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BMC Medical Informatics & Decision Making - Supplement, Volume 19S

Volume 19-S, Number 1, January 2019

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2018: medical informatics and decision making

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  Lindsay P. Zimmerman, Paul Reyfman, Angela D. R. Smith, Zexian Zeng, Abel N. Kho, L. Nelson Sanchez-Pinto, Yuan Luo:
  Early prediction of acute kidney injury following ICU admission using a multivariate panel of physiological measurements. 16:1-16:12
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  Zengjian Liu, Xiaolong Wang, Qingcai Chen, Buzhou Tang, Hua Xu:
  Temporal indexing of medical entity in Chinese clinical notes. 17:1-17:11
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  Tianzhong Yang, Yang Yang, Yugang Jia, Xiao Li:
  Dynamic prediction of hospital admission with medical claim data. 18:1-18:14
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  Tian Mei, Xiaoyan Wei, Ziyi Chen, Xianghua Tian, Nan Dong, Dongmei Li, Yi Zhou:
  Epileptic foci localization based on mapping the synchronization of dynamic brain network. 19:1-19:11
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  Guocai Chen, Yuxi Jia, Lisha Zhu, Ping Li, Lin Zhang, Cui Tao, W. Jim Zheng:
  Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD. 20:1-20:9
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  Yaoyun Zhang, Cui Tao, Yang Gong, Kai Wang, Zhongming Zhao:
  The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018). 21:1-21:3
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  Zhiheng Li, Zhihao Yang, Chen Shen, Jun Xu, Yaoyun Zhang, Hua Xu:
  Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text. 22:1-22:8

Volume 19-S, Number 2, April 2019

Proceedings from the 4th China Health Information Processing Conference (CHIP 2018)

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  Danqing Hu, Wei Dong, Xudong Lu, Huilong Duan, Kunlun He, Zhengxing Huang:
  Evidential MACE prediction of acute coronary syndrome using electronic health records. 9-17
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  Chao Yu, Yinzhao Dong, Jiming Liu, Guoqi Ren:
  Incorporating causal factors into reinforcement learning for dynamic treatment regimes in HIV. 19-29
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  Xuesi Zhou, Haoqi Xiong, Sihan Zeng, Xiangling Fu, Ji Wu:
  An approach for medical event detection in Chinese clinical notes of electronic health records. 31-37
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  Xieling Chen, Yonghui Lun, Jun Yan, Tianyong Hao, Heng Weng:
  Discovering thematic change and evolution of utilizing social media for healthcare research. 39-53
• 
  Suwen Liu, Yifan Shao, Longhua Qian, Guodong Zhou:
  Hierarchical sequence labeling for extracting BEL statements from biomedical literature. 55-65
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  Xuemeng Li, Jianfei Pang, Mei Li, Dongsheng Zhao:
  Discover high-risk factor combinations using Bayesian network from cohort data of National Stoke Screening in China. 67:1-67:8
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  Yan Gao, Lei Gu, Yefeng Wang, Yandong Wang, Feng Yang:
  Constructing a Chinese electronic medical record corpus for named entity recognition on resident admit notes. 67-78
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  Hai Long, Yan Zhu, Lirong Jia, Bo Gao, Jing Liu, Lihong Liu, Heinrich Herre:
  An ontological framework for the formalization, organization and usage of TCM-Knowledge. 79-89
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  Junqing He, Mingming Fu, Manshu Tu:
  Applying deep matching networks to Chinese medical question answering: a study and a dataset. 91-100
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  Xiaoling Cai, Shoubin Dong, Jinlong Hu:
  A deep learning model incorporating part of speech and self-matching attention for named entity recognition of Chinese electronic medical records. 101-109
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  Chao Yu, Jiming Liu, Hongyi Zhao:
  Inverse reinforcement learning for intelligent mechanical ventilation and sedative dosing in intensive care units. 111-120
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  Di Zhao, Jian Wang, Shengtian Sang, Hongfei Lin, Jiabin Wen, Chunmei Yang:
  Relation path feature embedding based convolutional neural network method for drug discovery. 121-130
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  Yafeng Ren, Hao Fei, Xiaohui Liang, Donghong Ji, Ming Cheng:
  A hybrid neural network model for predicting kidney disease in hypertension patients based on electronic health records. 131-138
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  Yang Xiang, Jun Xu, Yuqi Si, Zhiheng Li, Laila Rasmy, Yujia Zhou, Firat Tiryaki, Fang Li, Yaoyun Zhang, Yonghui Wu, Xiaoqian Jiang, W. Jim Zheng, Degui Zhi, Cui Tao, Hua Xu:
  Time-sensitive clinical concept embeddings learned from large electronic health records. 139-148
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  Bin Ji, Rui Liu, Shasha Li, Jie Yu, Qingbo Wu, Yusong Tan, Jiaju Wu:
  A hybrid approach for named entity recognition in Chinese electronic medical record. 149-158
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  Boyu Chen, Hao Jin, Zhiwen Yang, Yingying Qu, Heng Weng, Tianyong Hao:
  An approach for transgender population information extraction and summarization from clinical trial text. 159-170
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  Zhichang Zhang, Tong Zhou, Yu Zhang, Yali Pang:
  Attention-based deep residual learning network for entity relation extraction in Chinese EMRs. 171-177
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  Ying Xiong, Zhongmin Wang, Dehuan Jiang, Xiaolong Wang, Qingcai Chen, Hua Xu, Jun Yan, Buzhou Tang:
  A fine-grained Chinese word segmentation and part-of-speech tagging corpus for clinical text. 179-184
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  Fan Gong, Yilei Chen, Haofen Wang, Hao Lu:
  On building a diabetes centric knowledge base via mining the web. 185-197

Volume 19-S, Number 3, April 2019

Selected articles from the first International Workshop on Health Natural Language Processing (HealthNLP 2018)

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  V. G. Vinod Vydiswaran, Yaoyun Zhang, Yanshan Wang, Hua Xu:
  Special issue of BMC medical informatics and decision making on health natural language processing. 76:1-76:3
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  Chunhua Weng, Carol Friedman, Casey A. Rommel, John F. Hurdle:
  A two-site survey of medical center personnel's willingness to share clinical data for research: implications for reproducible health NLP research. 5-12
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  Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
  Discovering associations between problem list and practice setting. 13-22
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  Yanshan Wang, Saeed Mehrabi, Sunghwan Sohn, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu:
  Natural language processing of radiology reports for identification of skeletal site-specific fractures. 23-29
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  Liang Yao, Chengsheng Mao, Yuan Luo:
  Clinical text classification with rule-based features and knowledge-guided convolutional neural networks. 31-39
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  V. G. Vinod Vydiswaran, Manoj Reddy:
  Identifying peer experts in online health forums. 41-49
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  Yaoyun Zhang, Firat Tiryaki, Min Jiang, Hua Xu:
  Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison. 51-58
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  David A. Hanauer, Qiaozhu Mei, V. G. Vinod Vydiswaran, Karandeep Singh, Zach Landis-Lewis, Chunhua Weng:
  Complexities, variations, and errors of numbering within clinical notes: the potential impact on information extraction and cohort-identification. 59-69
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  Son Doan, Elly W. Yang, Sameer S. Tilak, Peter W. Li, Daniel S. Zisook, Manabu Torii:
  Extracting health-related causality from twitter messages using natural language processing. 71-77
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  Himanshu Sharma, Chengsheng Mao, Yizhen Zhang, Haleh Vatani, Liang Yao, Yizhen Zhong, Luke V. Rasmussen, Guoqian Jiang, Jyotishman Pathak, Yuan Luo:
  Developing a portable natural language processing based phenotyping system. 79-87
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  Buzhou Tang, Xiaolong Wang, Jun Yan, Qingcai Chen:
  Entity recognition in Chinese clinical text using attention-based CNN-LSTM-CRF. 89-97
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  Matthew J. Cook, Lixia Yao, Xiaoyan Wang:
  Facilitating accurate health provider directories using natural language processing. 99-106
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  Markus Kreuzthaler, Bastian Pfeifer, José Antonio Vera Ramos, Diether Kramer, Victor Grogger, Sylvia Bredenfeldt, Markus Pedevilla, Peter Krisper, Stefan Schulz:
  EHR problem list clustering for improved topic-space navigation. 107-114

Volume 19-S, Number 4, August 2019

Selected articles from the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018)

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  Jing Huang, Xinyuan Zhang, Jiayi Tong, Jingcheng Du, Rui Duan, Liu Yang, Jason H. Moore, Cui Tao, Yong Chen:
  Comparing drug safety of hepatitis C therapies using post-market data. 147:1-147:12
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  Zhe He, Jiang Bian, Cui Tao, Rui Zhang:
  Selected articles from the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018). 148:1-148:3
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  Somaieh Goudarzvand, Jennifer L. St. Sauver, Michelle M. Mielke, Paul Y. Takahashi, Yugyung Lee, Sunghwan Sohn:
  Early temporal characteristics of elderly patient cognitive impairment in electronic health records. 149:1-149:14
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  Xing He, Rui Zhang, Rubina F. Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, Mattia Prosperi, Jinhai Huo, Jordan Alpert, Jiang Bian:
  ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design. 150:1-150:18
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  Yuqing Yang, Xin Wang, Yu Huang, Ning Chen, Juhong Shi, Ting Chen:
  Ontology-based venous thromboembolism risk assessment model developing from medical records. 151:1-151:13
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  Muhammad Amith, Frank J. Manion, Chen Liang, Marcelline R. Harris, Dennis Wang, Yongqun He, Cui Tao:
  Architecture and usability of OntoKeeper, an ontology evaluation tool. 152:1-152:18

Volume 19-S, Number 5, December 2019

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  Yanshan Wang, Hua Xu, Özlem Uzuner:
  Editorial: The second international workshop on health natural language processing (HealthNLP 2019). 1
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  Liwei Wang, Lei Luo, Yanshan Wang, Jason A. Wampfler, Ping Yang, Hongfang Liu:
  Natural language processing for populating lung cancer clinical research data. 2
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  Feihong Yang, Haihong Guo, Jiao Li:
  TestIME: an application for evaluating the efficiency of Chinese input method engines in electronic medical record entry task. 3
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  Luqi Li, Jie Zhao, Li Hou, Yunkai Zhai, Jinming Shi, Fangfang Cui:
  An attention-based deep learning model for clinical named entity recognition of Chinese electronic medical records. 4
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  Go Eun Heo, Qing Xie, Min Song, Jeong-Hoon Lee:
  Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer's disease. 5
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  Xi Yang, Tianchen Lyu, Qian Li, Chih-Yin Lee, Jiang Bian, William R. Hogan, Yonghui Wu:
  A study of deep learning methods for de-identification of clinical notes in cross-institute settings. 6
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  Yueping Sun, Li Hou, Lu Qin, Yan Liu, Jiao Li, Qing Qian:
  RCorp: a resource for chemical disease semantic extraction in Chinese. 7
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  Jun Xu, Zhiheng Li, Qiang Wei, Yonghui Wu, Yang Xiang, Hee-Jin Lee, Yaoyun Zhang, Stephen Wu, Hua Xu:
  Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text. 8
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  Xuedong Li, Yue Wang, Dongwu Wang, Walter Yuan, Dezhong Peng, Qiaozhu Mei:
  Improving rare disease classification using imperfect knowledge graph. 9

Volume 19-S, Number 6, December 2019

Selected articles from the IEEE BIBM International Conference on Bioinformatics & Biomedicine (BIBM) 2018: medical informatics and decision making

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  Ming Huang, Nilay D. Shah, Lixia Yao:
  Evaluating global and local sequence alignment methods for comparing patient medical records. 263
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  Xintian Chen, Chunyang Ruan, Yanchun Zhang, Huijuan Chen:
  Heterogeneous information network based clustering for precision traditional Chinese medicine. 264
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  Hongzhe Guo, Bo Liu, Dengfeng Guan, Yilei Fu, Yadong Wang:
  Fast read alignment with incorporation of known genomic variants. 265
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  Tobore Igbe, Jingzhen Li, Abhishek Kandwal, Yuhang Liu, Ze-dong Nie, Lei Wang:
  Statistical and spectral analysis of ECG signal towards achieving non-invasive blood glucose monitoring. 266
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  Fenglong Ma, Yaqing Wang, Houping Xiao, Ye Yuan, Radha Chitta, Jing Zhou, Jing Gao:
  Incorporating medical code descriptions for diagnosis prediction in healthcare. 267
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  Ahmed Fares, Sheng-hua Zhong, Jianmin Jiang:
  EEG-based image classification via a region-level stacked bi-directional deep learning framework. 268
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  Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang:
  MultiSourcDSim: an integrated approach for exploring disease similarity. 269
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  Shuang Song, Chenbing Du, Ying Chen, Danni Ai, Hong Song, Yong Huang, Yongtian Wang, Jian Yang:
  Inter/intra-frame constrained vascular segmentation in X-ray angiographic image sequence. 270
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  Weichen Song, Yifeng Shen, Yanhua Zhang, Sufang Peng, Ran Zhang, Ailing Ning, Huafang Li, Xia Li, Guan Ning Lin, Shunying Yu:
  Expression alteration of microRNAs in Nucleus Accumbens is associated with chronic stress and antidepressant treatment in rats. 271
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  Afshin Khadangi, Eric Hanssen, Vijay Rajagopal:
  Automated segmentation of cardiomyocyte Z-disks from high-throughput scanning electron microscopy data. 272

Volume 19-S, Number 7, December 2019

Supplement special Issue on Biomedical and Health Informatics

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  Yifei Wang, Sophia Ananiadou, Jun'ichi Tsujii:
  Improving clinical named entity recognition in Chinese using the graphical and phonetic feature. 273
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  Rebecka Weegar, Alicia Pérez, Arantza Casillas, Maite Oronoz:
  Recent advances in Swedish and Spanish medical entity recognition in clinical texts using deep neural approaches. 274
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  Bin Ma, Chunxiao Li, Zhaolong Wu, Yulong Huang, Ada Chaeli van der Zijp-Tan, Shaobo Tan, Dongqi Li, Ada Fong, Chandan Basetty, Glen M. Borchert, Ryan Benton, Bin Wu, Jingshan Huang:
  Muscle fatigue detection and treatment system driven by internet of things. 275
• 
  Robinette Renner, Shengyu Li, Yulong Huang, Ada Chaeli van der Zijp-Tan, Shaobo Tan, Dongqi Li, Mohan Vamsi Kasukurthi, Ryan Benton, Glen M. Borchert, Jingshan Huang, Guoqian Jiang:
  Using an artificial neural network to map cancer common data elements to the biomedical research integrated domain group model in a semi-automated manner. 276

Volume 19-S, Number 8, December 2019

Selected articles from the IEEE BIBM International Conference on Bioinformatics & Biomedicine (BIBM) 2018: medical informatics and decision making (part 2)

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  Chunlei Tang, Joseph M. Plasek, Haohan Zhang, Min-Jeoung Kang, Haokai Sheng, Yun Xiong, David W. Bates, Li Zhou:
  A temporal visualization of chronic obstructive pulmonary disease progression using deep learning and unstructured clinical notes. 258
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  Tong Ruan, Liqi Lei, Yangming Zhou, Jie Zhai, Le Zhang, Ping He, Ju Gao:
  Representation learning for clinical time series prediction tasks in electronic health records. 259

Volume 19-S, Number 9, December 2019

Proceedings of the 2018 International Conference on Intelligent Computing (ICIC 2018) and Intelligent Computing and Biomedical Informatics (ICBI) 2018 conference: medical informatics and decision making

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  Domenico Buongiorno, Ilaria Bortone, Giacomo Donato Cascarano, Gianpaolo Francesco Trotta, Antonio Brunetti, Vitoantonio Bevilacqua:
  A low-cost vision system based on the analysis of motor features for recognition and severity rating of Parkinson's Disease. 243
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  Vitoantonio Bevilacqua, Antonio Brunetti, Giacomo Donato Cascarano, Andrea Guerriero, Francesco Pesce, Marco Moschetta, Loreto Gesualdo:
  A comparison between two semantic deep learning frameworks for the autosomal dominant polycystic kidney disease segmentation based on magnetic resonance images. 244
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  Min Pan, Yue Zhang, Qiang Zhu, Bo Sun, Tingting He, Xingpeng Jiang:
  An adaptive term proximity based rocchio's model for clinical decision support retrieval. 251
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  Giacomo Donato Cascarano, Claudio Loconsole, Antonio Brunetti, Antonio Lattarulo, Domenico Buongiorno, Giacomo Losavio, Eugenio Di Sciascio, Vitoantonio Bevilacqua:
  Biometric handwriting analysis to support Parkinson's Disease assessment and grading. 252
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  Mohamed Alloghani, Ahmed J. Aljaaf, Abir Hussain, Thar Baker, Jamila Mustafina, Dhiya Al-Jumeily, Mohammed Khalaf:
  Implementation of machine learning algorithms to create diabetic patient re-admission profiles. 253

Volume 19-S, Number 10, December 2019

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  Hong-Jie Dai:
  Family member information extraction via neural sequence labeling models with different tag schemes. 257
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  Sijia Liu, Yanshan Wang, Hongfang Liu:
  Selected articles from the BioCreative/OHNLP challenge 2018. 262
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  Xue Shi, Dehuan Jiang, Yuanhang Huang, Xiaolong Wang, Qingcai Chen, Jun Yan, Buzhou Tang:
  Family history information extraction via deep joint learning. 277