Dongyu Xue

20 papers A* 8Journal 12
YearRankTypeTitle / Venue / Authors
2025 J jnl
AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model.
CoRR
Changze Lv, Jiang Zhou, Siyu Long, Lihao Wang, Jiangtao Feng, Dongyu Xue, Yu Pei, Hao Wang, Zherui Zhang, Yuchen Cai, Zhiqiang Gao, Ziyuan Ma, Jiakai Hu, Chaochen Gao, Jingjing Gong, Yuxuan Song, Shuyi Zhang, Xiaoqing Zheng, Deyi Xiong, Lei Bai, Wanli Ouyang, Ya-Qin Zhang, Wei-Ying Ma, Bowen Zhou, Hao Zhou
2025 A* conf
An All-Atom Generative Model for Designing Protein Complexes.
ICML
Ruizhe Chen, Dongyu Xue, Xiangxin Zhou, Zaixiang Zheng, Xiangxiang Zeng, Quanquan Gu
2025 J jnl
An All-Atom Generative Model for Designing Protein Complexes.
CoRR
Ruizhe Chen, Dongyu Xue, Xiangxin Zhou, Zaixiang Zheng, Xiangxiang Zeng, Quanquan Gu
2025 A* conf
DPLM-2: A Multimodal Diffusion Protein Language Model.
ICLR
Xinyou Wang, Zaixiang Zheng, Fei Ye, Dongyu Xue, Shujian Huang, Quanquan Gu
2025 A* conf
Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling.
ICML
Xiangxin Zhou, Mingyu Li, Yi Xiao, Jiahan Li, Dongyu Xue, Zaixiang Zheng, Jianzhu Ma, Quanquan Gu
2025 J jnl
Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling.
CoRR
Xiangxin Zhou, Mingyu Li, Yi Xiao, Jiahan Li, Dongyu Xue, Zaixiang Zheng, Jianzhu Ma, Quanquan Gu
2025 A* conf
Elucidating the Design Space of Multimodal Protein Language Models.
ICML
Cheng-Yen Hsieh, Xinyou Wang, Daiheng Zhang, Dongyu Xue, Fei Ye, Shujian Huang, Zaixiang Zheng, Quanquan Gu
2025 J jnl
Elucidating the Design Space of Multimodal Protein Language Models.
CoRR
Cheng-Yen Hsieh, Xinyou Wang, Daiheng Zhang, Dongyu Xue, Fei Ye, Shujian Huang, Zaixiang Zheng, Quanquan Gu
2025 A* conf
ProteinBench: A Holistic Evaluation of Protein Foundation Models.
ICLR
Fei Ye, Zaixiang Zheng, Dongyu Xue, Yuning Shen, Lihao Wang, Yiming Ma, Yan Wang, Xinyou Wang, Xiangxin Zhou, Quanquan Gu
2024 A* conf
Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization.
NeurIPS
Xiangxin Zhou, Dongyu Xue, Ruizhe Chen, Zaixiang Zheng, Liang Wang, Quanquan Gu
2024 J jnl
Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization.
CoRR
Xiangxin Zhou, Dongyu Xue, Ruizhe Chen, Zaixiang Zheng, Liang Wang, Quanquan Gu
2024 J jnl
DPLM-2: A Multimodal Diffusion Protein Language Model.
CoRR
Xinyou Wang, Zaixiang Zheng, Fei Ye, Dongyu Xue, Shujian Huang, Quanquan Gu
2024 A* conf
Diffusion Language Models Are Versatile Protein Learners.
ICML
Xinyou Wang, Zaixiang Zheng, Fei Ye, Dongyu Xue, Shujian Huang, Quanquan Gu
2024 J jnl
Diffusion Language Models Are Versatile Protein Learners.
CoRR
Xinyou Wang, Zaixiang Zheng, Fei Ye, Dongyu Xue, Shujian Huang, Quanquan Gu
2024 J jnl
ProteinBench: A Holistic Evaluation of Protein Foundation Models.
CoRR
Fei Ye, Zaixiang Zheng, Dongyu Xue, Yuning Shen, Lihao Wang, Yiming Ma, Yan Wang, Xinyou Wang, Xiangxin Zhou, Quanquan Gu
2024 J jnl
ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design.
CoRR
Yiming Ma, Fei Ye, Yi Zhou, Zaixiang Zheng, Dongyu Xue, Quanquan Gu
2023 A* conf
Structure-informed Language Models Are Protein Designers.
ICML
Zaixiang Zheng, Yifan Deng, Dongyu Xue, Yi Zhou, Fei Ye, Quanquan Gu
2023 J jnl
Structure-informed Language Models Are Protein Designers.
CoRR
Zaixiang Zheng, Yifan Deng, Dongyu Xue, Yi Zhou, Fei Ye, Quanquan Gu
2023 J jnl
Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer.
Genom. Proteom. Bioinform.
Gongchen Zhang, Chenyu Zhu, Xiaohan Chen, Jifang Yan, Dongyu Xue, Zixuan Wei, Guohui Chuai, Qi Liu
2021 J jnl
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery.
Bioinform.
Shaoqi Chen, Dongyu Xue, Guohui Chuai, Qiang Yang, Qi Liu