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Medical concept normalization in French using multilingual terminologies and contextual embeddings J. Biomed. Inform. (IF 3.526) Pub Date : 2021-01-12 Perceval Wajsbürt; Arnaud Sarfati; Xavier Tannier
Introduction Concept normalization is the task of linking terms from textual medical documents to their concept in terminologies such as the UMLS®. Traditional approaches to this problem depend heavily on the coverage of available resources, which poses a problem for languages other than English. Objective We present a system for concept normalization in French. We consider textual mentions already
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Formative feedback generation in a VR-based dental surgical skill training simulator J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-27 Myat Su Yin; Peter Haddawy; Siriwan Suebnukarn; Farin Kulapichitr; Phattanapon Rhienmora; Varistha Jatuwat; Nuttanun Uthaipattanacheep
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Predicting neonatal respiratory distress syndrome and hypoglycaemia prior to discharge: Leveraging health administrative data and machine learning J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-05 Kim S. Betts; Steve Kisely; Rosa Alati
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Interpreting a Recurrent Neural Network’s Predictions of ICU Mortality Risk J. Biomed. Inform. (IF 3.526) Pub Date : 2021-01-07 Long V. Ho; Melissa Aczon; David Ledbetter; Randall Wetzel
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
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Identifying the essential nodes in network pharmacology based on multilayer network combined with random walk algorithm J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-25 Xianlai Chen; Mingyue Xu; Ying An
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Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-31 Yuqi Si; Jingcheng Du; Zhao Li; Xiaoqian Jiang; Timothy Miller; Fei Wang; W. Jim Zheng; Kirk Roberts
Objectives: Patient representation learning refers to learning a dense mathematical representation of a patient that encodes meaningful information from Electronic Health Records (EHRs). This is generally performed using advanced deep learning methods. This study presents a systematic review of this field and provides both qualitative and quantitative analyses from a methodological perspective. Methods:
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Enabling personalized decision support with patient-generated data and attributable components J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-13 Elliot G. Mitchell; Esteban G. Tabak; Matthew E Levine; Lena Mamykina; David J. Albers
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An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-13 Andrew Wen; Liwei Wang; Huan He; Sijia Liu; Sunyang Fu; Sunghwan Sohn; Jacob A. Kugel; Vinod C. Kaggal; Ming Huang; Yanshan Wang; Feichen Shen; Jungwei Fan; Hongfang Liu
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Discovering prescription patterns in pediatric acute-onset neuropsychiatric syndrome patients J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-28 Arturo Lopez Pineda; Armin Pourshafeie; Alexander Ioannidis; Collin McCloskey Leibold; Avis L. Chan; Carlos D. Bustamante; Jennifer Frankovich; Genevieve L. Wojcik
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Challenges and solutions to employing natural language processing and machine learning to measure patients’ health literacy and physician writing complexity: The ECLIPPSE study J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-11 William Brown; Renu Balyan; Andrew J. Karter; Scott Crossley; Wagahta Semere; Nicholas D. Duran; Courtney Lyles; Jennifer Liu; Howard H. Moffet; Ryane Daniels; Danielle S. McNamara; Dean Schillinger
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The role of explainability in creating trustworthy artificial intelligence for health care: A comprehensive survey of the terminology, design choices, and evaluation strategies J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-10 Aniek F. Markus; Jan A. Kors; Peter R. Rijnbeek
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Studying pediatric health outcomes with electronic health records using Bayesian clustering and trajectory analysis J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-11 Rebecca A. Hubbard; Jinyu Xu; Robert Siegel; Yong Chen; Ihuoma Eneli
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Analysis of the cognitive demands of electronic health record use J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-27 Mark S. Pfaff; Ozgur Eris; Charlene Weir; Amanda Anganes; Tina Crotty; Mohammad Rahman; Merry Ward; Jonathan R. Nebeker
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Hybrid collaborative filtering methods for recommending search terms to clinicians J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-09 Zhiyun Ren; Bo Peng; Titus K. Schleyer; Xia Ning
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A prediction and interpretation framework of acute kidney injury in critical care J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-16 Kaidi Gong; Hyo Kyung Lee; Kaiye Yu; Xiaolei Xie; Jingshan Li
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Domain specific word embeddings for natural language processing in radiology J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-15 Timothy L. Chen; Max Emerling; Gunvant R. Chaudhari; Yeshwant R. Chillakuru; Youngho Seo; Thienkhai H. Vu; Jae Ho Sohn
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A retrospective approach to evaluating potential adverse outcomes associated with delay of procedures for cardiovascular and cancer-related diagnoses in the context of COVID-19 J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-10 Neil S. Zheng; Jeremy L. Warner; Travis J. Osterman; Quinn S. Wells; Xiao-Ou Shu; Stephen A. Deppen; Seth J. Karp; Shon Dwyer; QiPing Feng; Nancy J. Cox; Josh F. Peterson; C. Michael Stein; Dan M. Roden; Kevin B. Johnson; Wei-Qi Wei
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Comparison of segmentation-free and segmentation-dependent computer-aided diagnosis of breast masses on a public mammography dataset J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-11 Rebecca Sawyer Lee; Jared A. Dunnmon; Ann He; Siyi Tang; Christopher Ré; Daniel L. Rubin
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Noise-tolerant similarity search in temporal medical data J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-25 Luca Bonomi; Liyue Fan; Xiaoqian Jiang
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Standardized Electronic Health Record Data Modeling and Persistence: A Comparative Review J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-25 Aya Gamal; Sherif Barakat; Amira Rezk
With the extensive adoption of electronic health records (EHRs) by several healthcare organizations, more efforts are needed to manage and utilize such massive, various, and complex healthcare data. Databases' performance and suitability to health care tasks are dramatically affected by how their data storage model and query capabilities are well-adapted to the use case scenario. On the other hand
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CMIID: A comprehensive medical information identifier for clinical search harmonization in Data Safe Havens J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-24 Michael A.P. Domingues; Rui Camacho; Pedro Pereira Rodrigues
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Annotating social determinants of health using active learning, and characterizing determinants using neural event extraction J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-05 Kevin Lybarger; Mari Ostendorf; Meliha Yetisgen
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Language models are an effective representation learning technique for electronic health record data J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-05 Ethan Steinberg; Ken Jung; Jason A. Fries; Conor K. Corbin; Stephen R. Pfohl; Nigam H. Shah
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Phenotype risk scores (PheRS) for pancreatic cancer using time-stamped electronic health record data: Discovery and validation in two large biobanks J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-03 Maxwell Salvatore; Lauren J. Beesley; Lars G. Fritsche; David Hanauer; Xu Shi; Alison M. Mondul; Celeste Leigh Pearce; Bhramar Mukherjee
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GenHITS: A Network Science Approach to Driver Gene Detection in Human Regulatory Network Using Gene’s Influence Evaluation J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-14 Mostafa Akhavan Safar; Babak Teimourpour; Mehrdad Kargari
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Smart conversational agents for the detection of neuropsychiatric disorders: A systematic review J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-02 Moisés R. Pacheco-Lorenzo; Sonia M. Valladares-Rodríguez; Luis E. Anido-Rifón; Manuel J. Fernández-Iglesias
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An hybrid ECG-based deep network for the early identification of high-risk to major cardiovascular events for hypertension patients J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-01 Giovanni Paragliola; Antonio Coronato
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Residual LSTM layered CNN for Classification of Gastrointestinal Tract Diseases J. Biomed. Inform. (IF 3.526) Pub Date : 2020-12-01 Şaban Öztürk; Umut Özkaya
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A hierarchical clustering and data fusion approach for disease subtype discovery J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-30 Bastian Pfeifer; Michael G. Schimek
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Evaluating warfarin dosing models on multiple datasets with a novel software framework and evolutionary optimisation J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-30 Gianluca Truda; Patrick Marais
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Pre-training phenotyping classifiers J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-28 Dmitriy Dligach; Majid Afshar; Timothy Miller
Recent transformer-based pre-trained language models have become a de facto standard for many text classification tasks. Nevertheless, their utility in the clinical domain, where classification is often performed at encounter or patient level, is still uncertain due to the limitation on the maximum length of input. In this work, we introduce a self-supervised method for pre-training that relies on
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A Review on Deep Learning Approaches in Healthcare Systems: Taxonomies, Challenges, and Open Issues J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-28 Shahab Shamshirband; Mahdis Fathi; Abdollah Dehzangi; Anthony Theodore Chronopoulos; Hamid Alinejad-Rokny
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Measuring the quality of patient–physician communication J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-06 Clint Cuffy; Nao Hagiwara; Scott Vrana; Bridget T. McInnes
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Potential circRNA-disease association prediction using DeepWalk and network consistency projection J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-18 Guanghui Li; Jiawei Luo; Diancheng Wang; Cheng Liang; Qiu Xiao; Pingjian Ding; Hailin Chen
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From electronic health records to terminology base: A novel knowledge base enrichment approach J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-21 Jiaying Zhang; Zhixing Zhang; Huanhuan Zhang; Zhiyuan Ma; Qi Ye; Ping He; Yangming Zhou
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A framework for patient-centered telemedicine: Application and lessons learned from vulnerable populations J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-10 Andrew H. Talal; Elisavet M. Sofikitou; Urmo Jaanimägi; Marija Zeremski; Jonathan N. Tobin; Marianthi Markatou
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Character level and word level embedding with bidirectional LSTM – Dynamic recurrent neural network for biomedical named entity recognition from literature J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-26 Sudhakaran Gajendran; Manjula D; Vijayan Sugumaran
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Best variable identification by means of data-mining and cooperative game theory J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-19 Stefan Bruch; Lisa Ernst; Mareike Schulz; Leonie Zieglowski; René H. Tolba
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A novel fitness function in genetic programming for medical data classification J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-14 Arvind Kumar; Nishant Sinha; Arpit Bhardwaj
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Treatment Selection for Life-Critical Shared Decision Making Under Ranges of Health-State Utility Scenarios J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-18 Evangelos Triantaphyllou; Juri Yanase
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An empirical characterization of fair machine learning for clinical risk prediction J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-18 Stephen R. Pfohl; Agata Foryciarz; Nigam H. Shah
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Learning Bayesian networks from demographic and health survey data J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-17 Neville Kenneth Kitson; Anthony C. Constantinou
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Weighted dimensionality reduction and robust Gaussian mixture model based cancer patient subtyping from gene expression data J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-11 Omar Rafique; A.H. Mir
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Detection of calibration drift in clinical prediction models to inform model updating J. Biomed. Inform. (IF 3.526) Pub Date : 2020-11-04 Sharon E. Davis; Robert A. Greevy; Thomas A. Lasko; Colin G. Walsh; Michael E. Matheny
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Deep learning with wearable based heart rate variability for prediction of mental and general health J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-31 Louise V. Coutts; David Plans; Alan W. Brown; John Collomosse
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Towards a goal-oriented methodology for clinical-guideline-based management recommendations for patients with multimorbidity: GoCom and its preliminary evaluation J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-06 Alexandra Kogan; Mor Peleg; Samson W. Tu; Raviv Allon; Natanel Khaitov; Irit Hochberg
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Detecting high-quality signals of adverse drug-drug interactions from spontaneous reporting data J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-24 Chen Zhan; Elizabeth Roughead; Lin Liu; Nicole Pratt; Jiuyong Li
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Reducing waiting time for remote patients in telemedicine with considering treated patients in emergency department based on body sensors technologies and hybrid computational algorithms: Toward scalable and efficient real time healthcare monitoring system J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-19 Omar Hussein Salman; Mohammed Imad Aal-Nouman; Zahraa K. Taha
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iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-20 Chunjiang Yu; Xin Qi; Yuxin Lin; Yin Li; Bairong Shen
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Learning multimorbidity patterns from electronic health records using Non-negative Matrix Factorisation J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-27 Abdelaali Hassaine; Dexter Canoy; Jose Roberto Ayala Solares; Yajie Zhu; Shishir Rao; Yikuan Li; Mariagrazia Zottoli; Kazem Rahimi; Gholamreza Salimi-Khorshidi
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A secure system for genomics clinical decision support J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-17 Seemeen Karimi; Xiaoqian Jiang; Robert H. Dolin; Miran Kim; Aziz Boxwala
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Using the contextual language model BERT for multi-criteria classification of scientific articles J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-13 Ashwin Karthik Ambalavanan; Murthy V. Devarakonda
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Concept placement using BERT trained by transforming and summarizing biomedical ontology structure J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-22 Hao Liu; Yehoshua Perl; James Geller
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Cross domains adversarial learning for Chinese named entity recognition for online medical consultation J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-23 Guihua Wen; Hehong Chen; Huihui Li; Yang Hu; Yanghui Li; Changjun Wang
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Automatic full conversion of clinical terms into SNOMED CT concepts J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-02 Rohit J. Kate
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Dementia Medical Screening using Mobile Applications: A Systematic Review with A New Mapping Model. J. Biomed. Inform. (IF 3.526) Pub Date : 2020-09-20 Fadi Thabtah,David Peebles,Jenny Retzler,Chanchala Hathurusingha
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Learning hidden patterns from patient multivariate time series data using convolutional neural networks: A case study of healthcare cost prediction J. Biomed. Inform. (IF 3.526) Pub Date : 2020-09-25 Mohammad Amin Morid; Olivia R. Liu Sheng; Kensaku Kawamoto; Samir Abdelrahman
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A deep learning–based, unsupervised method to impute missing values in electronic health records for improved patient management J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-01 Da Xu; Paul Jen-Hwa Hu; Ting-Shuo Huang; Xiao Fang; Chih-Chin Hsu
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A virtual reality methodology for cardiopulmonary resuscitation training with and without a physical mannequin J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-08 Fabio Buttussi; Luca Chittaro; Francesca Valent
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Defining facets of social distancing during the COVID-19 pandemic: Twitter analysis J. Biomed. Inform. (IF 3.526) Pub Date : 2020-10-14 Jiye Kwon; Connor Grady; Josemari T. Feliciano; Samah J. Fodeh