Zhe He (何辙), PhD, MS

[ How to pronounce my name? The pronunciation of "Zhe" is similar to "Germany" without "many" sound. The pronunciation of "He" is like "her" but without the "r" sound (the British accent). ]

Assistant Professor, School of Information, College of Communication and Information

Core Affiliate, Institute for Successful Longevity

Florida State University

271 Louis Shores Building

142 Collegiate Loop

Tallahassee FL, 32306-2100

Office: 850.644.5775

Email: zhe.he AT cci.fsu.edu OR zhe AT fsu.edu

[CV] [FSU CV] [Academic Genealogy] [GitHub] [Google Scholar] [ResearchGate] [NCBI] [OCRID]

Biography

Dr. Zhe He is an Assistant Professor in the School of Information at the Florida State University (Florida's iSchool) and a Core Affiliate of the Institute for Successful Longevity. Dr. He is an Associate Editor of BMC Medical Informatics and Decision Making.

Before joining FSU, Dr. He was a Postdoctoral Research Scientist (2014-2015) in the Department of Biomedical informatics at Columbia University, working with Dr. Chunhua Weng. In his postdoctoral research, he has developed methods for assessing the collective population representativeness of clinical studies with the goal of improving the transparency of study generalizability to the real-world population.

He obtained his Ph.D. in Computer Science at New Jersey Institute of Technology (2009-2014). He worked with Dr. James Geller and Dr. Yehoshua Perl in the Structural Analysis of Biomedical Ontologies Center (SABOC). His doctoral thesis introduced a set of quality assurance methodologies for controlled terminologies and ontologies, e.g., Unified Medical Language System (UMLS), SNOMED CT, and domain ontologies in BioPortal.

He has published over 50 peer-reviewed articles in leading biomedical informatics outlets, including 7 articles in Journal of Biomedical Informatics, 2 articles in Journal of Medical Internet Research, 2 articles in Artificial Intelligence in Medicine, 2 articles in Methods of Information in Medicine, 8 articles in American Medical Informatics Association (AMIA) Annual Symposium, and 2 articles in MEDINFO. His papers were nominated for the Student Paper Award of AMIA 2015 Summit on Clinical Research Informatics and MEDINFO 2015. His AMIA 2013 paper was selected as the representative paper on "Biomedical Ontologies" in the "Informatics Year In Review". His JBI 2016 and AMIA 2015 papers were selected into "Clinical Research Informatics 2016 Year in Review". He received two Distinguished Paper Awards from AMIA Annual Symposiums (in 2015 and 2017).

During his PhD studies, he was inducted into Alpha Epsilon Lambda National Graduate and Professional Honor Society. He received his MS from Columbia University and his BS from Beijing University of Posts and Telecommunications, both in Computer Science.

In his spare time, Zhe is interested in photography and traveling. This is his Photography Studio Website.

Research Interests

Dr. He has broad interests in biomedical and health informatics, clinical research informatics, knowledge discovery, knowledge representation, and ontology-enhanced data analytics. The overarching goal of his research is to improve the population health and advance biomedical research through the collection, analysis, and application of electronic health data from heterogeneous sources.

On the foundational track, he is developing semantic and structural methods to enhance controlled terminologies/ontologies and improve their utility in natural language processing, clinical decision support, data analytics, and electronic health records. On the application track, he has been developing novel data-driven methods and tools to assess the generalizability of clinical studies using the electronic data in clinical trial registries, public patient databases, and clinical data warehouses. His research aims to improve the representation of underserved population subgroups in clinical studies such as older adults with multiple chronic conditions. Another line of his research is to bridge the terminology gap between health information consumers and health professionals. His research has been funded by National Institutes of Health, Amazon, NVIDIA, FSU Council on Research and Creativity, and Institute for Successful Longevity.

Dr. He has published in the following topics:

  • Quality Assurance of Biomedical Ontologies and Controlled Vocabularies (e.g., SNOMED CT, UMLS)
  • Data-driven Concept Enrichment for Biomedical Ontologies and Controlled Vocabularies (e.g., SNOMED CT, NCIt)
  • Clinical Trial Generalizability Assessment and Improvements
  • Semantics-Powered Data Analytics
  • Vocabulary Gap between Health Information Consumers and Health Professionals
  • Consumer Information Seeking Behavior

Selected Publications (All Publications)

Clinical Research Informatics

  • 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. (SCIE, †: equal-contribution first authors, Impact Factor: 4.67) [Link] [PubMed]
  • 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 AMIA 2017 Annual Symposium. November 4-8, 2017. Washington DC. pp. 849-858. PMID: 29854151. PMCID: PMC5977671. [PDF] [PMC] (Distinguished Paper Award of AMIA 2017 Annual Symposium; three awards were selected from 105 accepted paper and 266 paper submissions) [Award Certificate] [Live Picture] [CCI News]
  • Zhe He, Zhiwei Chen, and Jiang Bian. Analysis of Temporal Constraints in Qualitative Eligibility Criteria of Cancer Clinical Studies. Proceedings of 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016). December 15-18, 2016. Shenzhen, China. pp. 717-722. PMID: 29263940. PMCID: PMC5733789. DOI: 10.1109/BIBM.2016.7822607. (Acceptance rate: 19%) [IEEE] [PDF] [PMC]
  • 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. pp. 2970-2973. PMID: 28268936 (Acceptance rate for orally-presented papers: 20%)
  • 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. (IF: 2.88, 5-Year IF: 3.12) [ScienceDirect] [PubMed] [PDF]
  • Zhe He, Praveen Chandar, Patrick Ryan, and Chunhua Weng. Simulation-based Evaluation of the Generalizability Index for Study Traits. Proceedings of AMIA 2015 Annual Symposium. November 14-18, 2015. San Francisco, CA. pp.594-602. PMID: 26958194 (Distinguished Paper Award of AMIA 2015 Annual Symposium [Official Announcement] [Award Certificate] [News Article]) [PDF] [PubMed]
  • 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. Studies in Health Technology and Informatics (MEDINFO 2015). 2015;216:569-73. PMID: 26262115 [PDF] [PubMed] [IOS Press] [Presentation Video] (Student Paper Award Nominee)
  • 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. (IF: 2.88, 5-Year IF: 3.12) [ScienceDirect] [PubMed] [PDF]
  • Zhe He, Simona Carini, Tianyong Hao, Ida Sim, and Chunhua Weng. A Method for Analyzing Commonalities in Clinical Trial Target Populations. Proceedings of AMIA 2014 Annual Symposium (AMIA 2014), November 15 - 19, 2014, Washington D.C. pp.1777-1786. PMID: 25954450. [PubMed] [PDF] [Talk Slides]

Quality Assurance of Biomedical Terminologies / Ontologies

Consumer Health Informatics

  • Biyang Yu and Zhe He. Exploratory Textual Analysis of Consumer Health Languages for People Who are D/deaf and Hard of Hearing. Proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine. November 13 - 16, 2017. Kansas City, MO. In press. [PDF]
  • 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 (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [PubMed] [ScienceDirect] [PDF]
  • 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 (Park MS and He Z are equal-contribution first authors) [JMIR] [PDF]

Selected Honors and Awards

  • Granted U.S. Permanent Residency under the category of "Aliens with Extraordinary Ability" (EB-1A), March 2018
  • FSU University-Wide Research Recognition Dinner Invitee, March 2018
  • Provost's Travel Grant (to present my paper in AMIA 2017), Florida State University, November 2017
  • Distinguished Paper Award of AMIA 2017 Annual Symposium, November 2017 [Certificate] [CCI News]
  • Outstanding Faculty Research Award, College of Communication & Information, Florida State University, April 2017
  • Provost's Travel Grant (to present my paper in AMIA 2016), Florida State University, November 2016
  • Amazon Web Services Cloud Credits for Research, December 2016 - November 2017
  • Travel Grant, NSF South Big Data Hub, September 2016
  • Travel Grant, NIH Future Research Leaders Conference, Bethesda, MD, September 2016
  • Planning Grant, Institute for Successful Longevity, May 2016
  • Two Papers Featured in Clinical Research Informatics 2016 Year in Review, March 2016 [Link]
  • Runner Up, Most Interesting Preliminary Results Paper Award, iConference 2016, March 2016
  • Travel Grant, Transatlantic Data Science Workshop, Bethesda, MD March 1-2, 2016
  • Florida State University First Year Assistant Professor Grant, May - August, 2016
  • Distinguished Paper Award of AMIA 2015 Annual Symposium ([Official Announcement] [Certificate] [News Article]), November 2015
  • Amazon Web Services Education Research Grant Award, December 2015 - November 2016
  • Provost's Travel Grant (to present my paper in AMIA 2015), Florida State University, September 2015
  • MEDINFO 2015 Student Paper Award Nominee, August 2015
  • AMIA 2015 Summit on Clinical Research Informatics Student Paper Award Nominee, April 2015
  • One Paper Featured in the "2014 Informatics Year in Review", November 2014 [Link]
  • Top Poster Award, 2014 Columbia University Postdoc Research and Career Symposium (One of the three awards among over 50 postdoc presenters)
  • Outstanding Leader Award 2013 - 2014, New Jersey Institute of Technology (One award is offered annually)
  • Distinguished College Graduate of Beijing China (10 out of over 400 graduates majored in Computer Science at BUPT )
  • Delegate of China in the 7th China Synergy Programme for Outstanding Youth (Highly selective 48 dedicates in mainland China)