title: An automatic system to identify heart disease risk factors in clinical texts over time.
abstract: Despite recent progress in prediction and prevention, heart disease remains a leading cause of death. One preliminary step in heart disease prediction and prevention is risk factor identification. Many studies have been proposed to identify risk factors associated with heart disease; however, none have attempted to identify all risk factors. In 2014, the National Center of Informatics for Integrating Biology and Beside (i2b2) issued a clinical natural language processing (NLP) challenge that involved a track (track 2) for identifying heart disease risk factors in clinical texts over time. This track aimed to identify medically relevant information related to heart disease risk and track the progression over sets of longitudinal patient medical records. Identification of tags and attributes associated with disease presence and progression, risk factors, and medications in patient medical history were required. Our participation led to development of a hybrid pipeline system based on both machine learning-based and rule-based approaches. Evaluation using the challenge corpus revealed that our system achieved an F1-score of 92.68%, making it the top-ranked system (without additional annotations) of the 2014 i2b2 clinical NLP challenge.
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: qingcai.chen@gmail.com.
authors.forename: Qingcai
authors.initials: Q
authors.lastname: Chen
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: Haodili.hit@gmail.com.
authors.forename: Haodi
authors.initials: H
authors.lastname: Li
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: tangbuzhou@gmail.com.
authors.forename: Buzhou
authors.initials: B
authors.lastname: Tang
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: wangxl@insun.hit.edu.cn.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: hit.liuxin@gmail.com.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: liuzengjian.hit@gmail.com.
authors.forename: Zengjian
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: liushuhit@outlook.com.
authors.forename: Shu
authors.initials: S
authors.lastname: Liu
authors.affiliation: Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: weida.wong@gmail.com.
authors.forename: Weida
authors.initials: W
authors.lastname: Wang
authors.affiliation: The Sixth People's Hospital of Shenzhen, Shenzhen 518052, China. Electronic address: qiwendeng@hotmail.com.
authors.forename: Qiwen
authors.initials: Q
authors.lastname: Deng
authors.affiliation: The Sixth People's Hospital of Shenzhen, Shenzhen 518052, China. Electronic address: 13809883596@163.com.
authors.forename: Suisong
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Department of Cardiology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou 510120, China. Electronic address: tjcyx1995@163.com.
authors.forename: Yangxin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Cardiology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou 510120, China. Electronic address: dr_wjf@hotmail.com.
authors.forename: Jingfeng
authors.initials: J
authors.lastname: Wang
mesh_terms: D000368:Aged; D002318:Cardiovascular Diseases / Q000175:diagnosis / Q000453:epidemiology*; D002681:China / Q000453:epidemiology; D015331:Cohort Studies; D015897:Comorbidity; D016494:Computer Security; D003219:Confidentiality; D057225:Data Mining / Q000379:methods*; D048909:Diabetes Complications / Q000175:diagnosis / Q000453:epidemiology*; D057286:Electronic Health Records / Q000458:organization & administration*; D005260:Female; D006801:Humans; D015994:Incidence; D008137:Longitudinal Studies; D008297:Male; D008875:Middle Aged; D033262:Narration; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods; D018570:Risk Assessment / Q000379:methods; D018875:Vocabulary, Controlled
keywords: Clinical information extraction; Heart disease; Machine learning; Risk factor identification