Ben Daniel Jones
Graduate Student, Department of Mathematics
Pronouns: he/him
Email: jones657@msu.edu
Website: https://www.benjones-math.com/
Bio
I am a 5th year math PhD candidate at Michigan State University working with Guo-Wei Wei to develop tools in **Geometric and Topological Deep Learning** for computational biology. Previously, I earned my MA in math, BS in computer science, and BS in math at The University of Alabama. A large amount of my dissertation work is on **Persistent Laplacians**, a generalization of the graph Laplacian to higher-dimensional multi-scale settings that generalizes persistent homology from topological data analysis (TDA). I developed **PETLS: Persistent Topological Laplacian Software**, which is a fast and flexible python library. Here are the links for the [PETLS Documentation](https://www.benjones-math.com/software/PETLS/index.html), the [PETLS Github](https://github.com/bdjones13/PETLS/), and the [arXiv paper](https://arxiv.org/abs/2508.11560).
Selected Publications
- Benjamin Jones and Guo-Wei Wei, "Khovanov Laplacian and Khovanov Dirac for Knots and Links," J. Phys. Complex. 6(2), 025014, 2025. View Publication
- Benjamin Jones and Guo-Wei Wei, "Persistent Directed Flag Laplacian," Foundations of Data Science, 7(3), 737-758, 2025. View Publication
- Benjamin Jones and Guo-Wei Wei, "PETLS: PErsistent Topological Laplacian Software," https://arxiv.org/abs/2508.11560, 2025. View Publication
- Chunhuan Zhang, Sean Cottrell, Benjamin Jones, Yueying Zhu, Huahai Qiu, Bengong Zhang, Tianshou Zhou, and Jian Jiang, "Meta-analysis and Topological Perturbation in Interactomic Network for Anti-opioid Addiction Drug Repurposing," J. Chem. Inf. Model. 65(22):12313-12330, 2025. View Publication
- Dong Chen, Gengzhuo Liu, Hongyan Du, Benjamin Jones, Junjie Wee, Rui Wang, Jiahui Chen, Jana Shen, and Guo-Wei Wei, "Drug Resistance Predictions Based on a Directed Flag Transformer," Advanced Science e02756, 2025. View Publication
- Mushal Zia, Benjamin Jones, Hongsong Feng, Guo-Wei Wei, "Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction," Journal of Chemical Theory and Computation 21(8), 4276-4285, 2025. View Publication
- Tobias Timofeyev, Christopher Potvin, Benjamin Jones, Kristin Kurianski, Miguel Lopez, and Sunia Tanweer, "Asymmetrically Weighted Dowker Persistence and Applications in Dynamical Systems," https://arxiv.org/abs/2601.04559, 2026. View Publication