Publications

A full list of my publications is available on Google Scholar.

Mathematical AI

• Faisal Suwayyid, Yuta Hozumi, Mushal Zia, JunJie Wee, Hongsong Feng, and Guo-Wei Wei. CAKR: commutative algebra k-mer representations for genomics. Nature Communications.
• Jian Liu and Hongsong Feng. Persistent local Laplacian prediction of protein-ligand binding affinities. Journal of Chemical Information and Modeling, 2026.
• Hongsong Feng, Li Shen, Jian Liu, and Guo-Wei Wei. Mayer homology learning prediction of protein-ligand binding affinities. Journal of Computational Biophysics and Chemistry, 2024, 1–14.
• Li Shen, Hongsong Feng, Fengling Li, Fengchun Lei, Jie Wu, and Guo-Wei Wei. Knot data analysis using multiscale Gauss link integral. Proceedings of the National Academy of Sciences, 121(42), e2408431121. (*Co-first authors.)

AI-aided drug design and discovery

• Hongsong Feng, Faisal Suwayyid, Mushal Zia, JunJie Wee, Yuta Hozumi, Chunlong Chen, and Guo-Wei Wei. CAML: Commutative algebra machine learning — a case study on protein-ligand binding affinity prediction. Journal of Chemical Information and Modeling, 2025.
• Hongsong Feng, Sean Cottrell, Yuta Hozumi, and Guo-Wei Wei. Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data. Computers in Biology and Medicine, 171 (2024), 108211.
• Hongsong Feng and Guo-Wei Wei. Virtual screening of DrugBank database for hERG blockers using topological Laplacian-assisted AI models. Computers in Biology and Medicine, 153 (2023), 106491.
• Hongsong Feng, Rui Wang, Chang-Guo Zhan, and Guo-Wei Wei. Multi-objective molecular optimization for opioid use disorder treatment using generative network complex. Journal of Medicinal Chemistry, 66 (2023), 12479–12498.
• Hongsong Feng, Kaifu Gao, Dong Chen, Li Shen, Alfred J. Robison, Edmund Ellsworth, and Guo-Wei Wei. Machine learning analysis of cocaine addiction informed by DAT, SERT, and NET-based interactome networks. Journal of Chemical Theory and Computation, 18 (2022), 2703–2719.
• Li Shen, Hongsong Feng, Yuchi Qiu, and Guo-Wei Wei. SVSBI: Sequence-based virtual screening of biomolecular interactions. Communications Biology, 6 (2023), 536.

Numerical algorithms for partial differential equations

• Hongsong Feng and Shan Zhao. FFT-based high order central difference schemes for the three-dimensional Poisson equation with various types of boundary conditions. Journal of Computational Physics, 410 (2020), 109391.
• Hongsong Feng and Shan Zhao. A fourth order finite difference method for solving elliptic interface problems with the FFT acceleration. Journal of Computational Physics, 419 (2020), 109677.
• Yiming Ren, Hongsong Feng, and Shan Zhao. FFT-based high order central difference schemes for Poisson’s equation on irregular domain. Journal of Computational Physics, 448 (2022), 110762.