Hanqun Cao

According to our database, Hanqun Cao authored at least 28 papers between 2022 and 2026.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2026

GeoCycler: Reward-Aligned 3D Diffusion for Constraint-Conditioned Cyclic Peptide Design.

Jingjie Zhang, Hanqun Cao, Haosen Shi, Mutian He, Yu Wang, Zijun Gao, Fang Wu, Xiaojun Yao, Chang-Yu Hsieh, Sinno Jialin Pan, Pranam Chatterjee, Chunbin Gu, Pheng-Ann Heng

CoRR, May, 2026

TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation.

Hanqun Cao, Aastha Pal, Sophia Tang, Yinuo Zhang, Jingjie Zhang, Pheng-Ann Heng, Pranam Chatterjee

CoRR, May, 2026

NoiseRater: Meta-Learned Noise Valuation for Diffusion Model Training.

Fang Wu, Haokai Zhao, Da Xing, Hanqun Cao, Tinson Xu, Yanchao Li, Xiangru Tang, Zehong Wang, Aaron Tu, Kuan Pang, Hanchen Wang, Hongbin Lin, Zeqi Zhou, Yinxi Li, Peng Xia, Li Erran Li, Molei Tao, Jure Leskovec, Aditya Joshi, Yejin Choi

CoRR, May, 2026

Proteo-R1: Reasoning Foundation Models for De Novo Protein Design.

Fang Wu, Weihao Xuan, Heli Qi, Hanqun Cao, Heng-Jui Chang, Zeqi Zhou, Haokai Zhao, Ma Jian, Carl Ma, Yu-Chi Cheng, Kuan Pang, Xiangru Tang, Zehong Wang, Guanlue Li, Hanchen Wang, Kejun Ying, Pan Lu, Chiho Im, Seungju Han, Peng Xia, Tinson Xu, Yinxi Li, Deyao Zhu, Pheng-Ann Heng, Naoto Yokoya, Masashi Sugiyama, Li Erran Li, Jure Leskovec, Yejin Choi

CoRR, May, 2026

RiboSphere: Learning Unified and Efficient Representations of RNA Structures.

Zhou Zhang, Hanqun Cao, Cheng Tan, Fang Wu, Pheng-Ann Heng, Tianfan Fu

CoRR, March, 2026

2025

CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design.

Zijun Gao, Mutian He, Shijia Sun, Hanqun Cao, Jingjie Zhang, Zihao Luo, Xiaorui Wang, Xiaojun Yao, Chang-Yu Hsieh, Chunbin Gu, Pheng-Ann Heng

CoRR, December, 2025

Learning the PTM Code through a Coarse-to-Fine, Mechanism-Aware Framework.

Jingjie Zhang, Hanqun Cao, Zijun Gao, Yu Wang, Shaoning Li, Jun Xu, Cheng Tan, Jun Zhu, Chang-Yu Hsieh, Chunbin Gu, Pheng-Ann Heng

CoRR, October, 2025

Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs.

Kai Zhuang, Jiawei Zhang, Yumou Liu, Hanqun Cao, Chunbin Gu, Mengdi Liu, Zhangyang Gao, Zitong Jerry Wang, Xuanhe Zhou, Pheng-Ann Heng, Lijun Wu, Conghui He, Cheng Tan

CoRR, October, 2025

From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?

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, Yejin Choi, Pheng-Ann Heng, Fang Wu

CoRR, October, 2025

Position: The Hidden Costs and Measurement Gaps of Reinforcement Learning with Verifiable Rewards.

Aaron Tu, Weihao Xuan, Heli Qi, Xu Huang, Qingcheng Zeng, Shayan Talaei, Yijia Xiao, Peng Xia, Xiangru Tang, Yuchen Zhuang, Bing Hu, Hanqun Cao, Wenqi Shi, Tianang Leng, Rui Yang, Yingjian Chen, Ziqi Wang, Irene Li, Nan Liu, Huaxiu Yao, Li Erran Li, Ge Liu, Amin Saberi, Naoto Yokoya, Jure Leskovec, Yejin Choi, Fang Wu

CoRR, September, 2025

A deep reinforcement learning platform for antibiotic discovery.

Hanqun Cao, Marcelo Der Torossian Torres, Jingjie Zhang, Zijun Gao, Fang Wu, Chunbin Gu, Jure Leskovec, Yejin Choi, Cesar de la Fuente-Nunez, Guangyong Chen, Pheng-Ann Heng

CoRR, September, 2025

PLAME: Leveraging Pretrained Language Models to Generate Enhanced Protein Multiple Sequence Alignments.

Hanqun Cao, Xinyi Zhou, Zijun Gao, Chenyu Wang, Xin Gao, Zhi Zhang, Chunbin Gu, Ge Liu, Pheng-Ann Heng

CoRR, July, 2025

Gated-GPS: enhancing protein-protein interaction site prediction with scalable learning and imbalance-aware optimization.

Xin Gao, Hanqun Cao, Jinpeng Li, Jiezhong Qiu, Guangyong Chen, Pheng-Ann Heng

Briefings Bioinform., May, 2025

R3Design: deep tertiary structure-based RNA sequence design and beyond.

Cheng Tan, Yijie Zhang, Zhangyang Gao, Hanqun Cao, Siyuan Li, Siqi Ma, Mathieu Blanchette, Stan Z. Li

Briefings Bioinform., January, 2025

GLID$^2$E: A Gradient-Free Lightweight Fine-tune Approach for Discrete Biological Sequence Design.

Hanqun Cao, Haosen Shi, Chenyu Wang, Sinno Jialin Pan, Pheng-Ann Heng

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2025, 2025

SAGEPhos: Sage Bio-Coupled and Augmented Fusion for Phosphorylation Site Detection.

Jingjie Zhang, Hanqun Cao, Zijun Gao, Xiaorui Wang, Chunbin Gu

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

ChemMiner: A Large Language Model Agent System for Chemical Literature Data Mining.

Kexin Chen, Yuyang Du, Junyou Li, Hanqun Cao, Menghao Guo, Xilin Dang, Lanqing Li, Jiezhong Qiu, Guangyong Chen, Pheng-Ann Heng

Proceedings of the IEEE/CVF International Conference on Computer Vision, ICCV 2025, 2025

2024

A Survey on Generative Diffusion Models.

Hanqun Cao, Cheng Tan, Zhangyang Gao, Yilun Xu, Guangyong Chen, Pheng-Ann Heng, Stan Z. Li

IEEE Trans. Knowl. Data Eng., July, 2024

DEL-Ranking: Ranking-Correction Denoising Framework for Elucidating Molecular Affinities in DNA-Encoded Libraries.

Hanqun Cao, Chunbin Gu, Mutian He, Ning Ma, Chang-Yu Hsieh, Pheng-Ann Heng

CoRR, 2024

Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries.

Chunbin Gu, Mutian He, Hanqun Cao, Guangyong Chen, Chang-Yu Hsieh, Pheng-Ann Heng

CoRR, 2024

Deep Learning-Based Quasi-Conformal Surface Registration for Partial 3D Faces Applied to Facial Recognition.

Yuchen Guo, Hanqun Cao, Lok Ming Lui

CoRR, 2024

An Autonomous Large Language Model Agent for Chemical Literature Data Mining.

Kexin Chen, Hanqun Cao, Junyou Li, Yuyang Du, Menghao Guo, Xin Zeng, Lanqing Li, Jiezhong Qiu, Pheng-Ann Heng, Guangyong Chen

CoRR, 2024

Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective.

Cheng Tan, Zhangyang Gao, Hanqun Cao, Xingran Chen, Ge Wang, Lirong Wu, Jun Xia, Jiangbin Zheng, Stan Z. Li

Proceedings of the Forty-first International Conference on Machine Learning, 2024

2023

ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling.

Odin Zhang, Jintu Zhang, Jieyu Jin, Xujun Zhang, Renling Hu, Chao Shen, Hanqun Cao, Hongyan Du, Yu Kang, Yafeng Deng, Furui Liu, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou

Nat. Mac. Intell., September, 2023

Efficient and accurate large library ligand docking with KarmaDock.

Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang, Zhe Wang, Ercheng Wang, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou

Nat. Comput. Sci., 2023

Learning Robust Classifier for Imbalanced Medical Image Dataset with Noisy Labels by Minimizing Invariant Risk.

Jinpeng Li, Hanqun Cao, Jiaze Wang, Furui Liu, Qi Dou, Guangyong Chen, Pheng-Ann Heng

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023

Fast Non-Markovian Diffusion Model for Weakly Supervised Anomaly Detection in Brain MR Images.

Jinpeng Li, Hanqun Cao, Jiaze Wang, Furui Liu, Qi Dou, Guangyong Chen, Pheng-Ann Heng

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023

2022

A Survey on Generative Diffusion Model.

Hanqun Cao, Cheng Tan, Zhangyang Gao, Guangyong Chen, Pheng-Ann Heng, Stan Z. Li

CoRR, 2022