Shaoning Li

PhD Student · AI for Science · CUHK

Shaoning Li

I'm a second-year PhD at The Chinese University of Hong Kong (CUHK), supervised by Prof. Pheng Ann Heng. Before that, I spent one year at Mila — Québec AI Institute with Prof. Jian Tang. I received my B.S. from Beihang University, advised by Prof. Hao Peng.

I was a research intern at Microsoft Research AI4Science with Dr. Bin Shao (Feb 2022 – Jun 2023), and worked at BioGeometry on de novo antibody design (Jun 2023 – Jun 2024). I also interned at Tencent (Aug 2024 – May 2025), and I'm currently interning at Anew Labs (Nov 2025 – present).

I work on AI for Science — protein structure prediction (AF2/3), de novo protein design, molecular dynamics, machine learning force fields, and protein–ligand docking. Representative papers are highlighted below. Feel free to reach out if these topics interest you.

Protein structure prediction De novo protein design Molecular dynamics ML force fields Protein–ligand docking

News

Jan 2026NewOne paper accepted at ICLR 2026.
Mar 2025One paper accepted at ICLR 2025 GEM workshop.
Sep 2024One paper accepted at Nature.
Sep 2024One paper accepted at NeurIPS 2024.
Jun 2024One paper accepted at ICML 2024 AI4Science workshop.
Jun 2024One paper accepted at Nature Communications.
Mar 2024One paper accepted at ICLR 2024 GEM workshop.

Selected Publications

* denotes equal contribution.

ProteinAE ProteinAE overview

ProteinAE: Protein Diffusion Autoencoders for Structure Encoding

Shaoning Li*, Le Zhuo*, Yusong Wang, Mingyu Li, Xinheng He, Fandi Wu, Hongsheng Li, Pheng-Ann Heng

14th International Conference on Learning Representations, ICLR 2026

Protein structure encoding · Diffusion autoencoders

Paper
Atomic Flow Matching

Design of Ligand-Binding Proteins with Atomic Flow Matching

Junqi Liu, Shaoning Li, Chence Shi, Zhi Yang, Jian Tang

13th International Conference on Learning Representations, ICLR 2025 GEM workshop

Protein design · Flow matching

Paper
AI2BMD

Ab initio characterization of protein molecular dynamics with AI2BMD

Tong Wang, Xinheng He, Mingyu Li, Yatao Li, Ran Bi, Yusong Wang, Chaoran Cheng, Xiangzhen Shen, Jiawei Meng, He Zhang, Haiguang Liu, Zun Wang, Shaoning Li, Bin Shao, Tie-Yan Liu

Nature, 2024

Molecular dynamics · Machine learning force fields

Paper Code Blog
Neural P3M

Neural P3M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs

Yusong Wang*, Chaoran Cheng*, Shaoning Li*, Yuxuan Ren, Bin Shao, Ge Liu, Pheng-Ann Heng, Nanning Zheng

38th Conference on Neural Information Processing Systems, NeurIPS 2024

Molecular representation learning · Long-range interaction · Geometric GNNs

Paper
AlphaFlow AlphaFlow detail

Improving AlphaFlow for Efficient Protein Ensembles Generation

Shaoning Li*, Mingyu Li*, Yusong Wang, Xinheng He, Nanning Zheng, Jian Zhang, Pheng-Ann Heng

41st International Conference on Machine Learning, ICML 2024 AI4Science workshop

Protein ensembles generation · Flow matching · AlphaFold

Paper
DeepGlycanSite

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite

Xinheng He, Lifen Zhao, Yinping Tian, Rui Li, Qinyu Chu, Zhiyong Gu, Mingyue Zheng, Yusong Wang, Shaoning Li, Hualiang Jiang, Yi Jiang, Liuqing Wen, Dingyan Wang, Xi Cheng

Nature Communications, NC 2024

Binding site prediction · Carbohydrates

Paper
F3low F3low detail

F3low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching

Shaoning Li*, Yusong Wang*, Mingyu Li*, Jian Zhang, Bin Shao, Nanning Zheng, Jian Tang

12th International Conference on Learning Representations, ICLR 2024 GEM workshop

Coarse-grained protein dynamics · SE(3) flow matching

Paper
ViSNet

Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing

Yusong Wang*, Shaoning Li*, Xinheng He, Mingyu Li, Zun Wang, Nanning Zheng, Bin Shao, Tie-Yan Liu

Nature Communications, NC 2024

Molecular dynamics · ML force fields · Equivariant graph neural networks

★ Editor's Highlights in AI and Bio
Paper Code Blog
Geoformer

Geometric Transformer with Interatomic Positional Encoding

Yusong Wang*, Shaoning Li*, Bin Shao, Nanning Zheng, Tie-Yan Liu

37th Conference on Neural Information Processing Systems, NeurIPS 2023

Molecule representation learning · Transformers · Positional encoding

Paper
Event Detection

Reinforced, Incremental and Cross-lingual Event Detection From Social Messages

Hao Peng, Ruitong Zhang, Shaoning Li, Yuwei Cao, Shirui Pan, Philip Yu

IEEE Transactions on Pattern Analysis and Machine Intelligence, T-PAMI 2022

Social event detection · Graph data mining · Reinforcement learning

★ Highly Cited Paper
Paper

Competitions & Awards

Aug 20231st PrizeFirst Global AI Drug Development Competition
Nov 20222nd PlaceOGB-LSC Graph Regression Track @ NeurIPS 2022
Nov 20223rd PlaceOpen Catalyst Project @ NeurIPS 2022
Apr 20211st PrizeNational Award on CCF Excellent Chinese University Students

Blogs

Collaboration

I have close collaborations with Dr. Yusong Wang, Dr. Mingyu Li, Dr. Xinheng He, Dr. Chaoran Cheng, Dr. Le Zhuo, and Dr. Chence Shi.