Huiyu CAI 蔡辉宇¶
I am a fifth-year PhD candidate at Mila - Quebec AI Institute and Department of Computer Science and Operations Research, University of Montreal, supervised by Prof. Jian Tang. I graduated from the Department of Machine Intelligence, Peking University as an Excellent Graduate in Beijing. I was previously a member of the Language Computing and Web Mining Group, led by Prof. Xiaojun Wan.
I am interested in deep generative models, geometric deep learning and their applications in biomolecular interaction modeling and protein de novo design.
Feel free to reach out (links at webpage footer)!
Publications¶
2026¶
- Generative AI-driven de novo design of high-affinity, epitope-specific antibodies targeting the CD93-IGFBP7 axis for cancer immunotherapy Open Access
Antibody Therapeutics, 2026
Yixin Qian, Youxin Feng, Ming Zou, Huiyu Cai, Jintong Ye, Ping Li, Jian Tang, Mi Deng
2025¶
- M3Site: multiclass multimodal learning for protein active site identification and classification
Briefings in Bioinformatics, 2025
Song Ouyang, Yong Luo, Huiyu Cai, Kehua Su, Fei Liao, Na Zhan, Huangxuan Zhao, Tailang Yin, Lin Zhao, Dongjing Shan
- Rapid restoration of potent neutralization activity against the latest Omicron variant JN.1 via AI rational design and antibody engineering
PNAS, 2025
Yunji Liao, Hang Ma, Zhenyu Wang, Shusheng Wang, Yang He, Yunsong Chang, Huifang Zong, Haoneng Tang, Lei Wang, Yong Ke, Huiyu Cai, Ping Li, Jian Tang, Hua Chen, Aleksandra Drelich, Bi-Hung Peng, Jason Hsu, Vivian Tat, Chien-Te K. Tseng, Jingjing Song, Yunsheng Yuan, Mingyuan Wu, Junjun Liu, Yali Yue, Xiaoju Zhang, Ziqi Wang, Li Yang, Jing Li, Xiaodan Ni, Hongshi Li, Yuning Xiang, Yanlin Bian, Baohong Zhang, Haiyang Yin, Dimiter S. Dimitrov, John Gilly, Lei Han, Hua Jiang, Yueqing Xie, and Jianwei Zhu
2024¶
- GearBind: Pretrainable geometric graph neural network for antibody affinity maturation
Nature Communications, 2024
Huiyu Cai*, Zuobai Zhang*, Mingkai Wang*, Bozitao Zhong*, Quanxiao Li, Yuxuan Zhong, Yanling Wu, Tianlei Ying, Jian Tang *Equal contribution
- MMSite: a multi-modal framework for the identification of active sites in proteins
NeurIPS, 2024
Song Ouyang, Huiyu Cai, Yong Luo, Kehua Su, Lefei Zhang, Bo Du
2023¶
- E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking
ICLR, 2023
Yangtian Zhang*, Huiyu Cai*, Chence Shi, Jian Tang *Equal contribution
2022¶
- Neural Structured Prediction for Inductive Node Classification
ICLR, 2022 (oral)
Meng Qu, Huiyu Cai, Jian Tang *Equal contribution
- Structured Multi-task Learning for Molecular Property Prediction
AISTATS, 2022
Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang
2021 and before¶
- Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data
Nature Communications, 2021 code
Yifan Zhao*, Huiyu Cai*, Zuobai Zhang, Jian Tang, Yue Li
*Equal contribution
- Multi-Modal Sarcasm Detection in Twitter with Hierarchical Fusion Model
ACL, 2019 data
Yitao Cai, Huiyu Cai, Xiaojun Wan
Projects¶
- TorchDrug: A powerful and flexible machine learning platform for drug discovery (Nov. 2021 - now)
- Implementation of the EWLS Algorithm for the Maximum Clique Problem (Dec. 2020 - Jan. 2021)
- Music Source Separation: Theory and Applications (Apr. 2020 - Jun. 2020)
- Raiden Game Implementation in Java (Jan. 2020 - Jun. 2020)
- Fine-grained Face Manipulation via DLGAN (Oct. 2019 - Jan. 2020)
- Bird Sound Classification with CNN (Mar. 2019 - Jun. 2019)
- Mahjong AI Based on Deep Supervised Learning (Mar. 2019 - Jun. 2019)
- Rule-based Doudizhu & Ataxx & Reversi & pysc2-minimap AI (Oct. 2017 - May. 2019)