Articles

A hybrid approach for named entity recognition in Chinese electronic medical record

With the rapid spread of electronic medical records and the arrival of medical big data era, the application of natural language processing technology in biomedicine has become a hot research topic.

Authors: Bin Ji, Rui Liu, Shasha Li, Jie Yu, Qingbo Wu, Yusong Tan and Jiaju Wu

Incorporating causal factors into reinforcement learning for dynamic treatment regimes in HIV

Reinforcement learning (RL) provides a promising technique to solve complex sequential decision making problems in health care domains. However, existing studies simply apply naive RL algorithms in discovering...

Authors: Chao Yu, Yinzhao Dong, Jiming Liu and Guoqi Ren

Relation path feature embedding based convolutional neural network method for drug discovery

Drug development is an expensive and time-consuming process. Literature-based discovery has played a critical role in drug development and may be a supplementary method to help scientists speed up the discover...

Authors: Di Zhao, Jian Wang, Shengtian Sang, Hongfei Lin, Jiabin Wen and Chunmei Yang

Applying deep matching networks to Chinese medical question answering: a study and a dataset

Medical and clinical question answering (QA) is highly concerned by researchers recently. Though there are remarkable advances in this field, the development in Chinese medical domain is relatively backward. I...

Authors: Junqing He, Mingming Fu and Manshu Tu

Discovering thematic change and evolution of utilizing social media for healthcare research

Social media plays a more and more important role in the research of health and healthcare due to the fast development of internet communication and information exchange. This paper conducts a bibliometric ana...

Authors: Xieling Chen, Yonghui Lun, Jun Yan, Tianyong Hao and Heng Weng

On building a diabetes centric knowledge base via mining the web

Diabetes has become one of the hot topics in life science researches. To support the analytical procedures, researchers and analysts expend a mass of labor cost to collect experimental data, which is also erro...

Authors: Fan Gong, Yilei Chen, Haofen Wang and Hao Lu

Mobile phone applications to overcome malnutrition among preschoolers: a systematic review

Malnutrition is one of the most important reasons for child mortality in developing countries, especially during the first 5 years of life. We set out to systematically review evaluations of interventions that...

Authors: Navisa Seyyedi, Bahlol Rahimi, Hamid Reza Farrokh Eslamlou, Toomas Timpka and Hadi Lotfnezhad Afshar

Facilitating accurate health provider directories using natural language processing

Accurate information in provider directories are vital in health care including health information exchange, health benefits exchange, quality reporting, and in the reimbursement and delivery of care. Maintain...

Authors: Matthew J. Cook, Lixia Yao and Xiaoyan Wang

Extracting health-related causality from twitter messages using natural language processing

Twitter messages (tweets) contain various types of topics in our daily life, which include health-related topics. Analysis of health-related tweets would help us understand health conditions and concerns encou...

Authors: Son Doan, Elly W. Yang, Sameer S. Tilak, Peter W. Li, Daniel S. Zisook and Manabu Torii

Developing a portable natural language processing based phenotyping system

This paper presents a portable phenotyping system that is capable of integrating both rule-based and statistical machine learning based approaches.

Authors: Himanshu Sharma, Chengsheng Mao, Yizhen Zhang, Haleh Vatani, Liang Yao, Yizhen Zhong, Luke Rasmussen, Guoqian Jiang, Jyotishman Pathak and Yuan Luo

Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison

A shareable repository of clinical notes is critical for advancing natural language processing (NLP) research, and therefore a goal of many NLP researchers is to create a shareable repository of clinical notes...

Authors: Yaoyun Zhang, Firat Tiryaki, Min Jiang and Hua Xu

Special issue of BMC medical informatics and decision making on health natural language processing

Authors: V. G. Vinod Vydiswaran, Yaoyun Zhang, Yanshan Wang and Hua Xu

Complexities, variations, and errors of numbering within clinical notes: the potential impact on information extraction and cohort-identification

Numbers and numerical concepts appear frequently in free text clinical notes from electronic health records. Knowledge of the frequent lexical variations of these numerical concepts, and their accurate identif...

Authors: David A. Hanauer, Qiaozhu Mei, V. G. Vinod Vydiswaran, Karandeep Singh, Zach Landis-Lewis and Chunhua Weng

Entity recognition in Chinese clinical text using attention-based CNN-LSTM-CRF

Clinical entity recognition as a fundamental task of clinical text processing has been attracted a great deal of attention during the last decade. However, most studies focus on clinical text in English rather...

Authors: Buzhou Tang, Xiaolong Wang, Jun Yan and Qingcai Chen

Natural language processing of radiology reports for identification of skeletal site-specific fractures

Osteoporosis has become an important public health issue. Most of the population, particularly elderly people, are at some degree of risk of osteoporosis-related fractures. Accurate identification and surveill...

Authors: Yanshan Wang, Saeed Mehrabi, Sunghwan Sohn, Elizabeth J. Atkinson, Shreyasee Amin and Hongfang Liu

EHR problem list clustering for improved topic-space navigation

The amount of patient-related information within clinical information systems accumulates over time, especially in cases where patients suffer from chronic diseases with many hospitalizations and consultations...

Authors: Markus Kreuzthaler, Bastian Pfeifer, Jose Antonio Vera Ramos, Diether Kramer, Victor Grogger, Sylvia Bredenfeldt, Markus Pedevilla, Peter Krisper and Stefan Schulz

Clinical text classification with rule-based features and knowledge-guided convolutional neural networks

Clinical text classification is an fundamental problem in medical natural language processing. Existing studies have cocnventionally focused on rules or knowledge sources-based feature engineering, but only a ...

Authors: Liang Yao, Chengsheng Mao and Yuan Luo

A two-site survey of medical center personnel’s willingness to share clinical data for research: implications for reproducible health NLP research

A shareable repository of clinical notes is critical for advancing natural language processing (NLP) research, and therefore a goal of many NLP researchers is to create a shareable repository of clinical notes...

Authors: Chunhua Weng, Carol Friedman, Casey A. Rommel and John F. Hurdle

Discovering associations between problem list and practice setting

The Health Information Technology for Economic and Clinical Health Act (HITECH) has greatly accelerated the adoption of electronic health records (EHRs) with the promise of better clinical decisions and patien...

Authors: Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad and Hongfang Liu

Identifying peer experts in online health forums

Online health forums have become increasingly popular over the past several years. They provide members with a platform to network with peers and share information, experiential advice, and support. Among the ...

Authors: V.G.Vinod Vydiswaran and Manoj Reddy

A hybrid neural network model for predicting kidney disease in hypertension patients based on electronic health records

Disease prediction based on Electronic Health Records (EHR) has become one hot research topic in biomedical community. Existing work mainly focuses on the prediction of one target disease, and little work is p...

Authors: Yafeng Ren, Hao Fei, Xiaohui Liang, Donghong Ji and Ming Cheng

QAnalysis: a question-answer driven analytic tool on knowledge graphs for leveraging electronic medical records for clinical research

While doctors should analyze a large amount of electronic medical record (EMR) data to conduct clinical research, the analyzing process requires information technology (IT) skills, which is difficult for most ...

Authors: Tong Ruan, Yueqi Huang, Xuli Liu, Yuhang Xia and Ju Gao

Correction to: Using decision fusion methods to improve outbreak detection in disease surveillance

Following publication of the original article [1], the authors reported that one of the authors’ names is spelled incorrectly.

Authors: Gaëtan Texier, Rodrigue S. Allodji, Loty Diop, Jean-Baptiste Meynard, Liliane Pellegrin and Hervé Chaudet

Predicting factors for survival of breast cancer patients using machine learning techniques

Breast cancer is one of the most common diseases in women worldwide. Many studies have been conducted to predict the survival indicators, however most of these analyses were predominantly performed using basic...

Authors: Mogana Darshini Ganggayah, Nur Aishah Taib, Yip Cheng Har, Pietro Lio and Sarinder Kaur Dhillon

Considering patient safety in autonomous e-mental health systems – detecting risk situations and referring patients back to human care

Digital health interventions can fill gaps in mental healthcare provision. However, autonomous e-mental health (AEMH) systems also present challenges for effective risk management. To balance autonomy and safe...

Authors: Myrthe L. Tielman, Mark A. Neerincx, Claudia Pagliari, Albert Rizzo and Willem-Paul Brinkman

The use of echocardiographic and clinical data recorded on admission to simplify decision making for elective percutaneous coronary intervention: a prospective cohort study

Coronary artery disease (CAD), a leading cause of mortality, affects patient health-related quality of life (HRQoL). Elective percutaneous coronary interventions (ePCIs) are usually performed to improve HRQoL ...

Authors: Rabah M. Al abdi, Hussam Alshraideh, Heba H. Hijazi, Mohamad Jarrah and Mohammad S. Alyahya

QL⁴MDR: a GraphQL query language for ISO 11179-based metadata repositories

Heterogeneous healthcare instance data can hardly be integrated without harmonizing its schema-level metadata. Many medical research projects and organizations use metadata repositories to edit, store and reus...

Authors: H. Ulrich, J. Kern, D. Tas, A. K. Kock-Schoppenhauer, F. Ückert, J. Ingenerf and M. Lablans

The validity of synthetic clinical data: a validation study of a leading synthetic data generator (Synthea) using clinical quality measures

Clinical data synthesis aims at generating realistic data for healthcare research, system implementation and training. It protects patient confidentiality, deepens our understanding of the complexity in health...

Authors: Junqiao Chen, David Chun, Milesh Patel, Epson Chiang and Jesse James

Automatically identifying social isolation from clinical narratives for patients with prostate Cancer

Social isolation is an important social determinant that impacts health outcomes and mortality among patients. The National Academy of Medicine recently recommended that social isolation be documented in elect...

Authors: Vivienne J Zhu, Leslie A Lenert, Brian E Bunnell, Jihad S Obeid, Melanie Jefferson and Chanita Hughes Halbert

Predicting hospital-acquired pneumonia among schizophrenic patients: a machine learning approach

Medications are frequently used for treating schizophrenia, however, anti-psychotic drug use is known to lead to cases of pneumonia. The purpose of our study is to build a model for predicting hospital-acquire...

Authors: Kuang Ming Kuo, Paul C. Talley, Chi Hsien Huang and Liang Chih Cheng

Accurate and rapid screening model for potential diabetes mellitus

Prediction or early diagnosis of diabetes is crucial for populations with high risk of diabetes.

Authors: Dongmei Pei, Yang Gong, Hong Kang, Chengpu Zhang and Qiyong Guo

Evaluating a South African mobile application for healthcare professionals to improve diagnosis and notification of pesticide poisonings

Mobile health is a fast-developing field. The use of mobile health applications by healthcare professionals (HCPs) globally has increased considerably. While several studies in high income countries have inves...

Authors: Siti Kabanda and Hanna-Andrea Rother

Recursive neural networks in hospital bed occupancy forecasting

Efficient planning of hospital bed usage is a necessary condition to minimize the hospital costs. In the presented work we deal with the problem of occupancy forecasting in the scale of several months, with a ...

Authors: Ekaterina Kutafina, Istvan Bechtold, Klaus Kabino and Stephan M. Jonas

Using decision fusion methods to improve outbreak detection in disease surveillance

When outbreak detection algorithms (ODAs) are considered individually, the task of outbreak detection can be seen as a classification problem and the ODA as a sensor providing a binary decision (outbreak yes o...

Authors: Gaëtan Texier, Rodrigue S. Allodji, Loty Diop, Jean-Baptiste Meynard, Liliane Pellegrin and Hervé Chaudet

Construction and application of service quality evaluation system in the preclinical research on cardiovascular implant devices

Services for the preclinical development and evaluation of cardiovascular implant devices (CVIDs) is a new industry. However, there is still no indicator system for quality evaluation. Our aim is to construct ...

Authors: Yongchun Cui, Fuliang Luo, Boqing Yang, Bin Li, Qi Zhang, Gopika Das, Guangxin Yue, Jiajie Li, Yue Tang and Xin Wang

Predicting life expectancy with a long short-term memory recurrent neural network using electronic medical records

Life expectancy is one of the most important factors in end-of-life decision making. Good prognostication for example helps to determine the course of treatment and helps to anticipate the procurement of healt...

Authors: Merijn Beeksma, Suzan Verberne, Antal van den Bosch, Enny Das, Iris Hendrickx and Stef Groenewoud

Who can you trust? A review of free online sources of “trustworthy” information about treatment effects for patients and the public

Information about effects of treatments based on unsystematic reviews of research evidence may be misleading. However, finding trustworthy information about the effects of treatments based on systematic review...

Authors: Andrew D. Oxman and Elizabeth J. Paulsen

Assessing factors militating against the acceptance and successful implementation of a cloud based health center from the healthcare professionals’ perspective: a survey of hospitals in Benue state, northcentral Nigeria

Cloud based health platforms (CBHP) have tremendous capacity to meet patient’s health needs. The benefits inherent in CBHP position it to be relevant for efficient healthcare delivery. Nonetheless, studies hav...

Authors: Patience E. Idoga, Mehmet Toycan, Halil Nadiri and Erbuğ Çelebi

Importance of medical data preprocessing in predictive modeling and risk factor discovery for the frailty syndrome

Increasing life expectancy results in more elderly people struggling with age related diseases and functional conditions. This poses huge challenges towards establishing new approaches for maintaining health a...

Authors: Andreas Philipp Hassler, Ernestina Menasalvas, Francisco José García-García, Leocadio Rodríguez-Mañas and Andreas Holzinger

Rare disease knowledge enrichment through a data-driven approach

Existing resources to assist the diagnosis of rare diseases are usually curated from the literature that can be limited for clinical use. It often takes substantial effort before the suspicion of a rare diseas...

Authors: Feichen Shen, Yiqing Zhao, Liwei Wang, Majid Rastegar Mojarad, Yanshan Wang, Sijia Liu and Hongfang Liu

A visual interactive analytic tool for filtering and summarizing large health data sets coded with hierarchical terminologies (VIADS)

Vast volumes of data, coded through hierarchical terminologies (e.g., International Classification of Diseases, Tenth Revision–Clinical Modification [ICD10-CM], Medical Subject Headings [MeSH]), are generated ...

Authors: Xia Jing, Matthew Emerson, David Masters, Matthew Brooks, Jacob Buskirk, Nasseef Abukamail, Chang Liu, James J. Cimino, Jay Shubrook, Sonsoles De Lacalle, Yuchun Zhou and Vimla L. Patel

A basic model for assessing primary health care electronic medical record data quality

The increased use of electronic medical records (EMRs) in Canadian primary health care practice has resulted in an expansion of the availability of EMR data. Potential users of these data need to understand th...

Authors: Amanda L. Terry, Moira Stewart, Sonny Cejic, J. Neil Marshall, Simon de Lusignan, Bert M. Chesworth, Vijaya Chevendra, Heather Maddocks, Joshua Shadd, Fred Burge and Amardeep Thind

Development and implementation of “Check of Medication Appropriateness” (CMA): advanced pharmacotherapy-related clinical rules to support medication surveillance

To improve medication surveillance and provide pharmacotherapeutic support in University Hospitals Leuven, a back-office clinical service, called “Check of Medication Appropriateness” (CMA), was developed, con...

Authors: Charlotte Quintens, Thomas De Rijdt, Tine Van Nieuwenhuyse, Steven Simoens, Willy E. Peetermans, Bart Van den Bosch, Minne Casteels and Isabel Spriet

Discovery of under immunized spatial clusters using network scan statistics

Clusters of under-vaccinated children are emerging in a number of states in the United States due to rising rates of vaccine hesitancy and refusal. As the measles outbreaks in California and other states in 20...

Authors: Jose Cadena, David Falcone, Achla Marathe and Anil Vullikanti

Clinical decision support system for the management of osteoporosis compared to NOGG guidelines and an osteology specialist: a validation pilot study

Although osteoporosis is an easily diagnosed and treatable condition, many individuals remain untreated. Clinical decision support systems might increase appropriate treatment of osteoporosis. We designed the ...

Authors: Haukur T. Gudmundsson, Karen E. Hansen, Bjarni V. Halldorsson, Bjorn R. Ludviksson and Bjorn Gudbjornsson

Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text

Extracting relations between important clinical entities is critical but very challenging for natural language processing (NLP) in the medical domain. Researchers have applied deep learning-based approaches to...

Authors: Zhiheng Li, Zhihao Yang, Chen Shen, Jun Xu, Yaoyun Zhang and Hua Xu

The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018)

In this editorial, we first summarize the 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) that was held on June 10–12, 2018 in Los Angeles, California, USA, and then briefly intr...

Authors: Yaoyun Zhang, Cui Tao, Yang Gong, Kai Wang and Zhongming Zhao

Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD

Disease comorbidity is very common and has significant impact on disease treatment. Revealing the associations among diseases may help to understand the mechanisms of diseases, improve the prevention and treat...

Authors: Guocai Chen, Yuxi Jia, Lisha Zhu, Ping Li, Lin Zhang, Cui Tao and W. Jim Zheng

Epileptic foci localization based on mapping the synchronization of dynamic brain network

Characterizing the synchronous changes of epileptic seizures in different stages between different regions is profound to understand the transmission pathways of epileptic brain network and epileptogenic foci....

Authors: Tian Mei, Xiaoyan Wei, Ziyi Chen, Xianghua Tian, Nan Dong, Dongmei Li and Yi Zhou

Early prediction of acute kidney injury following ICU admission using a multivariate panel of physiological measurements

The development of acute kidney injury (AKI) during an intensive care unit (ICU) admission is associated with increased morbidity and mortality.

Authors: Lindsay P. Zimmerman, Paul A. Reyfman, Angela D. R. Smith, Zexian Zeng, Abel Kho, L. Nelson Sanchez-Pinto and Yuan Luo