About me

I am a tenure-track assistant professor (AI Initiative) at the Department of Health Outcome and Biomedical Informatics, University of Florida. I completed my postdoctoral training at the Department of Biomedical Informatics, Harvard Medical School, working with Dr. Paul Avillach. Before that, I received my Ph.D. degree from the School of Computer Science and Engineering, Nanyang Technological University in 2020, under the supervision of Dr. Kwoh Chee Keong. My thesis is meta-analysis on the lethality of influenza A viruses using machine learning approaches, examined by dissertation advisory committee members Assoc. Professor Bo An, Assoc. Professor Erik Cambria and Assoc. Professor Sinno Jialin Pan. I obtained my bachelor’s degree and master’s degree from Shandong University and Central South University in 2013 and 2015, respectively.

Research Interest

  • Protein language model for downstream biomedical tasks (protein design, protein-protein interaction analysis)
  • Computational modeling in RNA viruses (influenza, coronaviruses, Zika, etc.)
  • Machine learning modeling to facilitate the diagnosis of cancer and rare/undiagnosed diseases
  • Genotype-phenotype association study for biomarker identification and novel discovery
  • Combination of clinical informatics and genomics to support clinical decision system
  • Interpretable and trustworthy AI to advance health equity
Recent News
  • [Dec.2023] Our paper “Developing Ethics and Equity Principles, Terms, and Engagement Tools to Advance Health Equity and Researcher Diversity in AI and Machine Learning: Modified Delphi Approach” was accepted by JMIR AI.
  • [Dec.2023] Our paper “LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism” was accepted by Bioinformatics.
  • [Nov.2023] Our paper “CLCAP: Contrastive Learning Improves Antigenicity Prediction for Influenza A Virus Using Convolutional Neural Networks” was accepted by Methods.
  • [Nov.2023] Qiang Yang joined my lab as a postdoc researcher, welcome!
  • [Oct.2023] Our paper “HSELDA: Heterogeneous Sub-Graph Learning for lncRNA-Disease Associations Prediction” was accepted by the 2023 IEEE International Conference on Bioinformatics and Biomedicine.
  • [Oct.2023] Our paper “PESI: Paratope-Epitope Set Interaction for SARS-CoV-2 Neutralization Prediction” was accepted by the 2023 IEEE International Conference on Bioinformatics and Biomedicine.
  • [Sep.2023] Our paper “Editorial: Computational Methods to Analyze RNA Data for Human Diseases” was accepted by Frontiers in Genetics.
  • [Sep.2023] I am serving as Editorial Board Member in the Journal of BMC Bioinformatics
  • [Sep.2023] Our proposal “Targeted protein design via constrained denoising diffusion probabilistic models” was funded by the Ministry of Education, Singapore
  • [Aug.2023] Our paper “Identification of Outcome-Oriented Progression Subtypes from Mild Cognitive Impairment to Alzheimer’s Disease Using Electronic Health Records” was accepted by the 2023 AMIA Annual Symposium
  • [Aug.2023] Our paper “MTLNFM: Multi-task Learning to Predict Patient Clinical Outcomes with Neural Factorization Machine” was accepted by the 2023 AMIA Annual Symposium
  • [Aug.2023] Pratyush Shukla joined our lab as a graduate research assistant, welcome!
  • [Jul.2023] I was invited to give a talk at the 2023 International Conference on Intelligent Biology and Medicine Workshop, with the topic “Leveraging the power of genomics to facilitate the diagnosis of undiagnosed diseases with machine learning models”
  • [Jul.2023] I am serving as the co-chair for the 2024 IEEE International Conference on Healthcare Informatics Tutorial.
  • [Jun.2023] Rohit Inampudi joined our lab as an undergraduate research assistant, welcome!
  • [Jun.2023] I was appointed as guest editor for the Special Issue “Computational Modeling in RNA Viruses” in the Journal of MDPI Viruses.
  • [May.2023] Our paper “COMET: Convolutional Dimension Interaction for Collaborative Filtering” was accepted by ACM Transactions on Intelligent Systems and Technology.
  • [May.2023] Our paper “ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences” was accepted by the Journal of Biomedical Informatics.
  • [Apr.2023] Hongru Zhao joined our lab as a graduate research assistant, welcome!
  • [Apr.2023] I am serving as a co-chair for the International Conference on Intelligent Biology and Medicine Workshop (ICIBM 2023).
  • [Mar.2023] Our proposal “Contrastive Convolutional Neural Networks to Predict High-confidence mRNA-miRNA Pairs in Colorectal Cancer Patients” was funded by UF Health Cancer Center as Artificial Intelligence Supplement Pilot & Exploratory Program.
  • [Mar.2023] I am serving as Program Committee member for IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2023).
  • [Feb.2023] I was appointed as the Guest Editor in the Journal of Computational Genomics of Frontiers in Genetics.
  • [Feb.2023] I joined UFHealth Cancer Center as a community member.
  • [Jan.2023] Our paper “CLCAP: Contrastive Learning Improves Antigenicity Prediction for Influenza A Virus Using Convolutional Neural Networks” was accepted by the 21st Asia Pacific Bioinformatics Conference.
  • [Jan.2023] Our paper “A review of the enzyme design in catalytic stability by artificial intelligence” was accepted by Briefings in Bioinformatics.
  • [Dec.2022] I officially started my position as an assistant professor at HOBI, University of Florida
  • [Nov.2022] Our paper “GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation” was accepted by Briefings in Bioinformatics.
  • [Nov.2022] I am serving as Program Committee member for the 21st Asia Pacific Bioinformatics Conference (APBC).
  • [Nov.2022] Xiangyu Chen joined our lab as a research intern, welcome!
  • [Oct.2022] Jiaxin Li joined our lab as a research undergraduate student, welcome!
  • [Oct.2022] Our collaborative proposal “Computational Drug Repurposing for AD/ADRD with Integrative Analysis of Real-World Data and Biomedical Knowledge was funded by NIA!
  • [Sep.2022] I am serving as Program Committee member for IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2022).
  • [Aug.2022] Xiaohan Li joined our lab as a research graduate student, welcome!
  • [Jun.2022] Our paper “A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods” was accepted by Briefings in Bioinformatics.
  • [May.2022] I was appointed as guest editor for Research Topic: Computational Methods to Analyze RNA Data for Human Diseases in the Journal of Frontiers In Genetics.
  • [May.2022] I accepted the offer from the University of Florida and will join the university as a tenure-track assistant professor this December.
  • [Apr.2022] I was invited to give a talk at Auburn University, Auburn, Alabama.
  • [Apr.2022] I was invited to give a talk at the University of Florida, Gainesville, Florida.
  • [Apr.2022] I was invited to give a talk at Emory University, Atlanta, Georgia.
  • [Mar.2022] New preprint “ViPal: A Framework for Virulence Prediction of Influenza Viruses with Prior Viral Knowledge Using Genomic Sequences” is released.
  • [Mar.2022] I was invited to give a talk at the University of California Irvine. (Virtual)
  • [Mar.2022] I was invited to give a talk at the University of Massachusetts, Boston, Massachusetts.
  • [Mar.2022] Our paper “Mendelian Randomization Analysis Suggests No Associations of Herpes Simplex Virus Infections With Multiple Sclerosis” was published at Frontiers in Neuroscience.
  • [Feb.2022] I was invited to give a talk at Boston University, Boston, Massachusetts.