1. Rationalized All-Atom Protein Design with Unified Multi-modal Bayesian Flow
Hanlin Wu, Yuxuan Song, Zhe Zhang, Zhilong Zhang,
Hao Zhou*, Wei-Ying Ma, and Jingjing Liu
In NeurIPS, 2025.
2. Accelerating 3D Molecule Generative Models with Trajectory Diagnosis
Zhilong Zhang, Yuxuan Song, Yichun Wang, Jingjing Gong, Hanlin Wu, Dongzhan Zhou,
Hao Zhou*, and Wei-Ying Ma
In NeurIPS, 2025.
3. DAPO: An Open-Source LLM Reinforcement Learning System at Scale
Qiying Yu, Zheng Zhang, Ruofei Zhu, Yufeng Yuan, Xiaochen Zuo, Yu Yue, Weinan Dai, Tiantian Fan, Gaohong Liu, Juncai Liu, LingJun Liu, Xin Liu, Haibin Lin, Zhiqi Lin, Bole Ma, Guangming Sheng, Yuxuan Tong, Chi Zhang, Mofan Zhang, Ru Zhang, Wang Zhang, Hang Zhu, Jinhua Zhu, Jiaze Chen, Jiangjie Chen, Chengyi Wang, Hongli Yu, Yuxuan Song, Xiangpeng Wei,
Hao Zhou*, Jingjing Liu, Wei-Ying Ma, Ya-Qin Zhang, Lin Yan, Yonghui Wu, and Mingxuan Wang*
In NeurIPS, 2025.
4. ShortListing Model: A Streamlined SimplexDiffusion for Discrete Variable Generation
Yuxuan Song, Zhe Zhang, Yu Pei, Jingjing Gong, Qiying Yu, Zheng Zhang, Mingxuan Wang,
Hao Zhou*, Jingjing Liu, and Wei-Ying Ma
In NeurIPS, 2025.
5. MOF-BFN: Metal-Organic Frameworks Structure Prediction via Bayesian Flow Networks
Rui Jiao, Hanlin Wu, Wenbing Huang, Yuxuan Song, Yawen Ouyang, Yu Rong, Tingyang Xu, Pengju Wang,
Hao Zhou*, Wei-Ying Ma, Jingjing Liu, and Yang Liu*
In NeurIPS, 2025.
6. Retro-R1: LLM-based Agentic Retrosynthesis
Wei Liu, Jiangtao Feng, Hongli Yu, Yuxuan Song, Yuqiang Li, Shufei Zhang, LEI BAI, Wei-Ying Ma, and
Hao Zhou*
In NeurIPS, 2025.
7. Enigmata: Scaling Logical Reasoning in Large Language Models with Synthetic Verifiable Puzzles
Jiangjie Chen, Qianyu He, Siyu Yuan, Aili Chen, Zhicheng Cai, Weinan Dai, Hongli Yu, Qiying Yu, Xuefeng Li, Jiaze Chen,
Hao Zhou, and Mingxuan Wang
In NeurIPS, 2025.
8. RetroDiff: Retrosynthesis as Multi-stage Distribution Interpolation
Yiming Wang, Yuxuan Song, Yiqun Wang, Minkai Xu, Rui Wang,
Hao Zhou*, and Wei-Ying Ma
In AISTATS, 2025.
9. Smooth Interpolation for Improved Discrete Graph Generative Models
Yuxuan Song, Juntong Shi, Jingjing Gong, Minkai Xu, Stefano Ermon,
Hao Zhou*, and Wei-Ying Ma
In ICML, 2025.
10. Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng,
Hao Zhou*, and Wei-Ying Ma
In ICML, 2025.
11. Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks
Keyue Qiu, Yuxuan Song, Jie Yu, Hongbo Ma, Ziyao Cao, Zhilong Zhang, Yushuai Wu, Mingyue Zheng,
Hao Zhou*, and Wei-Ying Ma
In ICML, 2025.
12. SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics
Suyuan Zhao, YIZHEN LUo, Ganbo Yang, Yan Zhong,
Hao Zhou*, and Zaiqing Nie
In ICML, 2025.
13. Steering Protein Family Design through Profile Bayesian Flow
Jingjing Gong, Yu Pei, Siyu Long, Yuxuan Song, Zhe Zhang, Wenhao Huang, Ziyao Cao, Shuyi Zhang,
Hao Zhou*, and Wei-Ying Ma
In ICLR, 2025.
14. A Periodic Bayesian Flow for Material Generation
Hanlin Wu, Yuxuan Song, Jingjing Gong, Ziyao Cao, Yawen Ouyang, Jianbing Zhang,
Hao Zhou*, Wei-Ying Ma, and Jingjing Liu
In ICLR, 2025.
