JunJie Wee

weejunji[at]msu.edu

Department of Mathematics
Michigan State University
C114 Wells Hall
619 Red Cedar Road
East Lansing, MI, 48824

My research develops advanced mathematical frameworks—commutative algebra, topological data analysis, spectral data analysis, and differential geometry—into practical tools for AI-driven molecular science. These methods span from foundational mathematical theory to applied problems in drug design, protein engineering, materials discovery, and viral evolution, alongside a continuing line of work in complex analysis and operator theory. Representative publications are linked under each theme below; the full list with abstracts and citation metrics is on the Publications page.

Mathematical Foundation of Data Science

Commutative Algebra, Topological data analysis, Spectral data analysis, Geometric data analysis
A review of topological data analysis and topological deep learning in molecular sciences, J. Chem. Inf. Model. (2025)
A cohomology-based Gromov-Hausdorff metric approach for quantifying molecular similarity, Scientific Reports (2025)
Persistent Dirac for molecular representation, Scientific Reports (2023)

Mathematical AI in Molecular Science [Poster]

Drug design, Protein-protein interactions, Protein engineering, Materials discovery
Evaluation of AlphaFold 3’s Protein–Protein Complexes for Predicting Binding Free Energy Changes upon Mutation, J. Chem. Inf. Model. (2024)
Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation, Computers in Biology and Medicine (2024)
Commutative algebra reveals genetic origin of diseases, arXiv preprint (2025)

Mathematical Virology and Therapeutic Discovery

Workflow diagram for predicting deep mutational scanning of SARS-CoV-2 spike protein RBD-ACE2 complexes using topological deep learning — Illustration of the workflow for predicting deep mutational scanning (DMS) of SARS-CoV-2 S protein RBD-ACE2 complexes using topological deep learning. [Paper, Poster]

Virus evolution, Cross-species transmission, Deep mutational scanning [Poster]
AI-driven therapeutic discovery
Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning, Virus Evolution (2025)
Preventing future zoonosis: SARS-CoV-2 mutations enhance human–animal cross-transmission, Computers in Biology and Medicine (2024)
Drug Resistance Predictions Based on a Directed Flag Transformer, Advanced Science (2024)

Complex Analysis and Operator Theory

Extremal Problems (Korenblum Maximum Principle)
Operators acting on complex function spaces
A Korenblum Maximum Principle for Weighted Hilbert spaces of entire Dirichlet series with real frequencies, Journal of Mathematics and Mathematical Sciences (2025)
Korenblum constants for various weighted Fock spaces, Complex Variables and Elliptic Equations (2022)
Korenblum constants for some function spaces, Proc. Amer. Math. Soc. (2020)

See the full list of publications, with abstracts and citation metrics, on the Publications page.