Standardizing and Harmonizing Behavioral and Social Science Research Factors in Alzheimer's Disease through Ontology-Based Approaches
Award Number: U01AG088076
NIH RePORTER Project Details: https://reporter.nih.gov/search/bGo56Rz6q0Sdz98guPjnjw/project-details/11180321
Principal Investigators
Overview
1.
Development of a formal ontological representation of BSSR elements related to ADRD that aligns with existing standards, involving iterative refinement;
2.
Development of advanced NLP systems to extract, normalize, and encode essential BSSR information pertaining to ADRD;
3.
LLMs-empowered ontology enrichment, semantic triple extraction, and KG generation;
4.
Systematic evaluation of the informatics solutions through conducting both EHRs-based observational demonstration studies and literature-driven knowledge validation.
Resources
Publications
Abdelhameed A, Sun Z, Yu Y, et al. Transformer-DAPT: AI-based dynamic assessment of ischemic and bleeding risks in patients on DAPT following PCI. npj Digit Med. 2026. https://doi.org/10.1038/s41746-026-02977-9 Epub ahead of print, 2026 Jul 14. PMID: 42448824.
Huang Y, Li Q, Chen A, et al. Feasibility of identifying factors related to Alzheimer's disease and related dementia in real-world data. JAMIA Open. 2026;9(2):ooag060. https://doi.org/10.1093/jamiaopen/ooag060 PMID: 42040178. PMCID: PMC13108722.
Amith M, Hao X, Manuel W, et al. Hootation: A GUI and API library for ontology validation and verbalization. Proc IEEE Int Conf Semant Comput. 2026;2026:128-132. https://doi.org/10.1109/ICSC67292.2026.00025 PMID: 42179940. PMCID: PMC13191566.
Li F, Li P, Bhandarkar A, et al. Artificial Intelligence-Empowered Multimodal Learning in Psychiatry: A Scoping Review. Biol Psychiatry Cogn Neurosci Neuroimaging. 2026. https://doi.org/10.1016/j.bpsc.2026.03.013 Epub ahead of print, 2026 Mar 30. PMID: 41921663. PMCID: PMC13377839.
Amith M, Ha V, Nguyen E, et al. Kinetic Human Movement Ontology: a semantic terminology model to symbolically represent physiological movement. Sci Data. 2026;13(1):696. https://doi.org/10.1038/s41597-026-06984-z Epub 2026 Mar 7. PMID: 41794846. PMCID: PMC13144411.
Yu Y, Hu X, Rajaganapathy S, et al. Accelerating AI innovation in healthcare: real-world clinical research applications on the Mayo Clinic Platform. npj Health Syst. 2026;3(1):17. https://doi.org/10.1038/s44401-026-00068-1 Epub 2026 Feb 16. PMID: 41710561. PMCID: PMC12909107.
Dai H, Huang Y, Liu Y, et al. Variational temporal deconfounder network for individualized treatment effect estimation with longitudinal observational data. J Biomed Inform. 2025;169:104880. https://doi.org/10.1016/j.jbi.2025.104880 Epub 2025 Jul 21. PMID: 40701259. PMCID: PMC12311642.
Hou Z, Liu H, Bian J, He X, Zhuang Y. Enhancing medical coding efficiency through domain-specific fine-tuned large language models. npj Health Syst. 2025;2(1):14. https://doi.org/10.1038/s44401-025-00018-3 Epub 2025 May 1. PMID: 40321467. PMCID: PMC12045799.
Amith M, Yu Y, Shi Y, et al. An ontology-based method for formalizing and encoding patient colonoscopy preparation using BPMN and OWL2 for automated tool development. J Clin Inform. 2025;1(1):8599. doi: 10.36922/jci.8599. Full text: https://pmc.ncbi.nlm.nih.gov/articles/PMC12461748/ Epub 2025 Apr 23. PMID: 41019254. PMCID: PMC12461748.
Hasan WU, Zaman KT, Wang X, Li J, Xie B, Tao C. Empowering Alzheimer's caregivers with conversational AI: a novel approach for enhanced communication and personalized support. npj Biomed Innov. 2024;1(1):3. https://doi.org/10.1038/s44385-024-00004-8 Epub 2024 Dec 4. PMID: 42032173. PMCID: PMC13055072.
Hao X, Cui L, Tao C, Roberts K, Amith M. Analyzing Llama 3-based Approach for Axiom Translation from Ontologies. CEUR Workshop Proc. 2024;3853:5. KBC-LM'24 workshop at ISWC 2024. https://ceur-ws.org/Vol-3853/paper5.pdf PMID: 40538705. PMCID: PMC12178606.
Team
Cui Tao
Principal Investigator
Cui Tao, PhD, Department of Artificial Intelligence and Informatics, Mayo Clinic, tao.cui@mayo.edu
Cui Tao is the inaugural Enterprise Chair of the Department of Artificial Intelligence and Informatics at Mayo Clinic. She serves as Vice President of Mayo Clinic Platform and the Enterprise Deputy Co-director of Data Science and Artificial Intelligence at the Mayo Clinic Comprehensive Cancer Center.
She is a Professor of Biomedical Informatics and an elected fellow of the American College of Medical Informatics. Her background is in clinical informatics and computer science, and her research interests include ontologies, knowledge graphs, predictive modeling, deep learning, large language models, as well as applying these technologies to clinical and translational studies.
She is a recipient of the Presidential Early Career Awards for Scientists and Engineers (PECASE), the highest honor bestowed by the United States Government on science and engineering professionals in the early stages of their independent research careers. Her collective research funding surpasses $30 million. She has a Ph.D. in computer science from Brigham Young University.
Jiang Bian
MPI
Jiang Bian, PhD, Regenstrief Institute, Indiana University, bianji@regenstrief.org
Fang Li
Co-Investigator
Fang Li, PhD, Department of Artificial Intelligence and Informatics, Mayo Clinic, li.fang@mayo.edu
Fang Li is an associate consultant and assistant professor at the Department of Artificial Intelligence and Informatics, Mayo Clinic. Her background is in medical informatics. Her research interests include ontologies, knowledge graphs, predictive modeling, and large language models.
She is the editorial board member of JAMIA and has over 40 journal and conference publications. She received her PhD degree in information and library science from the University of Chinese Academy of Sciences.
Lu Kang
Project Manager
Haifang Li
Researcher
Haifang Li, PhD, Department of Artificial Intelligence and Informatics, Mayo Clinic, Li.Haifang@mayo.edu
Haifang Li is a postdoctoral research fellow at Mayo Clinic. She earned her Ph.D. in Probability and Mathematical Statistics from the University of Chinese Academy of Sciences. Her research focuses on machine learning, natural language processing (NLP), and ontology-based knowledge representation, with applications in clinical and biomedical fields.
Yue Yu
Researcher/Working Group Lead
Yue Yu, PhD, Department of Artificial Intelligence and Informatics, Mayo Clinic, yu.yue1@mayo.edu
Yue Yu is an Assistant Professor of Biomedical Informatics and a Senior Data Science Analyst in the Department of Artificial Intelligence and Informatics at Mayo Clinic.
Dr. Yu's background is in biomedical informatics, and his research interests include medical data standardization, common data models, and machine learning, as well as the application of artificial intelligence technologies to support clinical and translational research. He earned his Ph.D. in Public Health from Jilin University.
Amit 'Tuan' Muhammad
Researcher
Weiguo Cao
Researcher
Weiguo Cao, PhD, Department of Artificial Intelligence and Informatics, Mayo Clinic, Cao.Weiguo@mayo.edu
Weiguo Cao is a postdoctoral research fellow in the Department of Artificial Intelligence and Informatics at Mayo Clinic. His background spans computer graphics, computer vision, medical image analysis, large language models, and machine learning.
Previously, he was a Postdoctoral Associate at Stony Brook University and a Senior Research Scientist at Alibaba Group. He holds a Ph.D. in computer science from the Institute of Computing Technology, Chinese Academy of Sciences.
Avanti Bhandarkar
Researcher
Avanti Bhandarkar, PhD, Department of Artificial Intelligence and Informatics, Mayo Clinic, Bhandarkar.Avanti@mayo.edu
Avanti Bhandarkar is a postdoctoral research fellow at Mayo Clinic. She received her PhD in Electrical and Computer Engineering from the University of Florida, where she specialized in natural language processing (NLP). She also holds an MS in Electrical and Computer Engineering from the University of Florida and a BE in Electronics and Telecommunication Engineering from G. H. Raisoni College of Engineering in India.
Dr. Bhandarkar's research focuses on NLP, applied artificial intelligence, and generative AI. Her work has led to over 10 publications in leading NLP, AI and interdisciplinary venues, including EACL, COLING, NAACL, IEEE, and the British Journal of Psychology.
Rakesh Kumar
Researcher
Rakesh Kumar, M.B.B.S., M.D., Department of Artificial Intelligence and Informatics, Mayo Clinic, Kumar.Rakesh@mayo.edu
Rakesh Kumar is a postdoctoral research fellow at Mayo Clinic. He holds an M.B.B.S. from Goa Medical College and an M.D. in Psychiatry from Guru Gobind Singh Medical College, where he also served as Chief Resident. Before joining Mayo Clinic, Dr. Kumar practiced psychiatry and served as a medical officer with the Government of India and State Government for nearly ten years.
His research focuses on the neurological mechanisms of mood disorders, development of objective biomarkers, and the application of artificial intelligence to advance psychiatric research and practice.
Xing He
Co-Investigator
Xing He, PhD, Indiana University School of Medicine / Regenstrief Institute
Xuguang Ai
Data Scientist
Xuguang Ai, MS, Center for Biomedical Informatics, Regenstrief Institute
Yuhang Jiang
Researcher
Yuhang Jiang, PhD, Department of Biostatistics and Health Data Science, Indiana University School of Medicine
Isaac H. Clark
Researcher
Isaac H. Clark, PhD, Department of Artificial Intelligence and Informatics, Mayo Clinic