BMC Medical Informatics & Decision Making - Supplement, Volume 20S

Volume 20-S, Number 1, April 2020

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  Ying Xiong, Shuai Chen, Haoming Qin, He Cao, Yedan Shen, Xiaolong Wang, Qingcai Chen, Jun Yan, Buzhou Tang:
  Distributed representation and one-hot representation fusion with gated network for clinical semantic textual similarity. 72
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  Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
  Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. 73

Volume 20-S, Number 2, March 2020

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  Yan-Bin Wang, Zhu-Hong You, Shan Yang, Hai-Cheng Yi, Zhan-Heng Chen, Kai Zheng:
  A deep learning-based method for drug-target interaction prediction based on long short-term memory neural network. 49
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  Xiaohui Yao, Tiffany Tsang, Qing Sun, Sara K. Quinney, Pengyue Zhang, Xia Ning, Lang Li, Li Shen:
  Mining and visualizing high-order directional drug interaction effects using the FAERS database. 50
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  Xia Ning, Chi Zhang, Kai Wang, Zhongming Zhao, Ewy A Mathé:
  The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions. 51

Volume 20-S, Number 3, July 2020

Health Information Processing

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  Liangliang Liu, Xiaojing Wu, Hui Liu, Xinyu Cao, Haitao Wang, Hongwei Zhou, Qi Xie:
  A semi-supervised approach for extracting TCM clinical terms based on feature words. 118
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  Xibin Jia, Yunfeng Liu, Zhenghan Yang, Dawei Yang:
  Multi-modality self-attention aware deep network for 3D biomedical segmentation. 119
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  Haifeng Xu, Jianfei Pang, Xi Yang, Mei Li, Dongsheng Zhao:
  Using predictive process monitoring to assist thrombolytic therapy decision-making for ischemic stroke patients. 120
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  Ming Cheng, Xiaolei Zhao, Xianfei Ding, Jianbo Gao, Shufeng Xiong, Yafeng Ren:
  Prediction of blood culture outcome using hybrid neural network model based on electronic health records. 121
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  Hetong Ma, Feihong Yang, Jiansong Ren, Ni Li, Min Dai, Xuwen Wang, An Fang, Jiao Li, Qing Qian, Jie He:
  ECCParaCorp: a cross-lingual parallel corpus towards cancer education, dissemination and application. 122
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  Zhichang Zhang, Yanlong Qiu, Xiaoli Yang, Minyu Zhang:
  Enhanced character-level deep convolutional neural networks for cardiovascular disease prediction. 123
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  Chao Yu, Guoqi Ren, Yinzhao Dong:
  Supervised-actor-critic reinforcement learning for intelligent mechanical ventilation and sedative dosing in intensive care units. 124
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  Nan Chen, Xiangdong Su, Tongyang Liu, Qizhi Hao, Ming Wei:
  A benchmark dataset and case study for Chinese medical question intent classification. 125
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  Lu Qin, Xiaowei Xu, Lingling Ding, Zixiao Li, Jiao Li:
  Identifying diagnosis evidence of cardiogenic stroke from Chinese echocardiograph reports. 126
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  Kuo-Kun Tseng, Jiaqian Li, Yih-Jing Tang, Ching-Wen Yang, Fang-Ying Lin:
  Healthcare knowledge of relationship between time series electrocardiogram and cigarette smoking using clinical records. 127
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  Fan Guo, Weiqing Li, Xin Zhao, Junfeng Qiu, Yuxiang Mai:
  A mobile app for Glaucoma diagnosis and its possible clinical applications. 128
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  Kaiwen Tan, Weixian Huang, Jinlong Hu, Shoubin Dong:
  A multi-omics supervised autoencoder for pan-cancer clinical outcome endpoints prediction. 129
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  Wang Zhao, Peixin Lu, Siwei Yu, Long Lu:
  Consumer health information needs in China - a case study of depression based on a Social Q&A community. 130
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  Peipei Chen, Wei Dong, Jinliang Wang, Xudong Lu, Uzay Kaymak, Zhengxing Huang:
  Interpretable clinical prediction via attention-based neural network. 131
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  Wenyan Tan, Haicheng Lin, Baoxin Lei, Aihua Ou, Zehui He, Ning Yang, Fujun Jia, Heng Weng, Tianyong Hao:
  The psychosis analysis in real-world on a cohort of large-scale patients with schizophrenia. 132
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  Yuyu Zheng, Xiangyu Meng, Pierre Zweigenbaum, Lingling Chen, Jingbo Xia:
  Hybrid phenotype mining method for investigating off-target protein and underlying side effects of anti-tumor immunotherapy. 133
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  Nan Li, Zhihao Yang, Ling Luo, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang:
  KGHC: a knowledge graph for hepatocellular carcinoma. 135
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  Xiaolong Zhang, Meng Zhang, Xuanping Zhang, Xiaoyan Zhu, Jiayin Wang:
  A prognostic index based on a fourteen long non-coding RNA signature to predict the recurrence-free survival for muscle-invasive bladder cancer patients. 136
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  Yidan Wang, Xuanping Zhang, Tao Wang, Jinchun Xing, Zhun Wu, Wei Li, Jiayin Wang:
  A machine learning framework for accurately recognizing circular RNAs for clinical decision-supporting. 137
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  Junyi Yang, Liang Xiao, Kangning Li:
  Modelling clinical experience data as an evidence for patient-oriented decision support. 138

Volume 20-S, Number 4, December 2020

Selected articles from the Fourth International Workshop on Semantics-Powered Data Analytics (SEPDA 2019)

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  Jiebin Chu, Wei Dong, Jinliang Wang, Kunlun He, Zhengxing Huang:
  Treatment effect prediction with adversarial deep learning using electronic health records. 139
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  Gilles Vandewiele, Bram Steenwinckel, Filip De Turck, Femke Ongenae:
  MINDWALC: mining interpretable, discriminative walks for classification of nodes in a knowledge graph. 191
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  Nur Hafieza Ismail, Ninghao Liu, Mengnan Du, Zhe He, Xia Hu:
  A deep learning approach for identifying cancer survivors living with post-traumatic stress disorder on Twitter. 254
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  Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts, Cui Tao:
  Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents. 259
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  Li Zhang, Jiamei Hu, Qianzhi Xu, Fang Li, Guozheng Rao, Cui Tao:
  A semantic relationship mining method among disorders, genes, and drugs from different biomedical datasets. 283
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  Hansi Zhang, Yi Guo, Mattia Prosperi, Jiang Bian:
  An ontology-based documentation of data discovery and integration process in cancer outcomes research. 292
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  Anderson Rossanez, Júlio Cesar dos Reis, Ricardo da Silva Torres, Hélène de Ribaupierre:
  KGen: a knowledge graph generator from biomedical scientific literature. 314
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  Zhe He, Cui Tao, Jiang Bian, Rui Zhang:
  Selected articles from the Fourth International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019). 315

Volume 20-S, Number 5, August 2020

Selected articles from the CIBB 2019 Special Session on Machine Learning in Healthcare Informatics and Medical Biology

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  Mafalda Falcão Ferreira, Rui Camacho, Luís Filipe Teixeira:
  Using autoencoders as a weight initialization method on deep neural networks for disease detection. 141
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  Andrea Seveso, Andrea Campagner, Davide Ciucci, Federico Cabitza:
  Ordinal labels in machine learning: a user-centered approach to improve data validity in medical settings. 142
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  Erica Tavazzi, Sebastian Daberdaku, Rosario Vasta, Andrea Calvo, Adriano Chiò, Barbara Di Camillo:
  Exploiting mutual information for the imputation of static and dynamic mixed-type clinical data with an adaptive k-nearest neighbours approach. 174

Volume 20-S, Number 7, September 2020

Proceedings of the 13th International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO 2019): medical informatics and decision making

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  Young-Min Kim, Taehoon Lee:
  Korean clinical entity recognition from diagnosis text using BERT. 242

Volume 20-S, Number 8, September 2020

Selected articles from the 15th International Symposium on Bioinformatics Research and Applications (ISBRA-19): medical informatics and decision making

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  Biao An, Qianwen Zhang, Yun Fang, Ming Chen, Yufang Qin:
  Iterative sure independent ranking and screening for drug response prediction. 224

Volume 20-S, Number 9, September 2020

Selected Articles from the 20th International Conference on Bioinformatics & Computational Biology (BIOCOMP 2019): medical informatics and decision making

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  Xiaoli Chen, Yong Zhu, Mayumi Jijiwa, Masaki Nasu, Junmei Ai, Shengming Dai, Bin Jiang, Jicai Zhang, Gang Huang, Youping Deng:
  Identification of plasma lipid species as promising diagnostic markers for prostate cancer. 223

Volume 20-S, Number 10, December 2020

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  Muhammad Amith, Kayo Fujimoto, Rebecca Mauldin, Cui Tao:
  Friend of a Friend with Benefits ontology (FOAF+): extending a social network ontology for public health. 269
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  Shiqiang Tao, Ningzhou Zeng, Isaac Hands, Joseph Hurt-Mueller, Eric B. Durbin, Licong Cui, Guo-Qiang Zhang:
  Web-based interactive mapping from data dictionaries to ontologies, with an application to cancer registry. 271
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  Vipina Kuttichi Keloth, James Geller, Yan Chen, Julia Xu:
  Extending import detection algorithms for concept import from two to three biomedical terminologies. 272
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  Fengbo Zheng, Rashmie Abeysinghe, Nicholas Sioutos, Lori Whiteman, Lyubov Remennik, Licong Cui:
  Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach. 273
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  Hugo J. Th. van Mens, Mirte M. van Eysden, Remko Nienhuis, Johannes J. M. van Delden, Nicolette F. de Keizer, Ronald Cornet:
  Evaluation of lexical clarification by patients reading their clinical notes: a quasi-experimental interview study. 278
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  Francisco Abad Navarro, Manuel Quesada-Martínez, Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis:
  Analysis of readability and structural accuracy in SNOMED CT. 284
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  Ling Zheng, Hua Min, Yan Chen, Vipina Kuttichi Keloth, James Geller, Yehoshua Perl, George Hripcsak:
  Outlier concepts auditing methodology for a large family of biomedical ontologies. 296
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  Ankur Agrawal, Licong Cui:
  Quality assurance and enrichment of biological and biomedical ontologies and terminologies. 301
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  Ling Zheng, Yan Chen, Hua Min, P. Lloyd Hildebrand, Hao Liu, Michael Halper, James Geller, Sherri de Coronado, Yehoshua Perl:
  Missing lateral relationships in top-level concepts of an ontology. 305
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  Luke T. Slater, Georgios V. Gkoutos, Robert Hoehndorf:
  Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. 311

Volume 20-S, Number 11, December 2020

Informatics and machine learning methods for health applications

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  Russell A. Li, Zhandong Liu:
  Stress detection using deep neural networks. 285
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  Jiancheng Ye, Liang Yao, Jiahong Shen, Rethavathi Janarthanam, Yuan Luo:
  Predicting mortality in critically ill patients with diabetes using machine learning and clinical notes. 295
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  Joseph Tassone, Peizhi Yan, Mackenzie Simpson, Chetan Harichandra Mendhe, Vijay Mago, Salimur Choudhury:
  Utilizing deep learning and graph mining to identify drug use on Twitter data. 304
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  Sundreen Asad Kamal, Changchang Yin, Buyue Qian, Ping Zhang:
  An interpretable risk prediction model for healthcare with pattern attention. 307
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  Gaurav Rao, Salimur Choudhury, Pawan Lingras, David W. Savage, Vijay Mago:
  SURF: identifying and allocating resources during Out-of-Hospital Cardiac Arrest. 313
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  Jacqueline Peng, Mengge Zhao, James M. Havrilla, Cong Liu, Chunhua Weng, Whitney Guthrie, Robert Schultz, Kai Wang, Yunyun Zhou:
  Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder. 322
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  Judy Hong, Anahita Davoudi, Shun Yu, Danielle L. Mowery:
  Annotation and extraction of age and temporally-related events from clinical histories. 338
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  Li Shen, Xinghua Shi, Zhongming Zhao, Kai Wang:
  Informatics and machine learning methods for health applications. 342
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  Chao-Chen Chen, Fu-Chiang Tsui:
  Comparing different wavelet transforms on removing electrocardiogram baseline wanders and special trends. 343

Volume 20-S, Number 12, December 2020

Slow Onset Detection in Epilepsy

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  Juan C. Mier, Yejin Kim, Xiaoqian Jiang, Guo-Qiang Zhang, Samden D. Lhatoo:
  Categorisation of EEG suppression using enhanced feature extraction for SUDEP risk assessment. 326
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  Bishal Lamichhane, Yejin Kim, Santiago Segarra, Guoqiang Zhang, Samden D. Lhatoo, Jaison Hampson, Xiaoqian Jiang:
  Automated detection of activity onset after postictal generalized EEG suppression. 327
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  Yejin Kim, Xiaoqian Jiang, Samden D. Lhatoo, Guoqiang Zhang, Shiqiang Tao, Licong Cui, Xiaojin Li, Robert D. Jolly, Luyao Chen, Michael Phan, Cung Ha, Marijane Detranaltes, Jiajie Zhang:
  A community effort for automatic detection of postictal generalized EEG suppression in epilepsy. 328
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  Cong Zhu, Yejin Kim, Xiaoqian Jiang, Samden D. Lhatoo, Hampson Jaison, Guo-Qiang Zhang:
  A lightweight convolutional neural network for assessing an EEG risk marker for sudden unexpected death in epilepsy. 329
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  Carroll Vance, Yejin Kim, Guo-Qiang Zhang, Samden D. Lhatoo, Shiqiang Tao, Licong Cui, Xiaojin Li, Xiaoqian Jiang:
  Learning to detect the onset of slow activity after a generalized tonic-clonic seizure. 330

Volume 20-S, Number 14, December 2020

Special Issue on Biomedical and Health Informatics

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  Jian Li, Zelin Zhang, Shengyu Li, Ryan Benton, Yulong Huang, Mohan Vamsi Kasukurthi, Dongqi Li, Jingwei Lin, Glen M. Borchert, Shaobo Tan, Gang Li, Bin Ma, Meihong Yang, Jingshan Huang:
  A partial encryption algorithm for medical images based on quick response code and reversible data hiding technology. 297
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  Bin Ma, Zhaolong Wu, Shengyu Li, Ryan Benton, Dongqi Li, Yulong Huang, Mohan Vamsi Kasukurthi, Jingwei Lin, Glen M. Borchert, Shaobo Tan, Gang Li, Meihong Yang, Jingshan Huang:
  Development of a support vector machine learning and smart phone Internet of Things-based architecture for real-time sleep apnea diagnosis. 298
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  Pete Yeh, Yiheng Pan, L. Nelson Sanchez-Pinto, Yuan Luo:
  Hyperchloremia in critically ill patients: association with outcomes and prediction using electronic health record data. 302
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  Haifeng Xu, Jianfei Pang, Xi Yang, Jinghui Yu, Xuemeng Li, Dongsheng Zhao:
  Modeling clinical activities based on multi-perspective declarative process mining with openEHR's characteristic. 303
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  Eva K. Lee, Karan Uppal:
  CERC: an interactive content extraction, recognition, and construction tool for clinical and biomedical text. 306
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  Sadiq Al-Insaif, Jochen Lang:
  Texture features in the Shearlet domain for histopathological image classification. 312
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  Qingfeng Wang, Qiyu Liu, Guoting Luo, Zhiqin Liu, Jun Huang, Yuwei Zhou, Ying Zhou, Weiyun Xu, Jie-Zhi Cheng:
  Automated segmentation and diagnosis of pneumothorax on chest X-rays with fully convolutional multi-scale ScSE-DenseNet: a retrospective study. 317
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  Ming Liang, Zhixing Zhang, Jiaying Zhang, Tong Ruan, Qi Ye, Ping He:
  Lab indicators standardization method for the regional healthcare platform: a case study on heart failure. 331