Publications & Presentations by Year

Publications by Types / Publications by Topics         [Google Scholar] [DBLP] [NCBI Bibliography] [arXiv] 

Manuscripts Under Review 

1. Navya Martin Kollapally, James Geller, Vipina Kuttichi Keloth, Zhe He, Julia Xu. Ontology Enrichment using a Large Language Model: Applying Lexical, Semantic, and Knowledge Network-Based Similarity for Concept Replacement. Submitted to the Journal of Biomedical Informatics.

2. Sivaraman Rajaganapathy, Shaika Chowdhury, Vincent Buchner, Zhe He, Xiaoqian Jiang, Ping Yang, James R Cerhan, Nansu Zong. Synoptic Reporting by Summarizing Cancer Pathology Reports using Large Language Models. Submitted to the Journal of the American Medical Informatics Association.

3. Forhan Bin Emdad, Balu Bhasuran, Gregor Stiglic, Zhe He. Evaluating AI Reporting Guideline Adherence of Medical AI Research Using Large Language Model-based Systems. To be submitted. 

4. Yuanying Pang, Ankita Singh, Shayok Chakraborty, Neil Charness, Walter R. Boot, Zhe He. Predicting Adherence to Gamified Cognitive Training Using Early Phase Game Performance Data: Towards a Just-In-Time Adherence Promotion Strategy. Submitted to PLOS ONE.

5. Mia Liza A. Lustria, Obianuju Aliche, and Zhe He. Enhancing Patient Engagement and Understanding: Is Providing Direct Access to Laboratory Results through Patient Portals Adequate? Submitted to the Journal of the American Medical Informatics Association.

6. Neelufar Payrovnaziri, Jonathan H. Chen, Karim Hanna, Benjamin Glicksberg, and Zhe He. Interpretable Deep Learning Model Based on Longitudinal and Snapshot EHR Data for Short-Term All-Cause Mortality Prediction of ICU Patients with Cardiovascular Diseases. To be submitted to Journal of Biomedical Informatics.

2024 (5 journal papers; 2 conference papers; 1 podium presentation)

1. Weisi Liu, Zhe He, Xiaolei Huang, Time Matters: Examine Temporal Effects on Biomedical Language Models. AMIA 2024 Annual Symposium. In press.

2. Wenshan Han, Balu Bhasuran, Victorine Muse, Søren Brunak, Lifeng Lin, Karim Hanna, Yu Huang, Jiang Bian, Zhe He.  Assessing the Seasonality of Lab Tests Among Patients with Alzheimer's Disease and Related Dementias in OneFlorida Data Trust. AMIA 2024 Annual Symposium. In press. [preprint on medRxiv]

3. Wenshan Han, Zheng Wang,  Mengli Xiao, Zhe He, Haitao Chu, Lifeng Lin. Tipping point analyses for the between-arm correlation in an arm-based evidence synthesis. BMC Medical Research Methodology. 2024. In press.

4. Ankita Singh, Shayok Chakraborty, Zhe He, Yuanying Pang, Shenghao Zhang, Ronast Subedi, Mia Liza A. Lustria, Neil Charness, Walter R. Boot. Predicting Adherence to Computer-based Cognitive Training Programs among Older Adults: Study of Domain Adaptation and Deep Learning. JMIR Aging. 2024. In press.

5. Shaika Chowdhury, Yongbin Chen, Pengyang Li, Sivaraman Rajaganapathy, Andrew Wen, Xiao Ma, Qiying Dai, Yue Yu, Sunyang Fu, Xiaoqian Jiang, Zhe He, Sunghwan Sohn, Xiaoke Liu, Suzette J Bielinski, Alanna Chamberlain, James Cerhan, Nansu Zong. Stratifying Heart Failure Patients with Graph Neural Network and Transformer using EHR to Optimize Drug Response Prediction. Journal of the American Medical Informatics Association.  2024. ocae137 [Link]

6. Zhe He, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu. Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of Medical Internet Research. 2024;26:e56655. doi: 10.2196/56655. PMID: 38630520 [Link]

7. Shenghao Zhang,  Michael Dieciuc, Andrew Dilanchian, Mia Liza A. Lustria, Dawn Carr, Neil Charness, Zhe He, Walter Boot. Adherence Promotion with Tailored Motivational Messages: Proof of Concept and Message Preferences in Older Adults. Gerontology and Geriatric Medicine.  In press. [PMC]

8. He Z, Bhasuran B, Jin Q, Tian S, Hanna K, Lu Z, Using Informatics and Generative AI to Support Older Adults’ Understanding of Lab Test Results. Presented at “East Meets West: Application of AI to Support Healthy Aging and Effective Care in Diverse Cultures” symposium of the Gerontological Society of America (GSA) 2024 Annual Scientific Meeting (GSA 2024), November 13-16, 2024, Seattle, WA.

2023 (6 journal papers; 10 conference papers; 3 podium presentations)

1. Shubo Tian, Pengfei Yin, Hansi Zhang, Arslan Erdengasileng, Jiang Bian and Zhe He. Parsing Clinical Trial Eligibility Criteria for Cohort Query by a Multi-Input Multi-Output Sequence Labeling Model.  2023 IEEE International Conference of Bioinformatics and Biomedicine (BIBM 2023). December 5-8, 2023. Istanbul, Turkey.  2023. pp. 4426-4430.  DOI: 10.1109/BIBM58861.2023.10385876 [medRxiv] [Link]

2. Alex Moerschbacher and Zhe He. Building Prediction Models for 30-Day Readmissions Among ICU Patients Using Both Structured and Unstructured Data in Electronic Health Records. 2023 IEEE International Conference of Bioinformatics and Biomedicine (BIBM 2023). December 5-8, 2023. Istanbul, Turkey.  pp. 4368-4373. DOI: 10.1109/BIBM58861.2023.10385612 [medRxiv] [Link]

3. Neel Jitesh Bhate, Ansh Mittal, Zhe He, Xiao Luo. Zero-shot Learning with Minimum Instruction to Extract Social Determinants and Family History from Clinical Notes using GPT Model. 2023 IEEE International Conference on Big Data (IEEE Big Data 2023). 2023. pp. 1476-1480, doi: 10.1109/BigData59044.2023.10386811. [Link]

4. Mohammad Ishtiaque Rahman, Forhan Bin Emdad, Chashi Mahiul Islam, and Zhe He. Uncovering the Interplay of Demographics and Healthcare Provider Availability on CMS HCC Risk Scores for Disabled Beneficiaries. The 11th edition of the International Conference on e-Health and Bioengineering (BHE 2023). IFMBE Proceedings Series. In press.

5. Lynette Hammond Gerido, Kenneth Resnicow, Elena Marinez Stoffel, Robert Cook-Deegan, Melissa Cline, Amy Coffin, Jill Holdren, Mary Anderlik Majumder, Zhe He. Big Advocacy, Little Recognition: The Hidden Work of Black Patients in Precision Medicine. Journal of Community Genetics. 2023. [Link]

6. Zhe He, Rui Zhang, Gayo Diallo, Zhengxing Huang, and Benjamin S. Glicksberg. Editorial: Explainable artificial intelligence for critical healthcare applications. Frontiers in Artificial Intelligence. 6:1282800. doi: 10.3389/frai.2023.1282800 [Link]

7. Qizhang Feng, Jiayi Yuan, Forhan Bin Emdad, Karim Hanna, Xia Hu, and Zhe He. Can Attention Be Used to Explain EHR-Based Mortality Prediction Tasks: A Case Study on Hemorrhagic Stroke. The 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2023). September 2023. Houston, TX. pp. 1-6. DOI: https://doi.org/10.1145/3584371.3613002 [Link]

8. Zhe He, Shubo Tian, Arslan Erdengsileng, Karim Hanna, Yang Gong, Xiao Luo, Zhan Zhang, Mia Liza A. Lustria. Annotation and Information Extraction of Consumer-Friendly Health Articles for Enhancing Laboratory Test Reporting. AMIA 2023 Annual Symposium. 2024 Jan 11;2023:407-416. PMID: 38222337; PMCID: PMC10785897. [Link]

9. Gregor Stiglic, Lucija Gosak, Primož Kocbek, Leon Kopitar, Prithwish Chakraborty, Pablo Meyer, Zhe He, and Jiang Bian. Improving Primary Healthcare Workflow Using Extreme Summarization of Scientific Literature Based on Generative AI. Accepted by KDD 2023 Workshop on Applied Data Science for Healthcare (KDD DSHealth 2023), 

10. Zhe He, Emily Pfaff, Serena Jingchuan Guo, Yi Guo, Yonghui Wu, Cui Tao, Gregor Stiglic, Jiang Bian. Enriching Real-world Data with Social Determinants of Health for Health Outcomes and Health Equity: Successes, Challenges, and Opportunities. IMIA Yearbook in Medical Informatics. 2023. 32(1):253-263. doi: 10.1055/s-0043-1768732. PMID: 38147867. PMCID: PMC10751148 [Link]

11. Michael O. Killian†, Shubo Tian†, Aiwen Xing, Dana Hughes, Dipankar Gupta, Xiaoyu Wang, and Zhe He†. Prediction of Outcomes After Heart Transplantation in Pediatric Patients Using National Registry Data: Evaluation of Machine Learning Approaches. JMIR Cardio. 2023;7:e45352. DOI: 10.2196/45352. PMID: 37338974 [Link] [PubMed]

12. Julia L Sheffler, Dimitris Kiosses, Zhe He, Bahram H Arjmandi, Neda S Akhavan, Kamelia Klejc, Sylvie Naar. Improving adherence to a Mediterranean ketogenic nutrition program for high-risk older adults: A pilot randomized trial. Nutrients. 2023. 15(10), 2329 [Link]

13. Yuanying Pang, Ankita Singh, Shayok Chakraborty, Neil Charness, Walter R. Boot, and Zhe He. Using Game Performance Data to Predict Adherence to Gamified Cognitive Training. The 7th International Workshop on Semantics-Powered Health Data Analytics (SEPDA 2023). June 12-15, 2023. Portoroz, Slovenia. In press.

14. Xiaoyu Wang,* Dipankar Gupta, Michael Killian, and Zhe He. Benchmarking Transformer-Based Models for Identifying Social Determinants of Health in Clinical Notes. 2023 the 11th IEEE International Conference on Healthcare Informatics (ICHI 2023).  2023 Jun;2023:570-574. doi: 10.1109/ichi57859.2023.00102. Epub 2023 Dec 11. PMID: 38239824; PMCID: PMC10795706.

15. Zhe He, Michael Dieciuc, Dawn Carr, Shayok Chakraborty, Ankita Singh, Ibukun E. Fowe, Shenghao Zhang, Mia Liza A. Lustria, Antonio Terracciano, Neil Charness, Walter R. Boot. New Opportunities for the Early Detection and Treatment of Cognitive Decline: Adherence Challenges and the Promise of Smart and Person-Centered Technologies. BMC Digital Health. 2023; 1(1):1-9. [Link]

16. Forhan Bin Emdad*, Shubo Tian*, Esha Nandy, Karim Hanna, and Zhe He. Towards Interpretable Multimodal Predictive Models for Early Mortality Prediction of Hemorrhagic Stroke Patients. AMIA 2023 Informatics Summit.  2023; 2023: 128–137. PMID: 37350906. PMCID: PMC10283097. [Link]

17. Zhe He, Shubo Tian, Arslan Erdengasileng, Mia Liza A. Lustria. Towards Semi-Automated Construction of Laboratory Test Result Comprehension Knowledgebase for a Patient-Facing Application. AMIA 2023 Informatics Summit, Seattle, WA. March 2023 (Podium presentation)

18. Michael Killian, Shubo Tian, Aiwen Xing, Diana Huges, Dipankar Gupta, Zhe He. Predicting Health Outcomes Using Machine Learning in Pediatric Heart Transplantation Using UNOS Data. The 43th Annual Meeting & Scientific Sessions of the International Society for Heart and Lung Transplantation (ISHLT 2023), Denver, CO, USA. April 2023. (Podium presentation)

19. Michael Killian, Shubo Tian, Aiwen Xing, Diana Huges, Dipankar Gupta, Zhe He. Predicting Health Outcomes through Machine Learning in Pediatric Heart Transplantation: Use of National Data from the United Network for Organ Sharing. The 27th Annual Conference of the Society for Social Work and Research (SSWR), Society for Social Work and Research, Phoenix, AZ. January 2023. (Podium presentation)

2022 (6 journal papers, 3 conference papers, 2 podium presentations)

1. Austin Mast, Shubo Tian, Zhe He, E Krimmel, M Buckley, S Gome, A Hennessey, A Horn, O Howell. Demonstration of the use of computational linguistics and machine learning to identify phenological anomalies described in the world's biodiversity specimen records. The 6th Annual Digital Data Conference, iDigBio, Virtual. May 2022. (Podium Presentation)

2. Mia Liza A. Lustria, Michael Dieciuc, Andrew Dilanchian, Shenghao Zhang, Walter R. Boot, Neil Charness, Dawn Carr, Zhe He, Shayok Chakraborty, Antonio Terracciano. I got training on the brain": Designing Messages to Improve Seniors' Adherence to Cognitive Assessment and Training Programs. 2022 Kentucky Conference on Health Communication, Department of Communication, University of Kentucky, Lexington, KY. April 2022. (Top Poster Award)  

3. Ankita Singh, Shayok Chakraborty, Zhe He, Shubo Tian, Shenghao Zhang, Mia Liza A. Lustria, Neil Charness, Nelson A Roque, Erin R Harrell, Walter R Boot. Deep Learning-based Predictions of Older Adults' Adherence to Cognitive Training to Support Training Efficacy. Frontiers in Psychology. 2022. 13:980778. doi: 10.3389/fpsyg.2022.980778. (Impact Factor: 4.232) [Link]

4. Arslan Erdengasileng, Shubo Tian, Sara Green, Sylvie Naar, Zhe He. Using Twitter Data Analysis to Understand the Perceptions, Awareness, and Barriers to the Wide Use of Pre-Exposure Prophylaxis in the United States. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2022). 2022 Dec. Las Vegas, NV.  pp. 3000-3007. [Link]

5. Zhe He, Shubo Tian, Ankita Singh, Shayok Chakraborty, Shenghao Zhang, Mia Liza A. Lustria, Neil Charness, Nelson Roque, Erin Harrell, Walter R. Boot. A Machine-Learning Based Approach for Predicting Older Adults’ Adherence to Technology-Based Cognitive Training. Information Processing and Management. 2022;  59(5): 103034. (Impact Factor: 7.47) [Free Access Link]

6. Sicheng Zhou, Dalton Schutte, Aiwen Xing, Jiyang Chen, Julian Wolfson, Zhe He, Fang Yu, Rui Zhang. Identification of Dietary Supplement Use from Electronic Health Records Using Transformer-based Language Models. BMC Medical Informatics and Decision Making. In press. (Impact Factor 3.298)

7. Laura A. Barrett, Aiwen Xing, Julia Sheffler, Elizabeth Steidley, Terrance Adam, Rui Zhang, and Zhe He. Assessing the use of prescription drugs and dietary supplements in obese respondents in the National Health and Nutrition Examination Survey. PLOS One.  2022; 17(6): e0269241. [Link]

8. Akhil Shiju and Zhe He. Classifying Drug Ratings Using User Reviews with Transformer-Based Language Models. The 10th IEEE International Conference on Healthcare Informatics (ICHI 2022). pp. 163-169. [Link]

9. Dawn Carr, Shubo Tian, Zhe He, Shayok Chakroborty, Michael Dieciuc, Nicolas Gray, Maedeh Agharazidermani, Mia Liza Lustria, Andrew Dilanchian, Shenghao Zhang, Neil Charness, Antonio Terracciano, Walter R. Boot, Motivation to Engage in Aging Research: Are There Typologies and Predictors? Gerontologist. 2022; 62(10): 1466-1476. DOI: 10.1093/geront/gnac035.. (Impact factor: 5.422) [Link]

10. Zhe He, Shubo Tian, Arslan Erdengasileng, Neil Charness, Jiang Bian. Temporal Subtyping of Alzheimer’s Disease Using Medical Conditions Preceding Alzheimer’s Disease Onset in Electronic Health Records. AMIA 2022 Informatics Summit. 2022; 2022: 226-235. PMID: 35854753. PMCID: PMC92851183 [Link]

11. Yu Lu, Laura A. Barrett, Rebecca Lin, Muhammad Amith, Cui Tao, and Zhe He. Understanding Information Needs and Barriers to Accessing Health Information Across All Stages of Pregnancy: A Systematic Review. JMIR Pediatrics and Parenting. 2022;5(1):e32235. doi: 10.2196/32235.  PMID: 35188477  [JMIR]

2021 (5 journal papers, 5 conference papers, 1 podium presentation)

1. Zhan Zhang, Lukas Kmoth, Xiao Luo, and Zhe He. User-Centered System Design for Communicating Clinical Laboratory Test Results: Design and Evaluation Study.  JMIR Human Factors. 2021; 8(4): e26017. (Acceptance rate: 25%) [JMIR]

2. Pengfei Yin, Hansi Zhang, Xing He, Matthew Diller, Qian Li, Shubo Tian, Arslan Erdengasileng, Zhe He, Cui Tao, and Jiang Bian. Toward Formal Computable Representation of Clinical Trial Eligibility Criteria for Alzheimer's Disease. The 6th International Workshop on Semantics-Powered Health Data Analytics (SEPDA 2021). November 3-5, 2021. Virtual.  In press.

3. Shubo Tian, Arslan Erdengasileng, Xi Yang, Yi Guo, Yonghui Wu, Jingfeng Zhang, Jiang Bian, and Zhe He. Transformer-Based Named Entity Recognition for Parsing Clinical Trial Eligibility Criteria. The 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB 2021).  Virtual. August 1-4, 2021. pp. 1-6. https://doi.org/10.1145/3459930.3469560 [Link]

4. Sicheng Zhou, Dalton Schutte, Aiwen Xing, Jiyang Chen, Julian Wolfson, Zhe He, Fang Yu and Rui Zhang. Identification of Dietary Supplement Use from  Electronic Health Records Using Transformer-based  Language Models. 2021 IEEE International Conference on Healthcare Informatics (ICHI 2021), 2021. pp. 513-514, doi: 10.1109/ICHI52183.2021.00096. [Link]

5. Zhe He, Arslan Erdengarsileng, Aiwen Xing, Xiao Luo, Neil Charness, Jiang Bian. How the clinical research community responded to the COVID-19 pandemic: An analysis of the COVID-19 clinical studies in ClinicalTrials.gov. JAMIA Open. 2021; 4(2): ooab032. PMID: 34056559. PMCID: PMC8083215 [medRxiv] [JAMIA] [PMC]

6. Zhaoyi Chen, Hansi Zhang, Yi Guo, Thomas J George Jr, Mattia Prosperi, William Hogan, Zhe He, Elizabeth Shenkman, Fei Wang, and Jiang Bian. Exploring the feasibility of using real-world data from a large clinical data research network to simulate clinical trials of Alzheimer’s Disease. npj Digital Medicine.  2021; 4(1): 84. PMID: 33990663. PMCID: PMC8121837 (Impact factor: 11.653) [Link] [PMC]

7. Michael O. Killian, Seyedeh Neelufar Payrovnaziri, Dipankar Gupta, Dev Desai, and Zhe He. Machine learning-based prediction of re-hospitalization in pediatric organ transplantation recipients. JAMIA Open. 4(1):  1-10. [Link] (Erratum for the deep learning model performance pending)

8. Yu Lu, Katherine Min, Zhan Zhang,  Xiao Luo, and Zhe He. Pregnancy-Related Information Seeking in Online Forums: A Qualitative Study. iConference 2021. March 28-31, 2021. Beijing, China. pp. 18-36. (Acceptance rate: 31%; 32/103 full paper submissions) [Link]

9. *Seyedeh Neelufar Payrovnaziri, Aiwen Xing, Shaeke Salman, Xiuwen Liu, Jiang Bian, and Zhe He. Assessing the Impact of Imputation on the Interpretations of Prediction Models: A Case Study on Mortality Prediction for Patients with Acute Myocardial Infarction. AMIA 2021 Informatics Summit. Virtual. March 22-25, 2021. pp. 465-474. [medRxiv] [AMIA]

10. Zhe He, Arslan Erdenasileng, Xiang Tang, Yiqi Xu, Qian Li, Neil Charness, William Hogan, Thomas J. George, Yi Guo, Jiang Bian. ctGATE: A Clinical Trial Generalizability Assessment Toolbox. AMIA 2021 Informatics Summit. (Podium Presentation)

11. Juan Xie*, Zhe He, Gary Burnett, and Ying Cheng. How do mothers exchange parenting-related information in online communities? A meta-synthesis.  Computers in Human Behavior. 2021; 115: 105531 (SSCI, Impact Factor: 6.829) [Free Access Link (till Jan 8, 2021)]

2020 (10 journal papers, 6 conference papers)

1. Zhan Zhang, Daniel Citardi, Aiwen Xing, Xiao Luo, Yu Lu, and Zhe He. Patient Challenges and Needs in Comprehending Lab Test Results: A Mixed-Methods Study. Journal of Medical Internet Research. 2020; 22(12). e18725 (Impact Factor: 5.43)  [Link]

2. Xiao Luo, Haoran Ding, Matthew Tang, Priyanka Gandhi, Zhan Zhang, and Zhe He. Attention Mechanism with BERT for Content Annotation and Categorization of Pregnancy-Related Questions on a Community Q&A Site. 2020 IEEE International Conference on Bioinformatics and Biomedicine. 2020: 1077-1081. PMCID: PMC7929090 [PMC]

3. Zhe He,  Cui Tao, Jiang Bian,  and Rui Zhang.  Selected articles from the Fourth International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019). BMC Medical Informatics and Decision Making. 2020. 20 (Suppl 4): 315. [Link] (Editorial of the journal supplement)

4. Jinchan Qu, Albert Steppi, Dongrui Zhong, Jie Hao, Jian Wang, Pei-Yau Lung, Tingting Zhao, Zhe He , and Jinfeng Zhang. Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. BMC Genomics. 2020; 21; 773. PMID: 33167858. PMCID: PMC7654050. (SCIE, Impact Factor 3.594) [Link]

5. Nur Hafieza Ismail, Mengnan Du, Ninghao Liu, Xia Hu, and Zhe He. A Deep Learning Approach for Identifying Cancer Survivors Living with Post-Traumatic Stress Disorder on Twitter. BMC Medical Informatics and Decision Making. 2020; 20 (suppl 4): 254. (SCIE, Impact Factor 2.276) [Link]

6. Juan Xie, Shi Xie, Ying Cheng, Zhe He. Beliefs and Information Seeking in Patients With Cancer in Southwest China: Survey Study. JMIR Cancer. 2020;6(2):e16138. DOI: 10.2196/16138. PMID: 32821061 [Link]

7. Anusha Bompelli, Jianfu Li, Yiqi Xu, Nan Wang, Terrance Adam, Zhe He, and Rui Zhang. Deep Learning Approaches to Extract Eligibility Criteria on Dietary Supplements Clinical Trials. AMIA 2020 Annual Symposium.  November 14-18, 2020. Virtual. pp. 243-252. PMID: 33936396. PMCID: PMC8075443 [medRxiv] [PMC]

8. Qian Li, Yi Guo, Zhe He, Hansi Zhang, Thomas J. George, and Jiang Bian. Using Real-World Data to Rationalize Clinical Trials Eligibility Criteria Design:  a Case Study of Alzheimer’s Disease Trials. AMIA 2020 Annual Symposium.  November 14-18, 2020. Virtual. pp. 717-726. PMID: 33936446. PMCID: PMC8075542. (1st Place of the 7th AMIA Knowledge Discovery and Data Mining Student Innovation Award) [medRxiv] [PMC]

9. Yu Lu, Xiao Luo, Zhan Zhang, and Zhe He. Retrieving Lab Test Related Questions from Social QA Sites By Combining Shallow Features and Deep Representations. AMIA 2020 Annual Symposium.  November 14-18, 2020. Virtual. pp. 717-726. PMID: 33936453. PMCID: PMC8075538. [medRxiv] [PMC]

10. Ling Zheng†, Zhe He†, Duo Wei, Vipina Keloth, Jung-Wei Fan, Luke Lindemann, Xinxin Zhu, James Cimino, and Yehoshua Perl. A review of auditing techniques for the Unified Medical Language System. Journal of the American Medical Informatics Association. 2020; 27(10): 1625-1638. PMID: 32766692. PMCID: PMC7566540 (SCI, Impact Factor: 4.497, Ling Zheng and Zhe He are equal-contribution first authors) [Free Access Link] [PMC]

11. *Seyedeh Neelufar Payrovnaziri, Zhaoyi Chen, Pablo Rengifo-Moreno, Tim Miller, Jiang Bian, Jonathan H. Chen, Xiuwen Liu, and Zhe He. Explainable artificial intelligence models using real-world electronic health record Data: a systematic scoping review. Journal of the American Medical Informatics Association. 2020; 27(7): 1173-1185. PMID: 32417928.  (SCI, Impact Factor: 4.497) [Free Access Link] [PubMed]

12. Shaeke Salman†, *Seyedeh Neelufar Payrovnaziri†, Xiuwen Liu, Pablo Rengifo-Moreno, and Zhe He. DeepConsensus: Consensus-based Interpretable Deep Neural Networks with Application to Mortality Prediction.  2020 International Joint Conference on Neural Networks (IJCNN 2020).  Glasgow, United Kingdom, 2020, pp. 1-8, doi: 10.1109/IJCNN48605.2020.9206678. [Link]

13. *Biyang Yu†, Zhe He†, Aiwen Xing, and Mia Liza Lustria.  An Informatics Framework to Assess Consumer Health Language Complexity Differences: Proof-of-Concept Study. Journal of Medical Internet Research. 2020;22(5):e16795. (Impact Factor: 5.43)  [Link]

14. Zhe He, Xiang Tang, Kelsa Bartley, Xi Yang, Yi Guo, Thomas J. George, Neil Charness, William Hogan, Jiang Bian. Clinical Trial Generalizability Assessment in the Big Data Era: A Review. Clinical and Translational Science. PMID: 32058639. 2020. DOI: 10.1111/cts.12764. 2020; 13(4): 675-684 (Impact Factor: 4.689) [Link] [PubMed] [Dataset Publication] [Commentary]

15. Zhe He, Laura A. Barrett, Rubina F. Rizvi, Xiang Tang, Seyedeh Neelufar Payrovnaziri, and Rui Zhang. Assessing the Use and Perception of Dietary Supplements Among Obese Patients with National Health and Nutrition Examination Survey. AMIA 2020 Informatics Summit. 2020; 231-40. PMID: 32477642 [Link] [PubMed] [PDF]

16. Zhe He, Wallace M Douglas, Michael Perlis, Andrea Barnes, Xiang Tang, Girardin Jean-Louis, and Natasha Williams. Reporting results in U.S. clinical trials for obstructive sleep apnea and insomnia: how transparent are they?  Sleep Health.  2020; 6(4): 529-533. doi: 10.1016/j.sleh.2019.11.009. PMID: 32179065 [PubMed] [Link]

2019 (1 edited book, 1 book chapter, 6 journal papers, 9 conference papers)

1. *Canlin Zhang†, *Daniel Biś†, Xiuwen Liu, and Zhe He. Biomedical Word Sense Disambiguation with Bidirectional Long Short-Term Memory and Attention-based Neural Networks. BMC Bioinformatics. 2019; 20: 502. [Link]

2. Lynette Hammond Gerido , Xiang Tang , Brittany Ernst , Aisha Langford, and Zhe He. Patient Engagement in Medical Research among Older Adults: Analysis of the Health Information National Trends Survey. Journal of Medical Internet Research. 2019;21(10):e16222. PMID: 31663860. PMCID: PMC6914241. [Link] [PubMed] [PMC]

3. Nur Hafieza Ismail, Ninghao Liu, Mengnan Du, Zhe He, and Xia Ben Hu. Using Deep Neural Network to Identify Cancer Survivors Living with Post-Traumatic Stress Disorder on Social Media. The 4th International Workshop on Semantics-Powered Data Mining and Analytics (SEPDA 2019). October 15, 2019. Aukland, New Zealand. CEUR WS Proceedings: 2417. pp. 48-52.  [Link]

4. Qian Li†, Zhe He†, Yi Guo†, Hansi Zhang, Thomas J George Jr, William Hogan, Neil Charness, Jiang Bian. Assessing the Validity of a a priori Patient-Trial Generalizability Score using Real-world Data from a Large Clinical Data Research Network: A Colorectal Cancer Clinical Trial Case Study. AMIA 2019 Annual Symposium.  November 14-18, 2019. Washington DC. pp.1101-1110. PMID: 32308907. PMCID: PMC7153072 (†:Co-first authors) (2nd Place of the Student Paper Competition) [PMC]

5. Nur Hafieza Ismail, Mengnan Du, Diego Martinez, and Zhe He. Multivariate Multi-step Deep Learning Time Series Approach in Forecasting Parkinson's Disease Future Severity Progression. The 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB 2019).  Niagara Falls, NY. pp. 383-389. (Acceptance rate: 39%) [Link]

6. Jiang Bian, Yi Guo, Zhe He, and Xia Hu. Social Web and Health Research - Benefits, Limitations and Best Practice. Springer International Publishing AG. 2019. Print ISBN: 978-3-030-14713-6. Online ISBN: 978-3-030-14714-3. DOI: https://doi.org/10.1007/978-3-030-14714-3 [Link]

7. Zhe He. Understanding and Bridging the Language and Terminology Gap between Health Professionals and Consumers Using Social Media. Social Web and Health Research: Benefits, Limitations, and Best Practices. In: Bian J., Guo Y., He Z., Hu X. (eds) Social Web and Health Research. Springer, Cham. 2019. pp. 103-121. DOI: 10.1007/978-3-030-14714-3_6. [Link]

8. Zhe He,  Jiang Bian, Cui Tao, and Rui Zhang.  Selected articles from the Third International Workshop on Semantics-Powered Data Analytics (SEPDA 2018). BMC Medical Informatics and Decision Making. 2019. 19 (Suppl 4):148.  DOI:  10.1186/s12911-019-0855-3. [Link] (Editorial of the journal supplement)

9. Xing He, Rui Zhang, Rubina 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. BMC Medical Informatics and Decision Making. 2019; 19 (Suppl 4) DOI: 10.1186/s12911-019-0857-1 [Link]

10. Seyedeh Neelufar Payrovnaziri, Laura A. Barrett, Daniel Bis, Jiang Bian, and Zhe He. Enhancing Prediction Models for One-Year Mortality in Patients with Acute Myocardial Infarction and Post Myocardial Infarction Syndrome. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:273-277. doi: 10.3233/SHTI190226. PMID: 31437928. PMCID: PMC6785831 [IOS Press] [PMC]

11.  Zhan Zhang, Yu Lu, Yubo Kou, Danny Wu, Jina Huh-Yoo, and Zhe He. Understanding Patient Information Needs about their Clinical Laboratory Results: A Study of Social Q&A Site. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:1403-1407. doi: 10.3233/SHTI190458. PMID: 31438157. [IOS Press]

12. Rubina F. Rizvi, Yefeng Wang, Thao Nguyen, Jake Vasilakes, Zhe He, and Rui Zhang. Analyzing Social Media Data to Understand Consumers’ Information Needs on Dietary Supplements. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:323-327. doi: 10.3233/SHTI190236.  PMID: 31437938.  PMCID: PMC6792048 [IOS Press] [PMC]

13. Francisco Modave, Yunpeng Zhao, Janice Krieger, Zhe He, Yi Guo, Jiang Bian. Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:1293-1297. doi: 10.3233/SHTI190435. PubMed PMID: 31438134. [Preprint] [IOS Press]

14. Vipina K. Keloth, Zhe He, Gai Elhanan, and James Geller. Alternative Classification of Identical Concepts in Different Terminologies: Different Ways to View the  World. Journal of Biomedical Informatics. 2019; 94. 103193. PMID: 31048072. PMCID: PMC7050413. DOI:  10.1016/j.jbi.2019.103193. [PubMed] [Link] [PMC]

15. Pei-Yau Lung, Zhe He, Tingting Zhao, Disa Yu, and Jinfeng Zhang. Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering. Database: The Journal of Biological Databases and Curation. 2019. 2019:1-8. PMID: 30624652.  [Link]

16. Zhe He, Rubina F. Rizvi, Fan Yang, Terrence J. Adam, and Rui Zhang. Comparing the Study Populations in Dietary Supplement and Drug Clinical Trials for Metabolic Syndrome Related Disorders. AMIA 2019 Informatics Summit. March 25-28, 2019. San Francisco, CA. pp. 799-808. PMID: 31259037. PMCID: PMC6568097 [AMIA]  [PMC]

17. *Laura A. Barrett, *Seyedeh Neelufar Payrovnaziri, Jiang Bian, and Zhe He. Building Computational Models to Predict One-Year Mortality in ICU Patients with Acute Myocardial Infarction and Post Myocardial Infarction Syndrome. AMIA 2019 Informatics Summit. March 25-28, 2019. San Francisco, CA. pp. 407-416. PMID: 31258994. PMCID: PMC6568097. (Finalist of the Student Paper Award) [Preprint] [AMIA] [PMC] (Media Report)

2018 (7 journal papers, 5 conference papers)

1. Zhe He, Vipina Kuttichi Keloth, Yan Chen, and James Geller. Extended Analysis of Topological-Pattern-Based Ontology Enrichment. Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. December 3-6, 2018, Madrid, Spain. pp.1641-1648. PMID: 30854243. PMCID: PMC6402505 [Link] [PMC]

2. Xing He, Rui Zhang, Rubina Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, and Jiang Bian. Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine. December 3-6, 2018, Madrid, Spain. pp. 1649-1652 [Link]

3. Tianyong Hao,  Raymond Wong, Zhe He, Haoran Xie, Tak-Lam Wong, and Fu Lee Wang. Natural Language Processing Empowered Mobile Computing. Wireless Communication and Mobile Computing. 2018. 2018: 1-2. DOI:  10.1155/2018/9130545. (Editorial of the special issue) [Link]

4. *Daniel Biś, *Canlin Zhang, Xiuwen Liu, and Zhe He. Layered Multistep Bidirectional Long Short-Term Memory Networks for Biomedical Word Sense Disambiguation. Proceedings of 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018). [Link] December 3-6, 2018, Madrid, Spain. pp. 313-320. (Acceptance Rate of Regular Paper: 19.6%) [Link]

5. Hansi Zhang, Zhe He, Xing He, Yi Guo, David R. Nelson, François Modave, Yonghui Wu, William Hogan, and Jiang Bian. Computable Eligibility Criteria through Ontology-Driven Data Access: A Case Study of Hepatitis C Virus Trials. Proceedings of AMIA 2018 Annual Symposium. November 3-8, 2018. San Francisco, CA. pp. 1601-1610.  (Finalist of the Student Paper Award, 8 out of 47 student papers were selected)

6. Vipina Kuttichi Keloth, Zhe He, Yan Chen, and James Geller. Leveraging Horizontal Density Differences Between Ontologies to Identify Missing Child Concepts: A Proof of Concept. Proceedings of AMIA 2018 Annual Symposium.  November 3-8, 2018. San Francisco, CA. pp. 644-653. [PDF]

7. 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 and Decision Making. 2018. 18 (Suppl 2) :56.  DOI: 10.1186/s12911-018-0624-8. PMID: 30066636. [Link] [PubMed] (Editorial of the journal supplement)

8. *Zhiwei Chen†, Zhe He†, Xiuwen Liu, and Jiang Bian. Evaluating semantic relations in neural word embeddings using biomedical and general domain knowledge bases. BMC Medical Informatics and Decision Making. 2018. 18 (Suppl 2) :65. DOI: 10.1186/s12911-018-0630-x. PMID: 30066651. [Link] [PubMed] [Correction Article] (†:Co-first authors)

9. Juan Antonio Lossio-Ventura, William Hogan, François Modave, Yi Guo, Zhe He, Xi Yang, Hansi Zhang, and Jiang Bian. OC-2-KB: Integration crowdsourcing into an obesity and cancer knowledge base curation system. BMC Medical Informatics and Decision Making. 2018. 2018. 18 (Suppl 2) :55. DOI: 10.1186/s12911-018-0635-5. PMID: 30066655. [Link] [PubMed]

10. Huanying Gu, Zhe He, Duo Wei, Gai Elhanan and Yan Chen. Validating UMLS Semantic Type Assignments Using SNOMED CT Semantic Tags. Methods of Information in Medicine. 2018; 57(1): 43-53. PMID: 29621830. [Link] [PubMed] [PMC]

11. Zhe He†, Jiang Bian†, Henry Carretta, Jiwon Lee, William Hogan, Elizabeth Shenkman, and Neil Charness.  Prevalence of Multiple Chronic Conditions Among Older Adults in Florida and the United States: Comparative Analysis of the OneFlorida Data Trust and National Inpatient Sample. Journal of Medical Internet Research. 2018; 20(4): e137. PMID: 29650502. PMCID: PMC5920146. (SCIE, †: equal-contribution first authors) [Link] [PubMed] [PMC]

12. Muhammad F. Amith†, Zhe He†, Jiang Bian, Juan Antonio Lossio-Ventura, and Cui Tao. Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.  Journal of Biomedical Informatics. 2018; 80:1-13. DOI: 10.1016/j.jbi.2018.02.010. PMID: 29462669. PMCID: PMC5882531 (†: equal-contribution first authors) [FSU CCI News] [ScienceDirect] [PubMed] [PMC]

2017 (3 journal papers & 8 conference papers)

1. Jiang Bian, Yunpeng Zhao, Ramzi G Salloum, Yi Guo, Mo Wang, Mattia Prosperi, Hansi Zhang, Xinsong Du, Laura J Ramirez-Diaz, Zhe He, Yuan Sun. Using Social Media Data to Understand the Impact of Promotional Information on Laypeople's Discussions: A Case Study of Lynch syndrome. Journal of Medical Internet Research. 2017;19(12):e414. DOI: 10.2196/jmir.9266. PMID: 29237586. PMCID: PMC5745354. [Link] [PMC]

2. Jinchan Qu, Albert Steppi, Jie Hao, Jian Wang, Pei-Yau Lung, Tinting Zhao, Zhe He and Jinfeng Zhang. Mining protein interactions affected by mutations using a NLP based machine learning approach. Proceedings of BioCreative VI Challenge and Workshop. October 18-20, 2017. Bethesda, MD. pp. 132-135. (Invited to give an oral presentation at BioCreative VI Track 4: Mining protein interactions and mutations for precision medicine) [Link]

3. Pei-Yau Lung, Tingting Zhao, Zhe He and Jinfeng Zhang. Extracting chemical-protein compound interactions from literature. Proceedings of BioCreative VI Challenge and Workshop. October 18-20, 2017. Bethesda, MD. pp. 160-163. (Invited to give an oral presentation at BioCreative VI Track 5: Text mining chemical protein interactions) [Link]

4. Juan Antonio Lossio-Ventura, William Hogan, Francois Modave, Yi Guo, Zhe He, Amanda Hicks, and Jiang Bian. OC-2-KB: A software pipeline to build an evidence-based obesity and cancer knowledge base. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp. 1284-1287. DOI: 10.1109/BIBM.2017.8217845. PMID: 29629236. PMCID: PMC5889048 [IEEE] [PMC]

5. Biyang Yu and Zhe He. Exploratory Textual Analysis of Consumer Health Languages for People Who are Deaf/Hard of Hearing. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp. 1288-1291. DOI: 10.1109/BIBM.2017.8217846 [IEEE]

6. Zhiwei Chen, Zhe He, Xiuwen Liu, and Jiang Bian. An Exploration of Semantic Relations in Neural Word Embeddings Using Extrinsic Knowledge. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp.1246-1251. DOI: 10.1109/BIBM.2017.8217836 [IEEE]

7. Zhe He, Yehoshua Perl, Gai Elhanan, Yan Chen, James Geller, and Jiang Bian. Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). November 13 - 16, 2017. Kansas City, MO. pp. 1262-1269. DOI: 10.1109/BIBM.2017.8217840. PMID: 29375930. PMCID: PMC5786167 [IEEE] [PMC] [PDF]

8. Zhe He*, Cui Tao, Jiang Bian, Michel Dumontier, and William Hogan. Semantics-Powered Healthcare Engineering and Data Analytics. Journal of Healthcare Engineering. 2017. DOI: https://doi.org/10.1155/2017/7983473. PMID: 29214005. PMCID: PMC5682067. (SCIE, Impact Factor: 1.295) [Link] [PubMed] [PMC] (Editorial of the Special Issue)

9. Zhe He, Arturo Gonzalez-Izquierdo, Spiros Denaxas, Andrei Sura, Yi Guo, William R. Hogan, Elizabeth Shenkman, Jiang Bian. Comparing and Contrasting A Priori and A Posteriori Generalizability Assessment of Clinical Trials on Type 2 Diabetes Mellitus. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp. 849-858. PMID: 29854151. PMCID: PMC5977671 (Distinguished Paper Award of AMIA 2017 Annual Symposium; three awards were selected from 105 accepted paper and 266 paper submissions) [Award Certificate] [CCI News] [PMC] 

10. Zhe He, Zhiwei Chen, Sanghee Oh, Jinghui Hou, and Jiang Bian. Enriching consumer health vocabulary through mining a social Q&A site: a similarity-based approach. Journal of Biomedical Informatics. 2017;69:75-85. PMID: 28359728.  [PubMed] [ScienceDirect]

11. Zhe He, Yan Chen, and James Geller. Perceiving the Usefulness of National Cancer Institute Metathesaurus for Enriching NCIt with Topological Patterns. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017). August 21-25, 2017. Hangzhou, China. Studies in Health Technology and Informatics. 2017;245: 863-867. PMID: 29295222. DOI:10.3233/978-1-61499-830-3-863 [IOS] [PubMed][PMC]

2016 (6 journal papers & 8 conference papers)

1. Juan Antonio Lossio-Ventura, William Hogan, François Modave, Amanda Hicks, Yi Guo, Zhe He, and Jiang Bian. Towards an Obesity-Cancer Knowledge Base: Biomedical Entity Identification and Relation Detection. Proceedings of the 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016). December 15-18, 2016. Shenzhen, China. pp. 1081-1088. DOI: 10.1109/BIBM.2016.7822672. PMID:  28503356. PMCID: PMC5426361. [IEEE] [PMC]

2. Min Sook Park†, Zhe He*†, Zhiwei Chen, Sanghee Oh, and Jiang Bian. Consumer's Use of UMLS Concepts on Social Media: Diabetes-Related Textual Data Analysis in Blog and Social Q&A Sites. JMIR Medical Informatics. 2016; 4(4):e41. PMID: 27884812. PMCID: PMC5146325 (†:Co-first authors) [JMIR] [PDF] [PMC] 

3. Zhe He, Zhiwei Chen, and Jiang Bian. Analysis of Temporal Constraints in Qualitative Eligibility Criteria of Cancer Clinical Studies. Proceedings of the 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016). pp. 717-722. PMID: 29263940. PMCID: PMC5733789. DOI: 10.1109/BIBM.2016.7822607. (Acceptance rate: 19%) [IEEE] [PMC]

4. Jiang Bian, Kenji Yoshigoe, Amanda Hicks, Jiawei Yuan, Zhe He, Mengjun Xie, Yi Guo, Mattia Prosperi, François Modave. Mining Twitter to assess the public perception of the "Internet of things". PLoS ONE. 2016;11(7): e0158450. PMID: 27391760. PMCID: PMC4938510  [Link] [PubMed] [PMC]

5. Zhe He, Yan Chen, Sherri de Coronado, Katrina Piskorski, and James Geller. Topological-Pattern-based Recommendation of UMLS Concepts for National Cancer Institute Thesaurus. Proceedings of American Medical Informatics Association 2016 Annual Symposium (AMIA 2016). 618-627. PMID: 28269858. PMCID: PMC5333219 [Talk Slides] [PMC]

6. Zhe He, Zhiwei Chen, Thomas J George, Gloria Lipori, and Jiang Bian. Assessing the Population Representativeness of Colorectal Cancer Treatment Clinical Trials. Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2016). August 16-20, 2016. Orlando, FL. 4 pages. pp.2970-2973. PMID: 28268936 PMCID: PMC5727892. (Acceptance rate for oral presentations: 20%) [IEEE] [PubMed] [PMC]

7. Zhe He and James Geller.  Preliminary Analysis of Difficulty of Importing Pattern-Based Concepts into the National Cancer Institute Thesaurus. Studies in Health Technology and Informatics. 2016. Volume 288: Exploring the Complexity in Health: An Interdisciplinary Systems Approach: 389-393. Medical Informatics Europe 2016 (MIE 2016). PMID: 27577410. [IOS Press] [PubMed] [PMC]

8. Christopher Ochs, Zhe He, Ling Zheng, James Geller, Yehoshua Perl, George Hripcsak, and Mark Musen. Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. Journal of Biomedical Informatics. 2016;61:63-76. PMID: 26988001. PMCID: PMC4893909 (SCI, Impact Factor: 2.950)  [ScienceDirect] [PubMed] [PMC]

9. Zhe He*, Patrick Ryan, Julia Hoxha, Shuang Wang, Simona Carini, Ida Sim, and Chunhua Weng. Multivariate analysis of the population representativeness of related clinical studies. Journal of Biomedical Informatics. 2016;60:66-76. PMID: 26820188.  PMCID: PMC4837055. [ScienceDirect] [PubMed] [PMC]

10. Huanying Gu*, Yan Chen, Zhe He, Michael Halper, and Ling Chen. Quality Assurance of UMLS Semantic Type Assignments Using SNOMED CT Hierarchies. Methods of Information in Medicine. 2016; 55(2):158-165. PMID: 25925776. [Schattauer] [PubMed] [PMC]

11. Zhe He, Neil Charness, Jiang Bian, and William R. Hogan. Assessing the Comorbidity Gap between Clinical Studies and Prevalence in Elderly Patient Populations.  Proceedings of 2016 IEEE International Conference on Biomedical and Health Informatics. February 24-27, 2016. Las Vegas, NV. pp.136-139. PMID: 27738664. [IEEE Xplore] [PMC]

12. Cilia Zayas, Zhe He, Jiawei Yuan, Mildred Maldonado-Molina, William R. Hogan, François Modave, and Jiang Bian. Examining Healthcare Utilization Patterns of Elderly and Mid-Aged Adults in the United States. Proceedings of the 29th International FLAIRS Conference (FLAIRS-29). May 16-18, 2016. Key Largo, FL. pp.361-366. PMID: 27430035. [AAAI] [PMC]

13. Zhe He*, Min Sook Park*, and Zhiwei Chen. UMLS-Based Analysis of Medical Terminology Coverage for Tags in Diabetes-Related Blogs (*: equal contribution). Proceedings of iConference 2016.  March 20-23, 2016. Philadelphia, PA. (Preliminary results paper. Acceptance rate: 30%)  (Runner up of the Most Interesting Preliminary Results Paper Award) [Link]

14. Julia Hoxha, Praveen Chandar, Zhe He, David Hanauer, James J Cimino, Chunhua Weng*. DREAM: Classification Scheme for Dialog Acts in Clinical Research Data Query Mediation. Journal of Biomedical Informatics. 2016;59:89-101. PMID: 26657707. [ScienceDirect] [PubMed]

2015 (2 journal papers & 4 conference papers) 

1. Zhe He, Praveen Chandar, Patrick Ryan, and Chunhua Weng. Simulation-based Evaluation of the Generalizability Index for Study Traits. Proceedings of American Medical Informatics Association 2015 Annual Symposium (AMIA 2015). November 14-18, 2015. San Francisco, CA. pp.594-603. PMID: 26958194 (Distinguished Paper Award of AMIA 2015 Annual Symposium [Official Announcement] [Award Certificate] [News Article]) [PubMed] [PMC] (Clinical Research Informatics 2016 Year in Review)

2. Praveen Chandar, Anil Yaman, Julia Hoxha, Zhe He, and Chunhua Weng. Similarity-based Recommendation of New Concepts to a Terminology. Proceedings of American Medical Informatics Association 2015 Annual Symposium (AMIA 2015). November 14-18, 2015. San Francisco, CA. pp.386-395. PMID: 26958170 [PubMed] [PMC]

3. Zhe He, Shuang Wang, Elhaam Borhanian, and Chunhua Weng. Assessing the Collective Population Representativeness of Type 2 Diabetes Trials by Combining Public Data from ClinicalTrials.gov and NHANES. Proceedings of MEDINFO 2015, August 19-23, 2015, Sao Paulo, Brazil. Studies in Health Technology and Informatics. IOS Press. 2015. 216:569-73. (Student Paper Award Nominee) [PubMed] [PMC] [IOS Press] 

4. Zhe He, and Chunhua Weng. Predicting New Target Conditions for Drug Retesting Using Temporal Patterns in Clinical Trials: A Proof of Concept. Proceedings of American Medical Informatics Association 2015 Joint Summits on Translational Science, March 23 - 27, 2015, San Francisco, CA. pp.445-449. PubMed] [PMC] [Talk Slides] (Student Paper Competition Finalist) 

5. Zhe He*, James Geller, and Yan Chen. A comparative analysis of the density of the SNOMED CT conceptual content for semantic harmonization. Artificial Intelligence in Medicine. 2015;64(1):29-40. PMID: 25890688. (SCI, Impact Factor: 3.574) [ScienceDirect] [PubMed] [PMC] (Invited Talk at IHTSDO Implementation SIG Webinar)

6. Zhe He, Simona Carini, Ida Sim, and Chunhua Weng*. Visual aggregate analysis of eligibility features of clinical trials. Journal of Biomedical Informatics. 2015;54:241-255. PMID: 25615940. [ScienceDirect] [PubMed] [PMC] [Link to VITTA System] (Clinical Research Informatics 2016 Year in Review)

2014 (1 journal paper & 3 conference papers)

1. Zhe He*, C. Paul Morrey, Yehoshua Perl, Gai Elhanan, Ling Chen, Yan Chen, and James Geller. Sculpting the UMLS Refined Semantic Network. Online Journal of Public Health Informatics. 2014;(6)2:e181. PMID: 25422719.  [PubMed] [PMC]

2. Zhe He, Simona Carini, Tianyong Hao, Ida Sim, and Chunhua Weng. A Method for Analyzing Commonalities in Clinical Trial Target Populations. Proceedings of American Medical Informatics Association 2014 Annual Symposium (AMIA 2014), November 15 - 19, 2014, Washington D.C. pp.1777-1786. PMID: 25954450. [PubMed] [PMC] [Talk Slides]

3. Chunhua Weng, Anil Yaman, Kuo Lin, and Zhe He. Trend and Network Analysis of Common Eligibility Features for Cancer Trials in ClinicalTrials.gov. Proceedings of 2014 International Conference for Smart Health, July 10 - 11, 2014, Beijing, China. Smart Health, Lecture Notes in Computer Science, Volume 8549:130-141. PMID: 26998530. [Springer] [PubMed]

4. Zhe He, James Geller, and Gai Elhanan. Categorizing the Relationships between Structurally Congruent Concepts from Pairs of Terminologies for Semantic Harmonization. Proceedings of 2014 American Medical Informatics Association Joint Summits on Translational Science, April 4 - 11, 2014, San Francisco, CA. pp. 48-53. PMID: 25717400 [PubMed] [Talk Slides]

2013 (2 journal papers & 3 conference papers)

1. Ankur Agrawal*, Zhe He, Duo Wei, Michael Halper, Yehoshua Perl, and Gai Elhanan. The readiness of SNOMED problem list concepts for meaningful use of electronic health records. Artificial Intelligence in Medicine. 2013;(58)2:73-80. PMID:23602702. [ScienceDirect] [PubMed](Highly Accessed)

2. James Geller, Zhe He*, Yehoshua Perl, C. Paul Morrey, and Julia Xu. Rule-based support system for multiple UMLS semantic type assignments. Journal of Biomedical Informatics, 2013;(46)1:97-110. PMID: 23041716. [ScienceDirect] [PubMed] (Highly Accessed)

3. Zhe He, Christopher Ochs, Ankur Agrawal, Yehoshua Perl, Dimitrios Zeginis, Konstantinos Tarabanis, Gai Elhanan, Michael Halper, Natasha Noy, and James Geller. A Family-Based Framework for Supporting Quality Assurance of Biomedical Ontologies in BioPortal. Proceedings of American Medical Informatics Association 2013 Annual Symposium (AMIA 2013), November 16 - 20, 2013, Washington D.C. pp. 581-90. PMID: 24551360. [PubMed] [Talk Slides] (Featured in "AMIA 2014 Year in Review")

4. Zhe He, Christopher Ochs, Larisa Soldatova, Yehoshua Perl, Sivaram Arabandi, and James Geller. Auditing Redundant Import in Reuse of a Top Level Ontology for the Drug Discovery Investigations Ontology. Proceedings of 2013 International Workshop on Vaccine and Drug Ontology Studies (co-located with ICBO 2013), July 7, 2013. Montreal, Qc, Canada.CEUR Proceedings Volume 1061 [Talk Slides]

5. Christopher Ochs, Zhe He, Yehoshua Perl, Sivaram Arabandi, James Geller, and Michael Halper. Choosing the Granularity of Abstraction Networks for Orientation and Quality Assurance of the Sleep Domain Ontology. Proceedings of the 4th International Conference on Biomedical Ontology (ICBO 2013), July 8 and 9, 2013. Montreal, Qc, Canada. CEUR Proceedings Volume 1060:84-9. 

2012 (2 conference/workshop papers)

1. Zhe He, Michael Halper, Yehoshua Perl, and Gai Elhanan. Clinical Clarity versus Terminological Order - the Readiness of SNOMED CT Concept Descriptors for Primary Care. Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems (MIXHS 2012) (co-located with CIKM 2012), Maui, HI, USA, October 29, 2012. pp.1-6. [ACM Digital Library] [Talk Slides]

2. Huanying Gu, Gai Elhanan, Michael Halper, and Zhe He. Questionable Relationship Triples in the UMLS. Proceedings of 2012 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI 2012), Hong Kong, January 2-7 2012. pp.713-6. [IEEE Xplore] [Talk Slides] 

Poster/Panel/Podium Presentation Abstracts

1. He, Z, Bhasuran, B., Wang, X., Gupta, D., & Killian, M. O.. Predicting Organ Rejections for Pediatric Heart Transplantations with a Combined Use of Transplant Registry Data and Electronic Health Records. Poster to be presented at 2024 American Transplant Congress, June 2024, Philadelphia, PA.

2. Zhe He, Ying Li, Serena Jingchuan Guo, Dipankar Gupta, Keran Moll, Hilda Klasky, Yonghui Wu, Hui Hu, AMIA KDDM Working Group Collaborative Workshop: Enriching Electronic Health Records with Social Determinants of Health to Improve Outcomes and Health Equity. Workshop at AMIA 2024 Informatics Summit, March 2024, Boston, MA.

3. Forhan Bin Emdad, Gregor Stiglic, Zhe He. Evaluating AI Reporting Guideline Adherence of Medical AI Research Using Large Language Model-based Systems. Poster presented at AMIA 2024 Informatics Summit, March 2024, Boston, MA.

4. He, Z, Bhasuran, B., Wang, X., Gupta, D., & Killian, M. O.. Predicting Organ Rejections for Pediatric Heart Transplantations with a Combined Use of Transplant Registry Data and Electronic Health Records. Poster presented at AMIA 2024 Informatics Summit, March 2024, Boston, MA.

5. Laura A. Barrett, Aiwen Xing, Elizabeth Steidley, Terrance Adam, Rui Zhang, and Zhe He. Assessing the Use of Prescription Drugs in Obese Respondents Using National Health and Nutrition Examination Survey Data. AMIA 2021 Annual Symposium. (Poster)

6. Zhan Zhang, Caleb Wilson, and Zhe He. Contextualizing Consumer Health Information Seeking. AMIA 2019 Annual Symposium. In press. (Poster)

7. Michael Dieciuc, Dawn Carr, Zhe He, Shayok Chakraborty, Neil Charness, Mia Lustria, Ankita Singh, Walter Boot. An Introduction to the Adherence Promotion With Person-Centered Technology Project. Gerontological Society of America Annual Meeting 2020 (GSA 2020). Innovation in Aging. 2020; 4(Suppl 1): 656. [PMC]

8. Zhe He, Rui Zhang, Olivier Bodenreider, Xinxin Zhu, Ronald Cornet, and Songmao Zhang. Developing Careers in Biomedical and Health Informatics. MEDINFO 2019. August 26-30, 2019, Lyon, France. (Panel)

9. Zhe He, Laura A. Barrett, Rubina F. Rizvi, Seyedeh Neelufar Payrovnaziri, and Rui Zhang. Exploring the Discrepancies in Actual and Perceived Benefits of Dietary Supplements Among Obese Patients. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:1474-1475. doi: 10.3233/SHTI190491. PMID: 31438188. (Poster).

10. Lynette Hammond Gerido and Zhe He. Improving Patient Participation in Cancer Clinical Trials: A qualitative analysis of HSRProj & RePORTER. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:1925-1926. doi: 10.3233/SHTI190716.  PMID: 31438410. (Poster).

11. Nur Hafieza Ismail, Ninghao Liu, Mengnan Du, Zhe He, Xia Ben Hu. Identification of Cancer Survivors Living with PTSD on Social Media. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. 2019 Aug 21;264:1468-1469. doi: 10.3233/SHTI190488. PMID: 31438185. (Poster).

12. Zhan Zhang, Yu Lu, Caleb Wilson, and Zhe He. Making Sense of Clinical Laboratory Results: An Analysis of Questions and Replies in a Social Q&A Community.  MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics.2 019 Aug 21;264:2009-2010. doi: 10.3233/SHTI190759. PMID: 31438453. (Poster).

13. Zhe He and Jiang Bian. Early Findings of a Survey on the Perception of Clinical Trial Generalizability Assessment and Eligibility Criteria Design. AMIA 2019 Informatics Summit. March 25-28, 2019. San Francisco, CA.  (Poster)

14. *Lynette Gerido and Zhe He. Opportunities to Improve Methods for Increasing Participation in Cancer Clinical Trials. AMIA 2018 Annual Symposium. November 3-8, 2018. San Francisco, CA (Poster)

15. *Lynette Gerido and Zhe He. Patient-Centered Strategies to Increase Participation in Cancer Clinical Trials. The Sixth IEEE International Conference on Healthcare Informatics (ICHI 2018), June 4-7, 2018. New York, NY.  pp. 361-362. DOI: 10.1109/ICHI.2018.00056. (Poster) [IEEE]

16. Biyang Yu, Lynette Gerido, Zhe He. Exploring Text Classification of Social Support in Online Health Communities for People Who are D/deaf and Hard of Hearing.  Proceedings of  the Association for Information Science and Technology (ASIS&T 2017), 54(1): 840-841.Washington DC. October 27 - November 1, 2017 (Poster)

17. Lynette Gerido, Michelle Kazmer, Zhe He, Marcia Mardis. Emergent Trends in Research to Increase Participation in Cancer Clinical Trials by Underrepresented Population: A Qualitative Analysis of the HSRProj Database.  Proceedings of  the Association for Information Science and Technology (ASIS&T 2017), 54(1): 677-678. Washington DC. October 27 - November 1, 2017 (Poster)

18. Zhe He, Zhiwei Chen, Sarah Mixon, Jiang Bian. A Visual Analysis Tool for Qualitative Eligibility Criteria of Clinical Studies. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp.2029. (Poster)

19. Jiang Bian, Andrei Sura, Yi Guo, François Modave, Zhe He, Elizabeth Shenkman, William Hogan.  Implementing a Hash-based Privacy-Preserving Entity Resolution Tool in the OneFlorida Clinical Data Research Network. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp.1953. (Poster)

20. Juan Antonio Lossio-Ventura, William Hogan, François Modave,  Amanda Hicks, Yi Guo, Zhe He, Mirela Vasconcelos, Jiang Bian. Building an Obesity and Cancer Semantic Web Knowledge Base. Proceedings of American Medical Informatics Association 2017 Annual Symposium (AMIA 2017). November 4-8, 2017. Washington DC. pp.2088 (Poster)

21. Zhe He and Aisha Langford. Comparative Analysis of Geriatric and Adult Drug Clinical Trials on ClinicalTrials.gov. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017).  August 21-25, 2017. Hangzhou, China.Studies in Health Technology and Informatics. 2017;245: 1265. PMID: 23295350 (Poster) [PubMed]

22. Tianyao Huo, Thomas J. George, Yi Guo, Zhe He, Mattia Prosperi, François Modave, and Jiang Bian. Explore Care Pathways of Colorectal Cancer Patients with Social Network Analysis. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017).  August 21-25, 2017. Hangzhou, China. Studies in Health Technology and Informatics. 2017;245: 1270. PMID: 29295255 (Poster) [PubMed]

23. Zhe He, Duo Wei, Jiang Bian, Jianlin Liu, and Yang Gong. Advancing Health Informatics Education and Health IT Workforce Development through Interdisciplinary Collaboration. Proceedings of the 16th World Congress on Medical and Health Informatics (MEDINFO 2017). August 21-25, 2017. Hangzhou, China. (Panel Presentation)

24. Aisha Langford and Zhe He, Eligibility Criteria for Hypertension-Related Interventions: Are Blacks Included? The 38th Annual Meeting and Scientific Sessions of the Society of Behavioral Medicine (SBM 2017). March 29 - April 1, 2017. San Diego, CA. (Poster)

25. Natasha Williams, Zhe He, Andrea Barnes, Aisha Langford, and Girardin Jean-Louis. Minority participation in clinical trials for obstructive sleep apnea and insomnia. SLEEP 2017, June 3-7, 2017.Boston, MA. (Poster). 

26. Amanda Hicks, William R. Hogan, Zhe He, Josh Hanna, Besty Shenkman, Jiawei Yuan, Jiang Bian. Using Semantic Queries for Cohort Discovery Across Research Networks. OHDSI Symposium 2015. October 20, 2015, Washington DC. (Poster)

27. Zhe He, Patrick Ryan, Shuang Wang, and Chunhua Weng. A Method for Assessing the Collective Population Representativeness of Multiple Related Clinical Trials Using Public Data. Proceedings of American Medical Informatics Association 2015 Joint Summits on Translational Science, March 23 - 27, 2015, San Francisco, CA. pp.255-256. (Podium Presentation) [Talk Slides]

28. James Geller, Christopher Ochs, Zhe He, and Yehoshua Perl. A Structural Meta-ontology for the BioPortal ontologies. Proceedings of Bio-ontologies 2013 (co-located with ISMB/ECCB 2013), July 20, Berlin, Germany. (Poster)