About me

My name is Gufeng Yu and I am from Yueyang in Hunan Province, China. I’m currently a Ph.D. candidate at the School of Computer Science, Shanghai Jiao Tong University, advised by Prof. Yang Yang. I obtained my Bachelor’s degree from School of Life Sciences and Biotechnology, Shanghai Jiao Tong University in 2023.

My research interest is AI for Science, with a specific focus on the application of AI in biochemistry and organic chemistry. Previously, my work centered on areas such as the reconstruction of gene regulatory networks and the chemical reaction prediction. Currently, I am concentrating on using generative models for the design of complex functional molecules and the analysis of intricate biomolecular dynamics. A key example of this is the de novo design of peptides within the immune system.

I am looking for visiting PhD student opportunities in the field of AI/ML research for Science starting from summer 2026! Please reach out if you find me interesting!

Recent News

• Mar. 2025, CLC-DB has been accepted by Journal of Cheminformatics!
• Dec. 2024, SubA has been accepted by Journal of Chemical Information and Modeling!
• Nov. 2023, MIGGRI has been accepted by PLOS Computational Biology!

Education

• Ph.D. in Computer Science and Technology, Shanghai Jiao Tong University, 2023-Now
• B.S. in Biotechnology (Bioinformatics), Shanghai Jiao Tong University, 2019-2023

Selected Publications

(#equal contribution, *corresponding)

1. Clc-db: an open-source online database of chiral ligands and catalysts
   Gufeng Yu#, Kaiwen Yu#, Xi Wang#, Chenxi Zhang, Yicong Luo, Xiaohong Huo*, Yang Yang*
   Journal of Cheminformatics, 2025, 17(1): 1-12.
   [Paper]
2. Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor
   Gufeng Yu#, Xi Wang#, Yicong Luo, Guanlin Li, Rui Ding, Runhan Shi, Xiaohong Huo*, Yang Yang*
   Journal of Chemical Information and Modeling, 2025, 65(1): 312-325.
   [Paper]
3. MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images
   Yuyang Huang#, Gufeng Yu#, Yang Yang*
   PLOS Computational Biology, 2023, 19(11): e1011623.
   [Paper]

Services

Teaching Assistant (TA): Intelligent Algorithms for Science CS7357 | Fall 2025, Shanghai Jiao Tong University

Honors and Awards

Excellent Graduate | Shanghai Jiao Tong University (2023)

Gold Medal and Best Software Project Nomination | iGEM (2021)