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2020 – today
- 2024
[j93]Jianfu Li, Yiming Li, Yuanyi Pan, Jinjing Guo, Zenan Sun, Fang Li, Yongqun He, Cui Tao:
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models. J. Biomed. Semant. 15(1): 14 (2024)- [j92]Zhao Li, Qiang Wei, Liang-Chin Huang, Jianfu Li, Yan Hu
, Yao-Shun Chuang, Jianping He, Avisha Das, Vipina Kuttichi Keloth, Yuntao Yang, Chiamaka S. Diala, Kirk E. Roberts, Cui Tao, Xiaoqian Jiang, W. Jim Zheng, Hua Xu:
Ensemble pretrained language models to extract biomedical knowledge from literature. J. Am. Medical Informatics Assoc. 31(9): 1904-1911 (2024) - [j91]Yiming Li, Jeff Zhao, Manqi Li, Yifang Dang, Evan Yu, Jianfu Li, Zenan Sun, Usama Hussein, Jianguo Wen, Ahmed M. Abdelhameed, Junhua Mai, Shenduo Li, Yue Yu, Xinyue Hu, Daowei Yang, Jingna Feng, Zehan Li, Jianping He, Wei Tao, Tiehang Duan, Yanyan Lou, Fang Li, Cui Tao:
RefAI: a GPT-powered retrieval-augmented generative tool for biomedical literature recommendation and summarization. J. Am. Medical Informatics Assoc. 31(9): 2030-2039 (2024) - [j90]Yiming Li, Xueqing Peng, Jianfu Li, Xu Zuo, Suyuan Peng, Donghong Pei, Cui Tao, Hua Xu, Na Hong:
Relation extraction using large language models: a case study on acupuncture point locations. J. Am. Medical Informatics Assoc. 31(11): 2622-2631 (2024) - [j89]Yiming Li, Wei Tao, Zehan Li, Zenan Sun, Fang Li, Susan H. Fenton, Hua Xu, Cui Tao:
Artificial intelligence-powered pharmacovigilance: A review of machine and deep learning in clinical text-based adverse drug event detection for benchmark datasets. J. Biomed. Informatics 152: 104621 (2024) - [j88]Sunyang Fu, Heling Jia, Maria Vassilaki, Vipina Kuttichi Keloth, Yifang Dang, Yujia Zhou, Muskan Garg, Ronald C. Petersen, Jennifer St Sauver, Sungrim Moon, Liwei Wang, Andrew Wen, Fang Li, Hua Xu, Cui Tao, Jungwei Fan, Hongfang Liu, Sunghwan Sohn:
FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. J. Biomed. Informatics 152: 104623 (2024) - [j87]Yiming Li, Qiang Wei, Xinghan Chen, Jianfu Li, Cui Tao, Hua Xu:
Improving tabular data extraction in scanned laboratory reports using deep learning models. J. Biomed. Informatics 159: 104735 (2024) - [j86]Jianping He, Fang Li, Jianfu Li, Xinyue Hu, Yi Nian, Yang Xiang, Jingqi Wang, Qiang Wei, Yiming Li, Hua Xu, Cui Tao:
Prompt Tuning in Biomedical Relation Extraction. J. Heal. Informatics Res. 8(2): 206-224 (2024) - [j85]Madhuri Sankaranarayanapillai, Su Wang, Hangyu Ji, Hsing-yi Song, Cui Tao:
Lessons learned from annotation of VAERS reports on adverse events following influenza vaccination and related to Guillain-Barré syndrome. BMC Medical Informatics Decis. Mak. 23-S(4): 298 (2024) - [j84]Xinyuan Zhang, Yixue Feng, Fang Li, Jin Ding, Danyal Tahseen, Ezekiel Hinojosa, Yong Chen, Cui Tao:
Evaluating MedDRA-to-ICD terminology mappings. BMC Medical Informatics Decis. Mak. 23-S(4): 299 (2024) - [j83]Tiehang Duan, Zhenyi Wang, Fang Li, Gianfranco Doretto, Donald A. Adjeroh, Yiyi Yin, Cui Tao:
Online continual decoding of streaming EEG signal with a balanced and informative memory buffer. Neural Networks 176: 106338 (2024) - [j82]Tiehang Duan, Zhenyi Wang, Li Shen, Gianfranco Doretto, Donald A. Adjeroh, Fang Li, Cui Tao:
Retain and Adapt: Online Sequential EEG Classification With Subject Shift. IEEE Trans. Artif. Intell. 5(9): 4479-4492 (2024) - [c134]Nicole Moore, Muhammad Amith, Ana Neumann, Jane Hamilton, Lu Tang, Lara S. Savas, Cui Tao:
Translating motivational interviewing for the HPV vaccine into a computable ontology model for automated AI conversational interaction. CHI Extended Abstracts 2024: 341:1-341:12 - [c133]Eloisa Nguyen, Rebecca Z. Lin, Yang Gong, Cui Tao, Muhammad Tuan Amith:
Developing a Computational Representation of Human Physical Activity and Exercise Using Open Ontology-Based Approach: A Tai Chi Use Case. ICHI 2024: 31-39 - [c132]Xubing Hao, Licong Cui, Cui Tao, Kirk Roberts, Muhammad Amith:
Analyzing Llama 3-based Approach for Axiom Translation from Ontologies. KBC-LM/LM-KBC@ISWC 2024 - [c131]Wordh Ul Hasan, Kimia Tuz Zaman, Mohammed Shalan, Xin Wang, Juan Li, Bo Xie, Cui Tao:
CareCompanion: A Personalized Virtual Assistant for Enhancing Support and Independence in ADRD Patients and Older Adults. SmartNets 2024: 1-10 - [i18]Song Wang, Yiliang Zhou, Ziqiang Han, Cui Tao, Yunyu Xiao, Ying Ding, Joydeep Ghosh, Yifan Peng:
Uncovering Misattributed Suicide Causes through Annotation Inconsistency Detection in Death Investigation Notes. CoRR abs/2403.19432 (2024) - [i17]Yiming Li, Xueqing Peng, Jianfu Li, Xu Zuo, Suyuan Peng, Donghong Pei, Cui Tao, Hua Xu, Na Hong:
Relation Extraction Using Large Language Models: A Case Study on Acupuncture Point Locations. CoRR abs/2404.05415 (2024) - [i16]Yiming Li, Deepthi Viswaroopan, William He, Jianfu Li, Xu Zuo, Hua Xu, Cui Tao:
Improving Entity Recognition Using Ensembles of Deep Learning and Fine-tuned Large Language Models: A Case Study on Adverse Event Extraction from Multiple Sources. CoRR abs/2406.18049 (2024) - 2023
- [j81]Meng Zhang, Madhuri Sankaranarayanapillai, Jingcheng Du, Yang Xiang, Frank J. Manion, Marcelline R. Harris, Cooper Stansbury, Huy Anh Pham, Cui Tao:
Machine learning-based donor permission extraction from informed consent documents. BMC Bioinform. 24(1): 477 (2023) - [j80]Song Wang, Yifang Dang, Zhaoyi Sun, Ying Ding, Jyotishman Pathak, Cui Tao, Yunyu Xiao, Yifan Peng:
An NLP approach to identify SDoH-related circumstance and suicide crisis from death investigation narratives. J. Am. Medical Informatics Assoc. 30(8): 1408-1417 (2023) - [j79]Yifang Dang, Fang Li, Xinyue Hu, Vipina Kuttichi Keloth, Meng Zhang, Sunyang Fu, Muhammad F. Amith, J. Wilfred Fan, Jingcheng Du, Evan Yu, Hongfang Liu, Xiaoqian Jiang, Hua Xu, Cui Tao:
Systematic design and data-driven evaluation of social determinants of health ontology (SDoHO). J. Am. Medical Informatics Assoc. 30(9): 1465-1473 (2023) - [j78]Xubing Hao, Xiaojin Li, Guo-Qiang Zhang, Cui Tao, Paul E. Schulz, Licong Cui:
An ontology-based approach for harmonization and cross-cohort query of Alzheimer's disease data resources. BMC Medical Informatics Decis. Mak. 23(1): 151 (2023) - [j77]Xinyuan Zhang, Rebecca Z. Lin, Muhammad Tuan Amith, Cynthia Wang, Jeremy Light, John Strickley, Cui Tao:
DEVO: an ontology to assist with dermoscopic feature standardization. BMC Medical Informatics Decis. Mak. 23-S(1): 162 (2023) - [c130]Tiehang Duan, Zhenyi Wang, Gianfranco Doretto, Fang Li, Cui Tao, Donald A. Adjeroh:
Replay with Stochastic Neural Transformation for Online Continual EEG Classification. BIBM 2023: 1874-1879 - [c129]Tiehang Duan, Zhenyi Wang, Gianfranco Doretto, Fang Li, Cui Tao, Donald A. Adjeroh:
Distributionally Robust Cross Subject EEG Decoding. ECAI 2023: 575-582 - [c128]Chloe Aguilar, Muhammad Amith, Lu Tang, Jane Hamilton, Lara S. Savas, Danniel Rhee, Tazrin Khan, Cui Tao:
Evaluating Domain-Independent Small Talk Conversations to Improve Clinical Communication Interaction for Human and Machine. HCI (18) 2023: 330-343 - [c127]Xin Wang, Wordh Ul Hasan, Juan Li, Rasha Hendawi, Yang Du, Bo Xie, Cui Tao:
Empowering Personalized Health Data Queries with Knowledge Graph and GPT-Enhanced Voice Assistant. HPCC/DSS/SmartCity/DependSys 2023: 1035-1042 - [c126]Yiming Li, Xueqing Peng, Jianfu Li, Suyuan Peng, Donghong Pei, Cui Tao, Hua Xu, Na Hong:
Development of a Natural Language Processing Tool to Extract Acupuncture Point Location Terms. ICHI 2023: 344-351 - [c125]Zehan Li, Iqra Ameer, Yan Hu, Ahmed Abdelhameed, Cui Tao, Salih Selek, Hua Xu:
Suicide Tendency Prediction from Psychiatric Notes Using Transformer Models. ICHI 2023: 481-483 - [c124]Zenan Sun, Cui Tao:
Named Entity Recognition and Normalization for Alzheimer's Disease Eligibility Criteria. ICHI 2023: 558-564 - [c123]Wordh Ul Hasan, Juan Li, Shadi Alian, Tianyi Liang, Vikram Pandey, Kimia Tuz Zaman, Jun Kong, Cui Tao:
Honoring Heritage, Managing Health: A Mobile Diabetes Self-Management App for Native Americans with Cultural Sensitivity and Local Factors. ISCC 2023: 1-6 - [c122]Kimia Tuz Zaman, Wordh Ul Hasan, Juan Li, Cui Tao:
Empowering Caregivers of Alzheimer's Disease and Related Dementias (ADRD) with a GPT-Powered Voice Assistant: Leveraging Peer Insights from Social Media. ISCC 2023: 1-7 - [c121]Muhammad Amith, Licong Cui, Kirk Roberts, Cui Tao:
Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research. WWW (Companion Volume) 2023: 820-825 - [i15]Muhammad Amith, Licong Cui, Kirk Roberts, Cui Tao:
Application of an ontology for model cards to generate computable artifacts for linking machine learning information from biomedical research. CoRR abs/2303.11991 (2023) - [i14]Fang Li, Yi Nian, Zenan Sun, Cui Tao:
Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions. CoRR abs/2306.10456 (2023) - [i13]Tiehang Duan, Zhenyi Wang, Gianfranco Doretto, Fang Li, Cui Tao, Donald A. Adjeroh:
Distributionally Robust Cross Subject EEG Decoding. CoRR abs/2308.11651 (2023) - [i12]Xinyue Hu, Zenan Sun, Yi Nian, Yifang Dang, Fang Li, Jingna Feng, Evan Yu, Cui Tao:
Explainable Graph Neural Network for Alzheimer's Disease And Related Dementias Risk Prediction. CoRR abs/2309.06584 (2023) - [i11]Yiming Li, Jianfu Li, Jianping He, Cui Tao:
AE-GPT: Using Large Language Models to Extract Adverse Events from Surveillance Reports-A Use Case with Influenza Vaccine Adverse Events. CoRR abs/2309.16150 (2023) - 2022
- [j76]Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao, Licong Cui:
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs. J. Biomed. Semant. 13(1): 22 (2022) - [j75]Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao:
Toward a standard formal semantic representation of the model card report. BMC Bioinform. 23(1): 281 (2022) - [j74]Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Larry Bu, Yuji Zhang, Yong Chen, Cui Tao:
Mining on Alzheimer's diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing. BMC Bioinform. 23-S(6): 407 (2022) - [c120]Mark A. Musen, Jiang Bian, Bruce Chorpita, Vimla Patel, Cui Tao:
Ontologies in the Behavioral Sciences: Accelerating Research and the Accessibility and Use of Knowledge. AMIA 2022 - [c119]Evan Yu, Cui Tao, Jingcheng Du, Degui Zhi, Yang Xiang, Kayo Fujimoto, Xi Luo, John A. Schneider:
Combining Transfer Learning with Graph Attention Models for HIV Risk Prediction. AMIA 2022 - [c118]Jianping He, Fang Li, Xinyue Hu, Jianfu Li, Yi Nian, Jingqi Wang, Yang Xiang, Qiang Wei, Hua Xu, Cui Tao:
Chemical-Protein Relation Extraction with Pre-trained Prompt Tuning. ICHI 2022: 608-609 - [i10]Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Yong Chen, Cui Tao:
Mining On Alzheimer's Diseases Related Knowledge Graph to Identity Potential AD-related Semantic Triples for Drug Repurposing. CoRR abs/2202.08712 (2022) - [i9]Yifang Dang, Fang Li, Xinyue Hu, Vipina Kuttichi Keloth, Meng Zhang, Sunyang Fu, Jingcheng Du, J. Wilfred Fan, Muhammad F. Amith, Evan Yu, Hongfang Liu, Xiaoqian Jiang, Hua Xu, Cui Tao:
Systematic Design and Evaluation of Social Determinants of Health Ontology (SDoHO). CoRR abs/2212.01941 (2022) - 2021
- [j73]Jingcheng Du, Yang Xiang, Madhuri Sankaranarayanapillai, Meng Zhang, Jingqi Wang, Yuqi Si, Huy Anh Pham, Hua Xu, Yong Chen, Cui Tao:
Extracting postmarketing adverse events from safety reports in the vaccine adverse event reporting system (VAERS) using deep learning. J. Am. Medical Informatics Assoc. 28(7): 1393-1400 (2021) - [j72]Jingcheng Du, Qing Wang, Jingqi Wang, Prerana Ramesh, Yang Xiang, Xiaoqian Jiang, Cui Tao:
COVID-19 trial graph: a linked graph for COVID-19 clinical trials. J. Am. Medical Informatics Assoc. 28(9): 1964-1969 (2021) - [j71]Muhammad Amith, Chidinma Onye, Tracey Ledoux, Grace Xiong, Cui Tao:
The ontology of fast food facts: conceptualization of nutritional fast food data for consumers and semantic web applications. BMC Medical Informatics Decis. Mak. 21-S(7): 275 (2021) - [j70]Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi:
Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction. npj Digit. Medicine 4 (2021) - [c117]Muhammad Amith, Marcelline R. Harris, Cooper Stansbury, Kathleen Ford, Frank J. Manion, Cui Tao:
Expressing and Executing Informed Consent Permissions using SWRL: The All of Us Use Case. AMIA 2021 - [c116]Daniel J. Stone, Sijia Liu, Yuan Luo, Andrew Wen, Nansu Zong, Luke V. Rasmussen, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Fei Wang, Cui Tao, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. AMIA 2021 - [c115]Yunpeng Zhao, Pengfei Yin, Yongqiu Li, Xing He, Jingcheng Du, Cui Tao, Yi Guo, Mattia Prosperi, Pierangelo Veltri, Xi Yang, Yonghui Wu, Jiang Bian:
Data and Model Biases in Social Media Analyses: A Case Study of COVID-19 Tweets. AMIA 2021 - [c114]Rebecca Z. Lin, Muhammad Tuan Amith, Xinyuan Zhang, Cynthia Wang, Jeremy Light, John Strickley, Cui Tao:
Developing Ontologies to Standardize Descriptions of Visual and Dermoscopic Elements. BIBM 2021: 1813-1817 - [c113]Patricia Ngantcha, Muhammad Tuan Amith, Kirk Roberts, John A. Valenza, Muhammad F. Walji, Cui Tao:
Dental EHR-infused Persona Ontologies to Enrich Dental Dialogue Interaction of Agents. BIBM 2021: 1818-1825 - [c112]Anna Zhu, Muhammad Amith, Lu Tang, Rachel Cunningham, Angela Xu, Julie A. Boom, Cui Tao:
Experimenting with a Prototype Interactive Narrative Game to Improve Knowledge and Beliefs for the HPV Vaccine. HCI (43) 2021: 186-201 - [c111]Patricia Ngantcha, Muhammad Amith, Cui Tao, Kirk Roberts:
Patient-Provider Communication Training Models for Interactive Speech Devices. HCI (16) 2021: 250-268 - [c110]Samuel Wang, Jingcheng Du, Lu Tang, Cui Tao:
Understanding Public Perceptions of Measles from Twitter Using Multi-Task Convolutional Neural Networks. MedInfo 2021: 607-611 - [i8]Muhammad Amith, Marcelline R. Harris, Cooper Stansbury, Kathleen Ford, Frank J. Manion, Cui Tao:
Expressing and Executing Informed Consent Permissions Using SWRL: The All of Us Use Case. CoRR abs/2108.10221 (2021) - [i7]Yi Nian, Jingcheng Du, Larry Bu, Fang Li, Xinyue Hu, Yuji Zhang, Cui Tao:
Knowledge Graph-based Neurodegenerative Diseases and Diet Relationship Discovery. CoRR abs/2109.06123 (2021) - 2020
- [j69]Qiang Wei, Yaoyun Zhang, Muhammad Amith, Rebecca Lin, Jenay Lapeyrolerie, Cui Tao, Hua Xu:
Recognizing software names in biomedical literature using machine learning. Health Informatics J. 26(1) (2020) - [j68]Jiang Bian, Yaoyun Zhang, Cui Tao:
Exploring the semantics in mental health research. Health Informatics J. 26(2): 723-725 (2020) - [j67]Fang Li, Guozheng Rao, Jingcheng Du, Yang Xiang, Yaoyun Zhang, Salih Selek, Jane Elizabeth Hamilton, Hua Xu, Cui Tao:
Ontological representation-oriented term normalization and standardization of the Research Domain Criteria. Health Informatics J. 26(2): 726-737 (2020) - [j66]Jianhong Luo, Jingcheng Du, Cui Tao, Hua Xu, Yaoyun Zhang:
Exploring temporal suicidal behavior patterns on social media: Insight from Twitter analytics. Health Informatics J. 26(2): 738-752 (2020) - [j65]Rui Duan, Xinyuan Zhang, Jingcheng Du, Jing Huang, Cui Tao, Yong Chen:
On the evidence consistency of pharmacovigilance outcomes between Food and Drug Administration Adverse Event Reporting System and electronic medical record data for acute mania patients. Health Informatics J. 26(2): 753-764 (2020) - [j64]Qiang Wei, Zongcheng Ji, Zhiheng Li, Jingcheng Du, Jingqi Wang, Jun Xu, Yang Xiang, Firat Tiryaki, Stephen Wu, Yaoyun Zhang, Cui Tao, Hua Xu:
A study of deep learning approaches for medication and adverse drug event extraction from clinical text. J. Am. Medical Informatics Assoc. 27(1): 13-21 (2020) - [j63]Hansi Zhang, Christopher Wheldon, Adam G. Dunn, Cui Tao, Jinhai Huo, Rui Zhang, Mattia Prosperi, Yi Guo, Jiang Bian:
Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States. J. Am. Medical Informatics Assoc. 27(2): 225-235 (2020) - [j62]Rubina F. Rizvi, Jake Vasilakes, Terrence J. Adam, Genevieve B. Melton, Jeffrey R. Bishop, Jiang Bian, Cui Tao, Rui Zhang:
iDISK: the integrated DIetary Supplements Knowledge base. J. Am. Medical Informatics Assoc. 27(4): 539-548 (2020) - [j61]Fang Li, Jingcheng Du, Yongqun He, Hsing-yi Song, Mohcine Madkour, Guozheng Rao, Yang Xiang, Yi Luo, Henry W. Chen, Sijia Liu, Liwei Wang, Hongfang Liu, Hua Xu, Cui Tao:
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J. Am. Medical Informatics Assoc. 27(7): 1046-1056 (2020) - [j60]Laila Rasmy, Firat Tiryaki, Yujia Zhou, Yang Xiang, Cui Tao, Hua Xu, Degui Zhi:
Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. J. Am. Medical Informatics Assoc. 27(10): 1593-1599 (2020) - [j59]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. BMC Medical Informatics Decis. Mak. 20-S(4): 259 (2020) - [j58]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. BMC Medical Informatics Decis. Mak. 20-S(4): 283 (2020) - [j57]Zhe He, Cui Tao, Jiang Bian, Rui Zhang:
Selected articles from the Fourth International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019). BMC Medical Informatics Decis. Mak. 20-S(4): 315 (2020) - [j56]Muhammad Amith, Kayo Fujimoto, Rebecca Mauldin, Cui Tao:
Friend of a Friend with Benefits ontology (FOAF+): extending a social network ontology for public health. BMC Medical Informatics Decis. Mak. 20-S(10): 269 (2020) - [c109]Rui Duan, Zhaoyi Chen, Jiayi Tong, Chongliang Luo, Tianchen Lyu, Cui Tao, Demetrius Maraganore, Jiang Bian, Yong Chen:
Leverage Real-World Longitudinal Data in Large Clinical Research Networks for Alzheimer's Disease and Related Dementia (ADRD). AMIA 2020 - [c108]Jiayi Tong, Zhaoyi Chen, Rui Duan, Wei-Hsuan Lo-Ciganic, Tianchen Lyu, Cui Tao, Peter A. Merkel, Henry R. Kranzler, Jiang Bian, Yong Chen:
Identifying Clinical Risk Factors for Opioid Use Disorder using a Distributed Algorithm to Combine Real-World Data from a Large Clinical Data Research Network. AMIA 2020 - [c107]Muhammad Amith, Jing Wang, Grace Xiong, Kirk Roberts, Cui Tao:
A health consumer ontology of fast food information. BIBM 2020: 1714-1719 - [c106]Angela Xu, Muhammad Amith, Jianfu Li, Lu Tang, Cui Tao:
An Interactive Game for Changing Youth Behavior Regarding E-cigarettes. HCI (38) 2020: 512-518 - [c105]Juan Li, Rasha Hendawi, Vikram Pandey, Rafa Alenezi, Xin Wang, Bo Xie, Cui Tao:
Development and Evaluation of ADCareOnto - an Ontology for Personalized Home Care for Persons with Alzheimer's Disease. HealthCom 2020: 1-6 - [c104]Qiang Wei, Yujia Zhou, Bo Zhao, Xinyue Hu, Qiaozhu Mei, Cui Tao, Hua Xu:
Named Entity Recognition from Table Headers in Randomized Controlled Trial Articles. ICHI 2020: 1-2 - [i6]Muhammad Amith, Rebecca Lin, Rachel Cunningham, Qiwei Luna Wu, Lara S. Savas, Yang Gong, Julie A. Boom, Lu Tang, Cui Tao:
Examining Potential Usability and Health Beliefs Among Young Adults Using a Conversational Agent for HPV Vaccine Counseling. CoRR abs/2001.02306 (2020) - [i5]Laila Rasmy, Yang Xiang, Ziqian Xie, Cui Tao, Degui Zhi:
Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction. CoRR abs/2005.12833 (2020) - [i4]Mohcine Madkour, Keith A. Butler, Eric Mercer, Ali Bahrami, Cui Tao:
Semantic based model of Conceptual Work Products for formal verification of complex interactive systems. CoRR abs/2008.01623 (2020)
2010 – 2019
- 2019
- [j55]Junguk Hur, Cui Tao, Yongqun He:
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). BMC Bioinform. 20-S(21): 705 (2019) - [j54]Muhammad Amith, Kirk Roberts, Cui Tao:
Conceiving an application ontology to model patient human papillomavirus vaccine counseling for dialogue management. BMC Bioinform. 20-S(21): 706 (2019) - [j53]Yang Xiang, Kayo Fujimoto, John A. Schneider, Yuxi Jia, Degui Zhi, Cui Tao:
Network context matters: graph convolutional network model over social networks improves the detection of unknown HIV infections among young men who have sex with men. J. Am. Medical Informatics Assoc. 26(11): 1263-1271 (2019) - [j52]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. J. Am. Medical Informatics Assoc. 26(11): 1279-1285 (2019) - [j51]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. BMC Medical Informatics Decis. Mak. 19-S(1): 20:1-20:9 (2019) - [j50]Yaoyun Zhang, Cui Tao, Yang Gong, Kai Wang, Zhongming Zhao:
The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018). BMC Medical Informatics Decis. Mak. 19-S(1): 21:1-21:3 (2019) - [j49]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. BMC Medical Informatics Decis. Mak. 19-S(2): 139-148 (2019) - [j48]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. BMC Medical Informatics Decis. Mak. 19-S(4): 147:1-147:12 (2019) - [j47]Zhe He, Jiang Bian, Cui Tao, Rui Zhang:
Selected articles from the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018). BMC Medical Informatics Decis. Mak. 19-S(4): 148:1-148:3 (2019) - [j46]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. BMC Medical Informatics Decis. Mak. 19-S(4): 152:1-152:18 (2019) - [j45]Jingcheng Du, Rachel Cunningham, Yang Xiang, Fang Li, Yuxi Jia, Julie A. Boom, Sahiti Myneni, Jiang Bian, Chongliang Luo, Yong Chen, Cui Tao:
Leveraging deep learning to understand health beliefs about the Human Papillomavirus Vaccine from social media. npj Digit. Medicine 2 (2019) - [c103]Marcelline R. Harris, Frank J. Manion, Madhuri Sankaranarayanapillai, Hsing-yi Song, Marisa Conte, Cui Tao:
A Scoping Review to Identify Biobank Classification and Permissions to Share Metadata. AMIA 2019 - [c102]Jonathan M. Vajda, J. Neil Otte, Cooper Stansbury, Marcelline R. Harris, Frank J. Manion, Cui Tao:
Refactoring and Expanding the Informed Consent Ontology (ICO). AMIA 2019 - [c101]Jonathan M. Vajda, J. Neil Otte, Cooper Stansbury, Marcelline R. Harris, Elizabeth Umberfield, Frank J. Manion, Cui Tao:
Expanding the Representation of Permissions and Deontic Roles in the Informed Consent Ontology (ICO). AMIA 2019 - [c100]Qiang Wei, Zongcheng Ji, Yuqi Si, Jingcheng Du, Jingqi Wang, Firat Tiryaki, Stephen Wu, Cui Tao, Kirk Roberts, Hua Xu:
Relation Extraction from Clinical Narratives Using Pre-trained Language Models. AMIA 2019 - [c99]Muhammad Amith, Licong Cui, Kirk Roberts, Hua Xu, Cui Tao:
Ontology of Consumer Health Vocabulary: providing a formal and interoperable semantic resource for linking lay language and medical terminology. BIBM 2019: 1177-1178 - [c98]Muhammad Tuan Amith, Kayo Fujimoto, Cui Tao:
NET-EXPO: A Gephi Plugin Towards Social Network Analysis of Network Exposure for Unipartite and Bipartite Graphs. HCI (35) 2019: 3-12 - [c97]Bikesh Maharjan, Juan Li, Jun Kong, Cui Tao:
Alexa, What Should I Eat? : A Personalized Virtual Nutrition Coach for Native American Diabetes Patients Using Amazon's Smart Speaker Technology. HealthCom 2019: 1-6 - [c96]Jonathan M. Vajda, J. Neil Otte, Cooper Stansbury, Frank J. Manion, Marcelline R. Harris, Cui Tao:
Using Stases to Enrich Queries for When and Where Regulations Are in Force. ICBO 2019: 1 - [c95]Fang Li, Mingqiang Wang, Huy Anh Pham, Yang Xiang, Muhammad Tuan Amith, Cui Tao, Jingcheng Du, Guozheng Rao:
Systematic Design of Drug Repurposing-Oriented Alzheimer's Disease Ontology. ICHI 2019: 1-5 - [c94]Muhammad Amith, Anna Zhu, Rachel Cunningham, Rebecca Lin, Lara S. Savas, Laura Shay, Yong Chen, Yang Gong, Julie Boom, Kirk Roberts, Cui Tao:
Early Usability Assessment of a Conversational Agent for HPV Vaccination. ITCH 2019: 17-23 - [c93]Ergin Soysal, Jeremy L. Warner, Jingqi Wang, Min Jiang, Krysten Harvey, Sandeep Kumar Jain, Xiao Dong, Hsing-yi Song, Harish Siddhanamatha, Liwei Wang, Qi Dai, Qingxia Chen, Xianglin Du, Cui Tao, Ping Yang, Joshua Charles Denny, Hongfang Liu, Hua Xu:
Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. MedInfo 2019: 1041-1045 - [c92]Graciela Gonzalez, Zhiyong Lu, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen, Jingcheng Du, Juliane Fluck, Casey S. Greene, John H. Holmes, Aditya Kashyap, Rikke Linnemann Nielsen, Zhengqing Ouyang, Sebastian Schaaf, Jaclyn N. Taroni, Cui Tao, Yuping Zhang, Hongfang Liu:
Text Mining and Machine Learning for Precision Medicine. PSB 2019: 449-454 - [c91]Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts, Cui Tao:
An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines. SEPDA@ISWC 2019: 24-30 - [c90]Guozheng Rao, Li Zhang, Xiaowang Zhang, Wenwen Li, Fang Li, Cui Tao:
A Multi-Source Linked Open Data Fusion Method for Gene Disorder Drug Relationship Querying. SEPDA@ISWC 2019: 31-35 - [e5]Zhe He, Jiang Bian, Cui Tao, Rui Zhang:
Proceedings of the 4th International Workshop on Semantics-Powered Data Mining and Analytics co-located with the 18th International Semantic Web Conference (ISWC 2019), Aukland, New Zealand, October 27, 2019. CEUR Workshop Proceedings 2427, CEUR-WS.org 2019 [contents] - [i3]Jingcheng Du, Chongliang Luo, Qiang Wei, Yong Chen, Cui Tao:
Exploring difference in public perceptions on HPV vaccine between gender groups from Twitter using deep learning. CoRR abs/1907.03167 (2019) - [i2]Hansi Zhang, Christopher Wheldon, Adam G. Dunn, Cui Tao, Jinhai Huo, Rui Zhang, Mattia Prosperi, Yi Guo, Jiang Bian:
Mining Twitter to Assess the Determinants of Health Behavior towards Human Papillomavirus Vaccination in the United States. CoRR abs/1907.11624 (2019) - 2018
- [j44]Muhammad Amith, Cui Tao:
Representing vaccine misinformation using ontologies. J. Biomed. Semant. 9(1): 22:1-22:13 (2018) - [j43]Li Wang, Yaoyun Zhang, Min Jiang, Jingqi Wang, Jiancheng Dong, Yun Liu, Cui Tao, Guoqian Jiang, Yi Zhou, Hua Xu:
Toward a normalized clinical drug knowledge base in China - applying the RxNorm model to Chinese clinical drugs. J. Am. Medical Informatics Assoc. 25(7): 809-818 (2018) - [j42]Muhammad Amith, Zhe He, Jiang Bian, Juan Antonio Lossio-Ventura, Cui Tao:
Assessing the practice of biomedical ontology evaluation: Gaps and opportunities. J. Biomed. Informatics 80: 1-13 (2018) - [j41]Hee-Jin Lee, Yaoyun Zhang, Min Jiang, Jun Xu, Cui Tao, Hua Xu:
Identifying direct temporal relations between time and events from clinical notes. BMC Medical Informatics Decis. Mak. 18(S-2): 23-34 (2018) - [j40]Zhe He, Cui Tao, Jiang Bian, Rui Zhang, Jingshan Huang:
Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017). BMC Medical Informatics Decis. Mak. 18(S-2): 56:1-56:4 (2018) - [j39]Xinyuan Zhang, Shiqi Wang, Jie Liu, Cui Tao:
Towards improving diagnosis of skin diseases by combining deep neural network and human knowledge. BMC Medical Informatics Decis. Mak. 18(S-2): 69-76 (2018) - [j38]Jingcheng Du, Yaoyun Zhang, Jianhong Luo, Yuxi Jia, Qiang Wei, Cui Tao, Hua Xu:
Extracting psychiatric stressors for suicide from social media using deep learning. BMC Medical Informatics Decis. Mak. 18(S-2): 77-87 (2018) - [j37]Rebecca Lin, Muhammad Amith, Chen Liang, Rui Duan, Yong Chen, Cui Tao:
Visualized Emotion Ontology: a model for representing visual cues of emotions. BMC Medical Informatics Decis. Mak. 18(S-2): 101-113 (2018) - [c89]Jing An, Mandana Salimi, Anupama E. Gururaj, Cui Tao, Degui Zhi, Hua Xu:
Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data. AMIA 2018 - [c88]Jingcheng Du, Fang Li, Yuxi Jia, Yang Xiang, Lu Tang, Sahiti Myneni, Cui Tao:
Mining Human Papillomavirus Vaccination Health Beliefs from Twitter Using Attentive Recurrent Neural Network. AMIA 2018 - [c87]Fang Li, Jingcheng Du, Guozheng Rao, Cui Tao:
Construction of Drug Repurposing-oriented Alzheimer's Disease Ontology. AMIA 2018 - [c86]Frank J. Manion, Marcelline R. Harris, Muhamamd F. Amith, Cui Tao:
Development and Validation of an Ontological Representation of the US Common Rule. AMIA 2018 - [c85]Jiayi Tong, Jing Huang, Jingcheng Du, Yi Cai, Cui Tao, Yong Chen:
Identification of Rare Adverse Events with Year-varying Reporting Rates for FLU4 Vaccine in VAERS. AMIA 2018 - [c84]Yang Xiang, Jun Xu, Jingcheng Du, Degui Zhi, Cui Tao:
Asthma Onset Prediction Using Structured EMR Data. AMIA 2018 - [c83]Xinyuan Zhang, Sicheng Zhou, Luca Giancardo, Cui Tao:
Computer Aided Diagnosis of Chest X-rays using by Combining Deep Convolutional Neural Networks. AMIA 2018 - [c82]Muhammad Amith, Frank J. Manion, Chen Liang, Marcelline R. Harris, Dennis Wang, Yongqun He, Cui Tao:
OntoKeeper: Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists. BIBM 2018: 1614-1617 - [c81]Qing Cong, Zhiyong Feng, Fang Li, Yang Xiang, Guozheng Rao, Cui Tao:
X-A-BiLSTM: a Deep Learning Approach for Depression Detection in Imbalanced Data. BIBM 2018: 1624-1627 - [c80]Qing Cong, Zhiyong Feng, Fang Li, Li Zhang, Guozheng Rao, Cui Tao:
Constructing Biomedical Knowledge Graph Based on SemMedDB and Linked Open Data. BIBM 2018: 1628-1631 - [c79]Jing Huang, Xinyuan Zhang, Jiayi Tong, Jingcheng Du, Rui Duan, Liu Yang, Jason H. Moore, Yong Chen, Cui Tao:
Comparing adverse effects of Hepatitis C drugs using FAERS data. BIBM 2018: 1653-1656 - [c78]Muhammad Amith, Rebecca Lin, Chen Liang, Yang Gong, Cui Tao:
VEO-Engine: Interfacing and Reasoning with an Emotion Ontology for Device Visual Expression. HCI (29) 2018: 349-355 - [c77]J. Neil Otte, Cooper Stansbury, Jonathan Vajda, Frank J. Manion, Elizabeth Umberfield, Yongqun He, Marcelline R. Harris, Jihad S. Obeid, Mathias Brochhausen, William D. Duncan, Cui Tao:
Coordinated Evolution of Ontologies of Informed Consent. ICBO 2018 - [c76]Jianhong Luo, Jingcheng Du, Cui Tao, Hua Xu, Yaoyun Zhang:
Exploring Temporal Patterns of Suicidal Behavior on Twitter. ICHI Workshops 2018: 55-56 - [c75]Xinyuan Zhang, Rui Duan, Jingcheng Du, Jing Huang, Yong Chen, Cui Tao:
Comparing Pharmacovigilance Outcomes Between FAERS and EMR Data for Acute Mania Patients. ICHI Workshops 2018: 57-59 - [c74]Fang Li, Guozheng Rao, Jingcheng Du, Yang Xiang, Yaoyun Zhang, Salih Selek, Jane Elizabeth Hamilton, Hua Xu, Cui Tao:
Term Standardization and Normalization for Research Domain Criteria (RDoC). ICHI Workshops 2018: 60-61 - [i1]Jingcheng Du, Qingyu Chen, Yifan Peng, Yang Xiang, Cui Tao, Zhiyong Lu:
ML-Net: multi-label classification of biomedical texts with deep neural networks. CoRR abs/1811.05475 (2018) - 2017
- [j36]Jingcheng Du, Jun Xu, Hsing-yi Song, Xiangyu Liu, Cui Tao:
Optimization on machine learning based approaches for sentiment analysis on HPV vaccines related tweets. J. Biomed. Semant. 8(1): 9:1-9:7 (2017) - [j35]Muhammad Amith, Cui Tao:
Modulated evaluation metrics for drug-based ontologies. J. Biomed. Semant. 8(1): 17:1-17:8 (2017) - [j34]Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute, Guoqian Jiang:
Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies. J. Biomed. Semant. 8(1): 19:1-19:11 (2017) - [j33]Muhammad Amith, Rachel Cunningham, Lara S. Savas, Julie Boom, Roger W. Schvaneveldt, Cui Tao, Trevor Cohen:
Using Pathfinder networks to discover alignment between expert and consumer conceptual knowledge from online vaccine content. J. Biomed. Informatics 74: 33-45 (2017) - [j32]Muhammad Amith, Hsing-yi Song, Yaoyun Zhang, Hua Xu, Cui Tao:
Lightweight predicate extraction for patient-level cancer information and ontology development. BMC Medical Informatics Decis. Mak. 17(2): 23-34 (2017) - [j31]Jingcheng Du, Jun Xu, Hsing-yi Song, Cui Tao:
Leveraging machine learning-based approaches to assess human papillomavirus vaccination sentiment trends with Twitter data. BMC Medical Informatics Decis. Mak. 17(2): 63-70 (2017) - [j30]Cui Tao, Yang Gong, Hua Xu, Zhongming Zhao:
Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data. BMC Medical Informatics Decis. Mak. 17(2): 77:1-77:3 (2017) - [j29]Yi Cai, Jingcheng Du, Jing Huang, Susan S. Ellenberg, Sean Hennessy, Cui Tao, Yong Chen:
A signal detection method for temporal variation of adverse effect with vaccine adverse event reporting system data. BMC Medical Informatics Decis. Mak. 17(2): 93-100 (2017) - [c73]Marcelline R. Harris, Frank J. Manion, Hsing-yi Song, Yongqun He, Muhamamd F. Amith, Cui Tao:
From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories. AMIA 2017 - [c72]Guoqian Jiang, Walter S. Campbell, Timothy Clark, Cui Tao, Mark A. Musen:
Big Data to Knowledge (BD2K) and the Application of Metadata. AMIA 2017 - [c71]Hansi Zhang, Yunpeng Zhao, Christopher Wheldon, Xinsong Du, Terrell Brown, Yi Guo, Stephanie Staras, Jingcheng Du, Cui Tao, Jiang Bian:
A Twitter Study of the Relationship between the Geographic Variations of HPV Vaccination Rates and Online Information in the United States. AMIA 2017 - [c70]Jingcheng Du, Yaoyun Zhang, Cui Tao, Hua Xu:
A pilot study of mining association between psychiatric stressors and symptoms in tweets. BIBM 2017: 1254-1257 - [c69]Hee-Jin Lee, Yaoyun Zhang, Jun Xu, Cui Tao, Hua Xu, Min Jiang:
Towards practical temporal relation extraction from clinical notes: An analysis of direct temporal relations. BIBM 2017: 1272-1275 - [c68]Rebecca Lin, Muhammad Tuan Amith, Chen Liang, Cui Tao:
Designing an ontology for emotion-driven visual representations. BIBM 2017: 1280-1283 - [c67]Xinyuan Zhang, Shiqi Wang, Jie Liu, Cui Tao:
Computer-aided diagnosis of four common cutaneous diseases using deep learning algorithm. BIBM 2017: 1304-1306 - [c66]Sijia Liu, Liwei Wang, Donna M. Ihrke, Vipin Chaudhary, Cui Tao, Chunhua Weng, Hongfang Liu:
Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose. CRI 2017 - [c65]Jingcheng Du, Jun Xu, Hsing-yi Song, Cui Tao:
Leveraging Machine Learning Based Approaches to Assess Human Papillomavirus Vaccination Sentiment Trends with Twitter. CRI 2017 - [c64]Rui Duan, Xinyuan Zhang, Jingcheng Du, Jing Huang, Cui Tao, Yong Chen:
Post-marketing Drug Safety Evaluation Using Data Mining Based on FAERS. DMBD 2017: 379-389 - [c63]Muhammad Amith, Yaoyun Zhang, Hua Xu, Cui Tao:
Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification. IEA/AIE (2) 2017: 386-395 - [c62]Muhammad Amith, Frank J. Manion, Marcelline R. Harris, Yaoyun Zhang, Hua Xu, Cui Tao:
Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. MedInfo 2017: 838-842 - [c61]Jingcheng Du, Jing Huang, Rui Duan, Yong Chen, Cui Tao:
Comparing the Human Papillomavirus Vaccination Opinions Trends from Different Twitter User Groups with a Machine Learning Based System and Semiparametric Nonlinear Regression. MedInfo 2017: 1218 - [c60]Jing Huang, Xinyuan Zhang, Jingcheng Du, Rui Duan, Liu Yang, Jason H. Moore, Yong Chen, Cui Tao:
Comparing Different Adverse Effects Among Multiple Drugs Using FAERS Data. MedInfo 2017: 1268 - 2016
- [j28]Cui Tao, Yongqun He, Sivaram Arabandi:
Vaccine and Drug Ontology Studies (VDOS 2014). J. Biomed. Semant. 7: 6 (2016) - [j27]Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li, Hua Xu:
Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J. Biomed. Semant. 7: 11 (2016) - [j26]Jingcheng Du, Yi Cai, Yong Chen, Cui Tao:
Trivalent influenza vaccine adverse symptoms analysis based on MedDRA terminology using VAERS data in 2011. J. Biomed. Semant. 7: 13 (2016) - [j25]Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li, Hua Xu:
Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J. Biomed. Semant. 7: 21 (2016) - [j24]Mohcine Madkour, Driss Benhaddou, Cui Tao:
Temporal data representation, normalization, extraction, and reasoning: A review from clinical domain. Comput. Methods Programs Biomed. 128: 52-68 (2016) - [c59]Jeffrey S. Grethe, Ibrahim Burak Özyurt, Hua Xu, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
A Scalable Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System. AMIA 2016 - [c58]Hua Xu, Jeffrey S. Grethe, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Yueling Li, Ibrahim Burak Özyurt, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Groundwork for Biomedical Data Discovery. AMIA 2016 - [c57]Mohcine Madkour, Hsing-yi Song, Jingcheng Du, Cui Tao:
A representational analysis of a temporal indeterminancy display in clinical events. BIBM 2016: 1089-1095 - [c56]Chen Liang, Jingchun Sun, Cui Tao:
Semantic Web Ontology and Data Integration: a Case Study in Aiding Psychiatric Drug Repurposing. CRI 2016 - [c55]Dennis Wang, Rachel Cunningham, Julie Boom, Muhammad Amith, Cui Tao:
Towards a HPV Vaccine Knowledgebase for Patient Education Content. Nursing Informatics 2016: 432-436 - [e4]Cui Tao, Guoqian Jiang, Dezhao Song, Jeff Heflin, Frank Schilder:
Proceedings of the First International Workshop on Biomedical Data Integration and Discovery (BMDID 2016) co-located with The 15th International Semantic Web Conference (ISWC 2016), Kobe, Japan, October 17, 2016. CEUR Workshop Proceedings 1709, CEUR-WS.org 2016 [contents] - 2015
- [j23]Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Andrew Lawson, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Humberto Lara-Guerra, Beate Litzenburger, Funda Meric-Bernstam, W. Jim Zheng:
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database J. Biol. Databases Curation 2015 (2015) - [j22]Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu:
Colorectal cancer drug target prediction using ontology-based inference and network analysis. Database J. Biol. Databases Curation 2015 (2015) - [j21]Muhammad Amith, Yang Gong, Rachel Cunningham, Julie Boom, Cui Tao:
Developing VISO: Vaccine Information Statement Ontology for patient education. J. Biomed. Semant. 6: 23 (2015) - [j20]Yuji Zhang, Puqiang Wu, Yi Luo, Cui Tao:
Identification of sex-associated network patterns in Vaccine-Adverse Event Association Network in VAERS. J. Biomed. Semant. 6: 33 (2015) - [j19]María Del Carmen Legaz-García, Marcos Menárguez Tortosa, Jesualdo Tomás Fernández-Breis, Christopher G. Chute, Cui Tao:
Transformation of standardized clinical models based on OWL technologies: from CEM to OpenEHR archetypes. J. Am. Medical Informatics Assoc. 22(3): 536-544 (2015) - [c54]Keith A. Butler, Eric Mercer, Ali Bahrami, Cui Tao:
Model Checking for Verification of Interactive Health IT Systems. AMIA 2015 - [c53]Guoqian Jiang, Harold R. Solbrig, Eric Prud'hommeaux, Cui Tao, Chunhua Weng, Christopher G. Chute:
Quality Assurance of Cancer Study Common Data Elements Using A Post-Coordination Approach. AMIA 2015 - [c52]Jie Long, Nathan C. Hulse, Cui Tao:
Analysis of empty responses from electronic resources in infobutton managers. AMIA 2015 - [c51]Sahiti Myneni, Muhammad Amith, Yimin Geng, Cui Tao:
Towards an Ontology-driven Framework to Enable Development of Personalized mHealth Solutions for Cancer Survivors' Engagement in Healthy Living. MedInfo 2015: 113-117 - [c50]Chen Liang, Jingchun Sun, Cui Tao:
Semantic Web Ontology and Data Integration: a Case Study in Aiding Psychiatric Drug Repurposing. MedInfo 2015: 1051 - [c49]Cui Tao, Jingcheng Du, Yi Cai, Yong Chen:
Trivalent Influenza Vaccine Adverse Event Analysis Based On MedDRA System Organ Classes Using VAERS Data. MedInfo 2015: 1076 - [c48]Muhammad Amith, Cui Tao:
A Web Application Towards Semiotic-based Evaluation of Biomedical Ontologies. BDM2I@ISWC 2015 - [e3]Dezhao Song, Adam Fermier, Cui Tao, Frank Schilder:
Proceedings of International Workshop on Biomedical Data Mining, Modeling, and Semantic Integration: A Promising Approach to Solving Unmet Medical Needs (BDM2I2015) co-located with The 14th International Semantic Web Conference (ISWC 2015), Bethlehem, United States, October 11th, 2015. CEUR Workshop Proceedings 1428, CEUR-WS.org 2015 [contents] - 2014
- [j18]Cui Tao, Puqiang Wu, Yi Luo, Yuji Zhang:
Linked vaccine adverse event data from VAERS for biomedical data analysis and longitudinal studies. BioData Min. 7: 36 (2014) - [j17]Cui Tao, Yongqun He, Sivaram Arabandi:
A 2013 workshop: vaccine and drug ontology studies (VDOS 2013). J. Biomed. Semant. 5: 16 (2014) - [j16]Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao, Barry Smith:
OAE: The Ontology of Adverse Events. J. Biomed. Semant. 5: 29 (2014) - [j15]Yuji Zhang, Cui Tao, Guoqian Jiang, Asha A. Nair, Jian Su, Christopher G. Chute, Hongfang Liu:
Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. J. Biomed. Semant. 5: 33 (2014) - [j14]Kimberly Clark, Deepak K. Sharma, Rui Qin, Christopher G. Chute, Cui Tao:
A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis. J. Biomed. Semant. 5: 49 (2014) - [c47]Craig Harrington, Cui Tao, Keith A. Butler, Jiajie Zhang:
Enhancing the TURF Framework with a Workflow Ontology. AMIA 2014 - [c46]Nathan C. Hulse, Jie Long, Xiaomin Xu, Cui Tao:
Enabling Locally-Developed Content For Access Through the Infobutton By Means of Automated Concept Annotation. AMIA 2014 - [c45]Jingchun Sun, Cui Tao, Kevin W. Zhu, W. Jim Zheng, Junjie Chen, Hua Xu:
An Integrative Framework for Drug Target Prediction and Repurposing. AMIA 2014 - [c44]Feichen Shen, Dingcheng Li, Hongfang Liu, Yugyung Lee, Jyotishman Pathak, Christopher G. Chute, Cui Tao:
Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. BHI 2014: 531-534 - [c43]Qian Zhu, Cui Tao:
Pharmacological class data representation in the Web Ontology Language (OWL). IEEE BigData 2014: 77-84 - [c42]Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann Balley, Funda Meric-Bernstam, W. Jim Zheng:
Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature. ICBO 2014: 66 - [c41]Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu:
Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches. ICBO 2014: 67 - [c40]Qian Zhu, Cui Tao:
Pharmacological Class Data Representation in the Web Ontology Language (OWL). ICBO 2014: 68-69 - [c39]Muhammad Amith, Cui Tao:
An Initial Framework for an Ontology-based Mobile Application for Vaccine Information Retrieval and Education. ICBO 2014: 81-83 - [c38]Yaoyun Zhang, Jingqi Wang, Cui Tao, Hua Xu:
Ontology-based Normalization for Disease-Lab test Relation Extraction. ICBO 2014: 87-89 - [c37]Muhammad Amith, Cui Tao:
A Prototype Mobile Virtual Assistant for Semantic-Based Vaccine Information Retrieval. ICSH 2014: 200-205 - [c36]Cui Tao, Puqiang Wu, Yuji Zhang:
Linked Vaccine Adverse Event Data Representation from VAERS for Biomedical Informatics Research. PAKDD Workshops 2014: 652-661 - [c35]Qian Zhu, Cui Tao, Feichen Shen, Christopher G. Chute:
Exploring the Pharmacogenomics Knowledge Base (PharmGKB) for Repositioning Breast Cancer Drugs by Leveraging Web Ontology Language (OWL) and Cheminformatics Approaches. Pacific Symposium on Biocomputing 2014: 172-182 - [c34]Guoqian Jiang, Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute:
Building a Semantic Web-based Metadata Repository for Facilitating Detailed Clinical Modeling in Cancer Genome Studies. SWAT4LS 2014 - [c33]Cui Tao, Nnaemeka Okafor, Amit M. Mehta, Charles L. Maddow, David J. Robinson, Brent King, Jiajie Zhang, Amy Franklin:
A Work Domain Ontology for Modeling Emergency Department Workflow. SWAT4LS 2014 - [c32]W. Jim Zheng, Jingcheng Du, Jijun Tang, Cui Tao:
GSO: A Semantic Web Ontology to Capture 3D Genome Structure. SWAT4LS 2014 - 2013
- [j13]Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu:
Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J. Biomed. Semant. 4: 33 (2013) - [j12]Cui Tao, Guoqian Jiang, Thomas A. Oniki, Robert R. Freimuth, Qian Zhu, Deepak K. Sharma, Jyotishman Pathak, Stanley M. Huff, Christopher G. Chute:
A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. J. Am. Medical Informatics Assoc. 20(3): 554-562 (2013) - [j11]Sunghwan Sohn, Kavishwar B. Wagholikar, Dingcheng Li, Siddhartha Jonnalagadda, Cui Tao, Ravikumar Komandur Elayavilli, Hongfang Liu:
Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. J. Am. Medical Informatics Assoc. 20(5): 836-842 (2013) - [j10]Cui Tao, Jyotishman Pathak, Harold R. Solbrig, Wei-Qi Wei, Christopher G. Chute:
Terminology representation guidelines for biomedical ontologies in the semantic web notations. J. Biomed. Informatics 46(1): 128-138 (2013) - [j9]Qian Zhu, Robert R. Freimuth, Zonghui Lian, Scott Bauer, Jyotishman Pathak, Cui Tao, Matthew J. Durski, Christopher G. Chute:
Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study. J. Biomed. Informatics 46(2): 286-293 (2013) - [j8]Cui Tao, Dezhao Song, Deepak K. Sharma, Christopher G. Chute:
Semantator: Semantic annotator for converting biomedical text to linked data. J. Biomed. Informatics 46(5): 882-893 (2013) - [c31]Nathan C. Hulse, Jie Long, Cui Tao:
Combining Infobuttons and Semantic Web Rules for Identifying Patterns and Delivering Highly-Personalized Education Materials. AMIA 2013 - [c30]Dingcheng Li, Liwei Wang, Cui Tao, Christopher G. Chute, Hongfang Liu:
Coreference Resolution from Medical Corpus with Topic Modeling. AMIA 2013 - [c29]Jie Long, Nathan C. Hulse, Cui Tao, Guilherme Del Fiol:
Adding Search Engine Functionality to Infobutton Manager Platform. AMIA 2013 - [c28]Cui Tao, Harold R. Solbrig, Craig Stancl, Kevin J. Peterson, Cory M. Endle, Scott Bauer, Deepak K. Sharma, Christopher G. Chute:
Introduction and Implementation of Common Terminology Services 2 (CTS2). AMIA 2013 - [c27]Yuji Zhang, Dingcheng Li, Cui Tao, Feichen Shen, Hongfang Liu:
An integrative computational approach to identify disease-specific networks from PubMed literature information. BIBM 2013: 72-75 - [c26]Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu:
Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. VDOS+DO@ICBO 2013 - [c25]Cui Tao, Dingcheng Li, Feichen Shen, Zonghui Lian, Jyotishman Pathak, Hongfang Liu, Christopher G. Chute:
Phenotyping on EHR Data Using OWL and Semantic Web Technologies. ICSH 2013: 31-32 - [c24]Catalina Martínez-Costa, Diego Boscá, María Del Carmen Legaz-García, Cui Tao, Jesualdo Tomás Fernández-Breis, Stefan Schulz, Christopher G. Chute:
Isosemantic Rendering of Clinical Information Using Formal Ontologies and RDF. MedInfo 2013: 1085 - [c23]Kimberly Clark, Deepak K. Sharma, Rui Qin, Christopher G. Chute, Cui Tao:
Ontology-based Temporal Analysis for Medical Device Adverse Event - A Use Case Study on Late Stent Thrombosis. SWAT4LS 2013 - [e2]Cui Tao, Yongqun He, Luca Toldo, Sivaram Arabandi, Selja Seppälä, Alan Ruttenberg:
Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th - 12th 2013. CEUR Workshop Proceedings 1061, CEUR-WS.org 2013 [contents] - 2012
- [j7]Yongqun He, Luca Toldo, Gully Burns, Cui Tao, Darrell R. Abernethy:
A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). J. Biomed. Semant. 3: 12 (2012) - [j6]Cui Tao, Yongqun He, Hannah Yang, Gregory A. Poland, Christopher G. Chute:
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. J. Biomed. Semant. 3: 13 (2012) - [j5]Stephen T. Wu, Hongfang Liu, Dingcheng Li, Cui Tao, Mark A. Musen, Christopher G. Chute, Nigam H. Shah:
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J. Am. Medical Informatics Assoc. 19(e1) (2012) - [j4]Susan Rea, Jyotishman Pathak, Guergana K. Savova, Thomas A. Oniki, Les Westberg, Calvin E. Beebe, Cui Tao, Craig G. Parker, Peter J. Haug, Stanley M. Huff, Christopher G. Chute:
Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project. J. Biomed. Informatics 45(4): 763-771 (2012) - [c22]Cui Tao, Harold R. Solbrig, Pradip Kanjamala, Kevin J. Peterson, Craig Stancle, Christopher G. Chute:
Common Terminology Services 2 (CTS2) for Biomedical Community. AMIA 2012 - [c21]Dingcheng Li, Cui Tao, Hongfang Liu, Christopher G. Chute:
Ontology-Based Temporal Relation Modeling with MapReduce Latent Dirichlet Allocations for Big EHR Data. CGC 2012: 708-715 - [c20]Hongfang Liu, Stephen T. Wu, Cui Tao, Christopher G. Chute:
Modeling UIMA type system using web ontology language: towards interoperability among UIMA-based NLP tools. MIX-HS 2012: 31-36 - [c19]Matt-Mouley Bouamrane, Frances S. Mair, Cui Tao:
An overview of electronic health information management systems quality assessment. MIX-HS 2012: 37-46 - [c18]Cui Tao, Yuji Zhang, Guoqian Jiang, Matt-Mouley Bouamrane, Christopher G. Chute:
Optimizing semantic MEDLINE for translational science studies using semantic web technologies. MIX-HS 2012: 53-58 - [c17]Cui Tao, Matt-Mouley Bouamrane:
Managing interoperability and compleXity in health systems - MIXHS'12. CIKM 2012: 2758-2759 - [c16]Cui Tao, Guoqian Jiang, Thomas A. Oniki, Robert R. Freimuth, Jyotishman Pathak, Qian Zhu, Deepak K. Sharma, Stanley M. Huff, Christopher G. Chute:
A Semantic-Web Oriented Representation of Clinical Element Model for Secondary Use of Electronic Healthcare Data. HISB 2012: 133 - [c15]Cui Tao, Krist Wongsuphasawat, Kimberly Clark, Catherine Plaisant, Ben Shneiderman, Christopher G. Chute:
Towards event sequence representation, reasoning and visualization for EHR data. IHI 2012: 801-806 - [e1]Cui Tao, Matt-Mouley Bouamrane:
Proceedings of the 2nd International Workshop on Managing Interoperability and compleXity in Health Systems, MIX-HS, Maui, HI, USA, October 29, 2012. ACM 2012, ISBN 978-1-4503-1710-8 [contents] - 2011
- [c14]Cui Tao, Natalya Fridman Noy, Harold R. Solbrig, Nigam H. Shah, Mark A. Musen, Christopher G. Chute:
Proposed SKOS Extensions for BioPortal Terminology Services. JIST 2011: 342-349 - [c13]Wen Chen, Lei Kong, Yun Wu, Xiaohui Liao, Cui Tao:
Wireless extensions of CANBUS in industrial applications. BMEI 2011: 2187-2191 - [c12]Matt-Mouley Bouamrane, Cui Tao:
Managing interoperability and complexity inhealth systems: MIXHS'11 workshop summary. CIKM 2011: 2635-2636 - [c11]Cui Tao, Guoqian Jiang, Kimberly Clark, Deepak K. Sharma, Christopher G. Chute:
Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-Based Approaches. ICBO 2011 - 2010
- [c10]David W. Embley, Stephen W. Liddle, Deryle W. Lonsdale, Aaron P. Stewart, Cui Tao:
KBB: A Knowledge-Bundle Builder for Research Studies. ER Workshops 2010: 148-157 - [c9]Cui Tao, Harold R. Solbrig, Deepak K. Sharma, Wei-Qi Wei, Guergana K. Savova, Christopher G. Chute:
Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. ISWC (2) 2010: 241-256
2000 – 2009
- 2009
- [j3]Cui Tao, David W. Embley:
Automatic hidden-web table interpretation, conceptualization, and semantic annotation. Data Knowl. Eng. 68(7): 683-703 (2009) - [c8]Cui Tao, David W. Embley, Stephen W. Liddle:
FOCIH: Form-Based Ontology Creation and Information Harvesting. ER 2009: 346-359 - 2008
- [c7]David W. Embley, Stephen W. Liddle, Cui Tao:
A Web of Knowledge: A Conceptual-Modeling Perspective. The Evolution of Conceptual Modeling 2008: 137-160 - [c6]David W. Embley, Stephen W. Liddle, Deryle W. Lonsdale, George Nagy, Yuri A. Tijerino, Robert Clawson, Jordan Crabtree, Yihong Ding, Piyushee Jha, Zonghui Lian, Stephen Lynn, Raghav K. Padmanabhan, Jeff Peters, Cui Tao, Robby Watts, Charla Woodbury, Andrew Zitzelberger:
A Conceptual-Model-Based Computational Alembic for a Web of Knowledge. ER 2008: 532-533 - 2007
- [c5]Cui Tao, David W. Embley:
Seed-Based Generation of Personalized Bio-ontologies for Information Extraction. ER Workshops 2007: 74-84 - [c4]Cui Tao, David W. Embley:
Automatic Hidden-Web Table Interpretation by Sibling Page Comparison. ER 2007: 566-581 - 2006
- [c3]Cui Tao, Yihong Ding, Deryle W. Lonsdale:
Automatic Creation of Web Services from Extraction Ontologies. ER (Workshops) 2006: 415-424 - [c2]Cui Tao:
Toward Making Online Biological Data Machine Understandable. ISWC 2006: 992-993 - 2005
- [j2]David W. Embley, Cui Tao, Stephen W. Liddle:
Automating the extraction of data from HTML tables with unknown structure. Data Knowl. Eng. 54(1): 3-28 (2005) - 2003
- [j1]Cui Tao, Taiyi Zhang:
Speaker-independent speech recognition based on fast neural network. Int. J. Artif. Intell. Tools 12(4): 481-487 (2003) - 2002
- [c1]David W. Embley, Cui Tao, Stephen W. Liddle:
Automatically Extracting Ontologically Specified Data from HTML Tables of Unknown Structure. ER 2002: 322-337
Coauthor Index
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