - including, for example, predi…
Xerox（施乐公司）；SUNY Buffalo（纽约州立大学布法罗分校）；Conduent Labs US（Conduent美国实验室）；University of Rochester（罗切斯特大学）；United Technologies Research Center（联合技术研究中心）
Predicting the future health information of patients from the historical Electronic Health Records (EHR) is a core research task in the development of personalized healthcare. Patient EHR data consist of sequences of visits over time, where each visit contains multiple medical codes, including diagnosis, medication, and procedure codes. The most important challenges for this task are to model the temporality and high dimensionality of sequential EHR data and to interpret the prediction results. Existing work solves this problem by employing recurrent neural networks (RNNs) to model EHR data an…
University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；University of Massachusetts Lowell（马萨诸塞大学洛厄尔分校）；Bedford VA Medical Center（贝德福德退伍军人事务医疗中心）
Question: Can an encoder-decoder architecture pretrained on a large dataset of longitudinal electronic health records improves patient outcome predictions? Findings: In this prognostic study of 6.8 million patients, our denoising sequence-to-sequence prediction model of multiple outcomes outperformed state-of-the-art models scuh pretrained BERT on a broad range of patient outcomes, including intentional self-harm and pancreatic cancer. Meaning: Deep bidirectional and autoregressive representation improves patient outcome prediction.
Online forums and social media platforms provide noisy but valuable data every day. In this paper, we propose a novel end-to-end neural network-based user embedding system, Author2Vec. The model incorporates sentence representations generated by BERT (Bidirectional Encoder Representations from Transformers) with a novel unsupervised pre-training objective, authorship classification, to produce better user embedding that encodes useful user-intrinsic properties. This user embedding system was pre-trained on post data of 10k Reddit users and was analyzed and evaluated on two user classification …
Electronic Health Records-Based Data-Driven Diabetes Knowledge Unveiling and Risk Prognosis
Georgia Institute of Technology（佐治亚理工学院）；McGill University（麦吉尔大学）；Carnegie Mellon University（卡内基梅隆大学）；Oregon State University（俄勒冈州立大学）；University of Pennsylvania（宾夕法尼亚大学）；Northeastern University（东北大学）；University of California, San Diego（加州大学圣地亚哥分校）
One major impediment to the wider use of deep learning for clinical decision making is the difficulty of assigning a level of confidence to model predictions. Currently, deep Bayesian neural networks and sparse Gaussian processes are the main two scalable uncertainty estimation methods. However, deep Bayesian neural network suffers from lack of expressiveness, and more expressive models such as deep kernel learning, which is an extension of sparse Gaussian process, captures only the uncertainty from the higher level latent space. Therefore, the deep learning model under it lacks interpretabili…
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…
Sberbank Artificial Intelligence Laboratory（俄罗斯联邦储蓄银行人工智能实验室）；New York University（纽约大学）
In this paper we study the problem of predicting clinical diagnoses from textual Electronic Health Records (EHR) data. We show the importance of this problem in medical community and present comprehensive historical review of the problem and proposed methods. As the main scientific contributions we present a modification of Bidirectional Encoder Representations from Transformers (BERT) model for sequence classification that implements a novel way of Fully-Connected (FC) layer composition and a BERT model pretrained only on domain data. To empirically validate our model, we use a large-scale Ru…
Multivariate time-series data are used in many classification and regression predictive tasks, and recurrent models have been widely used for such tasks. Most common recurrent models assume that time-series data elements are of equal length and the ordered observations are recorded at regular intervals. However, real-world time-series data have neither a similar length nor a same number of observations. They also have missing entries, which hinders the performance of predictive tasks. In this paper, we approach these issues by presenting a model for the combined task of imputing and predicting…
CDMT-EHR: A Continuous-Time Diffusion Framework for Generating Mixed-Type Time-Series Electronic Health Records
Department of Core Informatics, Graduate School of Informatics, Osaka Metropolitan University（核心信息学系，信息学研究生学校，大阪 Metropolitan 大学）；Smart Data & Knowledge Services Department, German Research Center for Artificial Intelligence (DFKI GmbH)（智能数据与知识服务部，德国人工智能研究中心（DFKI GmbH））；Department of Hematology and Department of Laboratory Medicine and Medical Informatics, Graduate School of Medicine, Osaka Metropolitan University（血液科和实验室医学与医学信息学系，医学研究生学校，大阪 Metropolitan 大学）
School of Engineering and Applied Sciences, Harvard University（哈佛大学工程与应用科学学院）；Massachusetts General Hospital（麻省总医院）
Supervisory signals can help topic models discover low-dimensional data representations that are more interpretable for clinical tasks. We propose a framework for training supervised latent Dirichlet allocation that balances two goals: faithful generative explanations of high-dimensional data and accurate prediction of associated class labels. Existing approaches fail to balance these goals by not properly handling a fundamental asymmetry: the intended task is always predicting labels from data, not data from labels. Our new prediction-constrained objective trains models that predict labels fr…
Decoding language representations directly from the brain can enable new Brain-Computer Interfaces (BCI) for high bandwidth human-human and human-machine communication. Clinically, such technologies can restore communication in people with neurological conditions affecting their ability to speak. In this study, we propose a novel deep network architecture Brain2Char, for directly decoding text (specifically character sequences) from direct brain recordings (called Electrocorticography, ECoG). Brain2Char framework combines state-of-the-art deep learning modules --- 3D Inception layers for multi…
Bidirectional recurrent imputation and abundance estimation of LULC classes with MODIS multispectral time series and geo-topographic and climatic data
Dept. of Computer Science and Artificial Intelligence, DaSCI University of Granada（计算机科学与人工智能系，DaSCI格拉纳达大学）；Dept. of Botany Faculty of Science, University of Granada（植物学系，格拉纳达大学）
提出融合 MODIS 多光谱时间序列与地理地形、气候辅助信息的端到端 LSTM 解混框架，并发布安达卢西亚像元级丰度标注数据集。
School of Biomedical Informatics, University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心生物医学信息学院）
Deep learning (DL) based predictive models from electronic health records (EHR) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required to achieve high accuracy, hindering the adoption of DL-based models in scenarios with limited training data size. Recently, bidirectional encoder representations from transformers (BERT) and related models have achieved tremendous successes in the natural language processing domain. The pre-training of BERT on a very large training corpus generates contextualized embeddings that can boost the performance of mo…
Dalian University of Technology（大连理工大学）；Worcester Polytechnic Institute（伍斯特理工学院）；Indiana University（印第安纳大学）；Alibaba DAMO Academy（阿里巴巴达摩院）
Objective: Ubiquitous internet access is reshaping the way we live, but it is accompanied by unprecedented challenges in preventing chronic diseases that are usually planted by long exposure to unhealthy lifestyles. This paper proposes leveraging online shopping behaviors as a proxy for personal lifestyle choices to improve chronic disease prevention literacy, targeted for times when e-commerce user experience has been assimilated into most people's everyday lives. Methods: Longitudinal query logs and purchase records from 15 million online shoppers were accessed, constructing a broad spectrum…
