I am 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. I also hold a courtesy appointment with the Department of Computer Science. I am also the Lead of the Method Core of the Center for Translational Behavioral Science, as well as the FSU's Informatics Lead of the FSU-UF Joint Clinical and Translational Science Institute. I am an Associate Editor of BMC Medical Informatics and Decision Making.
My research lies in biomedical and health informatics, clinical research informatics, knowledge discovery, knowledge representation, and ontology-enhanced data analytics. At FSU, I lead the eHealth Lab. The overarching goal of our 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, we develop 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, we devise 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. Our research aims to improve the representation of underserved population subgroups in clinical studies such as older adults with multiple chronic conditions. Another line of our research is to bridge the terminology gap between health information consumers and health professionals through the analysis of the textual content in the online social media. Our research has been funded by National Institutes of Health, Amazon, NVIDIA, FSU Council on Research and Creativity, and Institute for Successful Longevity.
Before joining FSU in Fall 2015, I was a Postdoctoral Research Scientist in the Department of Biomedical informatics at Columbia University between 2014 and 2015, working with Dr. Chunhua Weng. In my postdoctoral research, I developed informatics methods to assess the collective population representativeness of clinical studies, with the goal of improving the transparency of study generalizability to the real-world population. I received my Ph.D. in Computer Science at New Jersey Institute of Technology in 2014, where I worked with Dr. James Geller and Dr. Yehoshua Perl in the Structural Analysis of Biomedical Ontologies Center (SABOC). My doctoral thesis is centered on quality assurance methodologies for controlled biomedical vocabularies - Unified Medical Language System (UMLS), SNOMED CT, and domain ontologies in BioPortal. My postdoctoral and doctoral research was supported by three R01 grants funded by the National Library of Medicine and Columbia's CTSA grant funded by the National Center for Advancing Translational Sciences.
I have published over 60 peer-reviewed articles in leading biomedical informatics venues, including Journal of Biomedical Informatics, Journal of Medical Internet Research, BMC Medical Informatics and Decision Making, Artificial Intelligence in Medicine, Methods of Information in Medicine, American Medical Informatics Association (AMIA) Annual Symposium, and MEDINFO. My first-author papers received many prestigious recognitions in the field of biomedical informatics, including (1) two Distinguished Paper Awards of AMIA Annual Symposiums (AMIA 2015 paper and AMIA 2017 paper), (2) paper selection in "AMIA 2014 Informatics Year In Review" (AMIA 2013 paper), (3) Finalists of the Student Paper Award of AMIA 2015 Summit on Clinical Research Informatics and MEDINFO 2015, and (4) paper selection in "Clinical Research Informatics 2016 Year in Review" (JBI 2016 and AMIA 2015 paper)
In 2014, I was inducted into Alpha Epsilon Lambda National Graduate and Professional Honor Society. I received my MS from Columbia University and BS from Beijing University of Posts and Telecommunications, both in Computer Science.
In my spare time, I am interested in photography and traveling. This is my Photography Studio.
Education
- Postdoctoral Training. 2015: Columbia University, Biomedical Informatics
- Ph.D. 2014; New Jersey Institute of Technology (NJIT), Computer Science
- M.S. 2009; Columbia University, Computer Science
- B.E. 2007; Beijing University of Posts and Telecommunications, Computer Science
Research Interests
Dr. He has broad interests in biomedical and health informatics, clinical research informatics, knowledge discovery, and ontology-based data analytics. 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, 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. He has published in the following topics:
- Quality assurance of biomedical ontologies (e.g, domain ontologies in BioPortal)
- Quality assurance of controlled vocabularies (e.g., SNOMED CT, UMLS)
- Data-driven conceptual content enrichment for ontologies/terminologies (e.g., SNOMED CT, NCIt)
- Clinical trial generalizability assessment and improvement
- Consumer Health Vocabulary
Teaching Interests
Health Information Technology, Data Mining, Machine Learning, Database Management Systems
Publications & Research
Selected Publications (All Publications)
- Qian Li, Zhe He, Yi Guo, Hansi Zhang, Thomas J George Jr, William Hogan, Neil Charness, Jiang Bian, Assessing the Validity of a a prior 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. In press. (Qian Li, Zhe He, and Yi Guo are co-first authors)
- 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)
- 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, Impact Factor: 4.67) [Link] [PubMed] [PMC]
- 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; three awards were selected from 105 accepted paper and 266 paper submissions) [Award Certificate] [Live Picture] [CCI News]
- 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. (Impact Factor: 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 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. (Impact Factor: 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
- 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. DOI: 10.1016/j.jbi.2019.103193. [PubMed] [Link]
- 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. (†: equal-contribution first authors, SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [FSU CCI News] [ScienceDirect] [PubMed]
- 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 AMIA 2016 Annual Symposium. November 12-16, 2016. Chicago, IL. pp. 618-627. PMID: 28269858 [Talk Slides] [PMC]
- 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. (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [ScienceDirect] [PubMed][PDF]
- 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: 2.88, 5-Year Impact Factor: 2.86)[ScienceDirect] [PDF] (Invited Talk at IHTSDO Implementation SIG Webinar [Slides] [Video]) (#14 Hottest Article April - June 2015)
- 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] [PDF]
- 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 AMIA 2013 Annual Symposium (AMIA 2013) , November 16 - 20, 2013, Washington D.C. pp. 581-90. PMID: 24551360. [PubMed] [PDF] [Talk Slides] (Featured in "AMIA 2014 Year in Review")
- 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. (SCI, Impact Factor: 2.88, 5-Year Impact Factor: 3.12) [ScienceDirect] [PubMed] [PDF] (Highly Accessed)
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. pp. 1288-1291. DOI: 10.1109/BIBM.2017.8217846 [IEEE] [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]
Machine Learning and Artificial Intelligence
- 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). (Acceptance rate: 39%)
- 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. In press.
- 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. In press. (Finalist of the Student Paper Award) (Media Report)
Grants & Awards
Research Grants
- Program: NIH Research Grant Award (R01)
- Sponsor: National Institute on Aging / National Institutes of Health
- Date: 08/2019- 03/2024
- Total Amount: $2.9 million
- Role: Co-Investigator (PI: Walter Boot)
Posttransplant Health Outcomes in Pediatrics Organ Transplantation
- Program: Clinical and Translational Science Institute’s (CTSI) Precision Health Initiative Pilot Award
- Sponsor: National Institutes of Health (Parent UL1TR001427)
- Date: 07/2019 - 06/2020
- Total Amount: $40,834
- Role: Co-Principle Investigator (MPI: Michael Killian)
- Program: NIH Exploratory/Developmental Research Grant Program (R21)
- Sponsor: National Institute on Aging / National Institutes of Health
- Date: 01/2019 - 11/2020
- Total Amount: $422,382
- Role: Principle Investigator (Contact PI, MPI with Jiang Bian)
Measuring Prevalence of Autism Spectrum Disorder and Benchmarking Utilization Using the OneFlorida Consortium Data
- Program: Planning Grant
- Sponsor: Institute for Successful Longevity, Florida State University
- Date: 05/2018 - 05/2019
- Total Amount: $15,500
- Role: Co-Principle Investigator (PI: Henry Carretta)
Testing a New Approach for Academic Work Evaluations
- Program: Small Business Innovation Research Awarded to Pevals LLC; FSU subcontract
- Sponsor: National Institutes of Health
- Date: 09/2017 - 08/2018
- Total Amount: $20,000
- Role: Co-Principle Investigator (PI: Minjing Tao)
VATEC: A Visual Analysis Tool of Qualitative Eligibility Criteria of Clinical Studies
- Program: AWS Cloud Credits for Research
- Sponsor: Amazon Inc.
- Date: 12/2016 - 12/2017
- Total Amount: $1,200
- Role: Principle Investigator
Assessing the Representation of Older Adults with Multiple Chronic Conditions in Cancer Clinical Trials
- Program: Planning Grant
- Sponsor: Institute for Successful Longevity, Florida State University
- Date: 05/2016 - 05/2018
- Total Amount: $15,500
- Role: Principle Investigator (Co-PI: Henry Carretta)
Towards Data-Driven Assessment of the Population Representativeness of Clinical Trials
- Program: First Year Assistant Professor Award (FYAP)
- Sponsor: Council on Research and Creativity, Florida State University
- Date: 05/2016 - 08/2016
- Total Amount: $20,000
- Role: Principle Investigator
Resource and Travel Grants
Developing Data-Driven Tools for Assessing the Population Representativeness of Clinical Trials
- Program: Amazon Web Services Research Grant
- Sponsor: Amazon Inc.
- Date: 12/2015 - 12/2016
- Total Amount: $2,000
- Role: Principle Investigator
- Project Title: Accelerating Data-Driven Biomedical and Health Informatics Research with GPU
- Amount: $1,200
- Date: 02/2018
Provost's Travel Grant, Provost's Office, Florida State University
- Purpose: Attending American Medical Informatics Association 2017 Annual Symposium
- Amount: $823
- Date: 11/2017
Undergraduate Research Opportunity Program Materials Grant
- Sponsor: Center for Undergraduate Research and Academic Engagement, Florida State University
- Date: 11/2016
Provost's Travel Grant, Provost's Office, Florida State University
- Purpose: Attending American Medical Informatics Association 2016 Annual Symposium
- Amount: $1,000
- Date: 11/2016
Provost's Travel Grant, Provost's Office, Florida State University.
- Purpose: Attending American Medical Informatics Association 2015 Annual Symposium
- Amount: $1,000
- Date: 11/2015
Awards
- 2018-2019 Outstanding Faculty Research Award, College of Communication & Information, Florida State University, April 2019
- Distinguished Paper Award of AMIA 2017 Annual Symposium, November 2017 [CCI News]
- 2016-2017 Outstanding Faculty Research Award, College of Communication & Information, Florida State University, April 2017
- Travel Grant, NSF South Big Data Hub, September 2016
- Travel Grant, NIH Future Research Leaders Conference, Bethesda, MD, September 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
- Distinguished Paper Award of AMIA 2015 Annual Symposium ([Official Announcement] [Certificate] [News Article]), November 2015
- 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
- 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 given annually)
- Distinguished College Graduate of Beijing (10 out of over 400 graduates majored in Computer Science at BUPT )