Hanqun Cao

Hanqun Cao(Hank)

Third-year Ph.D. Student, Computer Science & Engineering, CUHK
Visiting Researcher, Perelman School of Medicine, UPenn

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About

I am a third-year Ph.D. student in the Department of Computer Science and Engineering at The Chinese University of Hong Kong, advised by Prof. Pheng-Ann Heng. I am currently a visiting researcher at the University of Pennsylvania Perelman School of Medicine, working with Prof. Cesar de la Fuente-Nunez in the Machine Biology Group.

My research develops deep generative models and reinforcement learning methods for biomolecular design. I build AI systems that design functional proteins, antimicrobial peptides, RNA, and small molecules — and validate them experimentally. I hold a B.Sc. in Mathematics from CUHK, 2 US patents, and have published in Nature Communications, Nature Machine Intelligence, Nature Computational Science, IEEE TKDE, NeurIPS, ICLR, ICML, ICCV, and MICCAI.

News

2026.05AcceptedSF-Cluster (first) accepted as Oral at ICML 2026 AI4Science Workshop.
2026.05Accepted4 papers at ICML 2026 GenBio Workshop, including Proteo-R1 as Oral.
2026.05AcceptedCA-DEL (co-first) accepted by KDD 2026 Datasets & Benchmark Track.
2026.05AcceptedThe Forgetting-Learning Trade-off (first) accepted by KDD 2026 AI4Sciences Track.
2026.05Accepted3 first/co-first author papers accepted by ICML 2026.

Selected Publications

Selected first/co-first/corresponding author works. Full list on Google Scholar.  * equal contribution  # corresponding

Protein / peptide design
TD3B: transition-directed discrete diffusion for allosteric binder generation
Hanqun Cao, Aastha Pal, Sophia Tang, Yinuo Zhang, Jingjie Zhang, Pheng-Ann Heng, Pranam Chatterjee
ICML 2026Spotlight
Proteo-R1: reasoning foundation models for de novo protein design
Fang Wu*, Weihao Xuan*, Heli Qi*, Hanqun Cao*, Heng-Jui Chang*, Zeqi Zhou*, ..., Pheng-Ann Heng, ..., Jure Leskovec, Yejin Choi
ICML 2026
Learning the PTM code through a coarse-to-fine, mechanism-aware framework
Jingjie Zhang*, Hanqun Cao*, Zijun Gao, ..., Chang-Yu Hsieh, Chunbin Gu
Nat. Commun.Nature Communications, 2026
The forgetting-learning trade-off: making reinforcement learning work for protein language models
Hanqun Cao, Hongrui Zhang, Junde Xu, Zhou Zhang, Lingdong Shen, Minghao Sun, Ge Liu, Jinbo Xu, Wu-Jun Li, Jinren Ni, Cesar de la Fuente-Nunez, Tianfan Fu, Shuting Jin, Pheng-Ann Heng, Fang Wu
KDD 2026AI4Sciences Track
SF-Cluster: frustration-aware MSA subsampling for protein conformation modeling
Hanqun Cao, Zijun Gao, Chunbin Gu, Ge Liu, Pheng-Ann Heng, Pranam Chatterjee
ICML '26 WSAI4Science · Oral
AlloGen: conformation-selective binder design with differential state scoring
Hanqun Cao, Aastha Pal, Sumi Kimura, Yesol Kim, Jingjie Zhang, Pheng-Ann Heng, Pranam Chatterjee
ICML '26 WSGenBio
Structure-guided reinforcement learning for high-affinity antibody design
Hanqun Cao, Shuaike Shen, Weihao Xuan, Jian Ma, Pheng-Ann Heng, Fang Wu
ICML '26 WSGenBio
Bi-TEAM: a unified cross-scale representation learning framework for chemically modified biomolecules
Chunbin Gu*, Zijun Gao*, ..., Hanqun Cao#, Jiajun Bu#, Chang-Yu Hsieh#
PreprintarXiv, 2026
Corresponding author
A deep reinforcement learning platform for antibiotic discovery
Hanqun Cao, Marcelo D.T. Torres, Jingjie Zhang, Zijun Gao, Fang Wu, Chunbin Gu, Jure Leskovec, Yejin Choi, Cesar de la Fuente-Nunez, Guangyong Chen, Pheng-Ann Heng
PreprintbioRxiv, 2025
arXivbioRxiv
ODesign: a world model for biomolecular interaction design
Odin Zhang, ..., Hanqun Cao, ..., et al.
PreprintarXiv, 2025
GLID²E: a gradient-free lightweight fine-tune approach for discrete biological sequence design
Hanqun Cao, Haosen Shi, Chenyu Wang, Sinno Jialin Pan, Pheng-Ann Heng
NeurIPS 2025
SAGEPhos: sage bio-coupled and augmented fusion for phosphorylation site detection
Jingjie Zhang*, Hanqun Cao*, Zijun Gao, Xiaorui Wang, Chunbin Gu
ICLR 2025
InstructPLM: aligning protein language models to follow protein structure instructions
Jiezhong Qiu*, Junde Xu*, Jie Hu*, Hanqun Cao*, et al.
PreprintbioRxiv, 2024
bioRxiv
RNA design
RiboSphere: learning unified and efficient representations of RNA structures
Zhou Zhang*, Hanqun Cao*, Cheng Tan, Fang Wu, Pheng-Ann Heng, Tianfan Fu
ICML 2026
Base-and-sugar dual-frame flow matching for RNA co-design
Junzhe Li, Lijian Peng, Yuhao Li, Yize Zhou, Hanqun Cao, Cheng Tan, Shengchao Liu
ICML '26 WSGenBio
RiboPO: preference optimization for structure- and stability-aware RNA design
Minghao Sun*, Hanqun Cao*, Zhou Zhang*, et al.
PreprintarXiv, 2025
ODesign: a world model for biomolecular interaction design
Odin Zhang, ..., Hanqun Cao, ..., et al.
PreprintarXiv, 2025
R3Design: deep tertiary structure-based RNA sequence design and beyond
Cheng Tan, ..., Hanqun Cao, ..., Stan Z. Li
BIBBriefings in Bioinformatics, 2025
Deciphering RNA secondary structure prediction: a probabilistic K-rook matching perspective
Cheng Tan, Zhangyang Gao, Hanqun Cao, Xingran Chen, et al.
ICML 2024
Small molecule design
CA-DEL: an open multi-target, multi-modal benchmark for learning from DNA-encoded library screens
Mutian He*, Hanqun Cao*, Cheng Tan, Zijun Gao, Xiaojun Yao, Chunbin Gu, Pheng-Ann Heng
KDD 2026Datasets & Benchmark Track
* Co-first author
ODesign: a world model for biomolecular interaction design
Odin Zhang, ..., Hanqun Cao, ..., et al.
PreprintarXiv, 2025
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling
Odin Zhang, ..., Hanqun Cao, ..., et al.
Nat. Mach. Intell.Nature Machine Intelligence, 2023
Efficient and accurate large library ligand docking with KarmaDock
Xujun Zhang, ..., Hanqun Cao, ..., et al.
Nat. Comput. Sci.Nature Computational Science, 2023

Education & Experience

Jun 2025 –
Aug 2026
Visiting Researcher
University of Pennsylvania, Perelman School of Medicine
Machine Biology Group · Host: Prof. Cesar de la Fuente-Nunez · AI-driven antibiotic discovery
Aug 2023 –
Jul 2027
Ph.D. in Computer Science & Engineering
The Chinese University of Hong Kong
Advisor: Prof. Pheng-Ann Heng · Protein design, generative models, RL for biology
Sep 2019 –
Jul 2023
B.Sc. in Mathematics
The Chinese University of Hong Kong
SURP & UROP research scholarships · FYP with Prof. Ronald Lui
Aug 2021 –
Jun 2022
Research Assistant
CUHK CSE, Prof. Yu Li
Protein structural design with score-based diffusion models
May 2021 –
Sep 2021
Summer Research
CUHK Mathematics, Prof. Jun Zou
Inverse problems in elastic wave scattering (FEM)