Dongyu Xue

According to our database, Dongyu Xue authored at least 13 papers between 2021 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2026

AMix-2: Establishing Protein as a Native Modality in Large Language Models.

Keyue Qiu, Yixin Wu, Lihao Wang, Yawen Ouyang, Jixiang Yu, Zihan Zhou, Changze Lv, Dongyu Xue, Yuxuan Song, Xinbo Zhang, Hao Wang, Jiangtao Feng, Zhiqiang Gao, Lijun Wu, Xiaoqing Zheng, Ka-Chun Wong, Lei Bai, Ya-Qin Zhang, Wei-Ying Ma, Dahua Lin, Bowen Zhou, Hao Zhou

CoRR, May, 2026

2025

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model.

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

CoRR, July, 2025

Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling.

Xiangxin Zhou, Mingyu Li, Yi Xiao, Jiahan Li, Dongyu Xue, Zaixiang Zheng, Jianzhu Ma, Quanquan Gu

Proceedings of the Forty-second International Conference on Machine Learning, 2025

Elucidating the Design Space of Multimodal Protein Language Models.

Cheng-Yen Hsieh, Xinyou Wang, Daiheng Zhang, Dongyu Xue, Fei Ye, Shujian Huang, Zaixiang Zheng, Quanquan Gu

Proceedings of the Forty-second International Conference on Machine Learning, 2025

An All-Atom Generative Model for Designing Protein Complexes.

Ruizhe Chen, Dongyu Xue, Xiangxin Zhou, Zaixiang Zheng, Xiangxiang Zeng, Quanquan Gu

Proceedings of the Forty-second International Conference on Machine Learning, 2025

ProteinBench: A Holistic Evaluation of Protein Foundation Models.

Fei Ye, Zaixiang Zheng, Dongyu Xue, Yuning Shen, Lihao Wang, Yiming Ma, Yan Wang, Xinyou Wang, Xiangxin Zhou, Quanquan Gu

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

DPLM-2: A Multimodal Diffusion Protein Language Model.

Xinyou Wang, Zaixiang Zheng, Fei Ye, Dongyu Xue, Shujian Huang, Quanquan Gu

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

2024

ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design.

Yiming Ma, Fei Ye, Yi Zhou, Zaixiang Zheng, Dongyu Xue, Quanquan Gu

CoRR, 2024

Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization.

Xiangxin Zhou, Dongyu Xue, Ruizhe Chen, Zaixiang Zheng, Liang Wang, Quanquan Gu

Proceedings of the Advances in Neural Information Processing Systems 37: Annual Conference on Neural Information Processing Systems 2024, 2024

Diffusion Language Models Are Versatile Protein Learners.

Xinyou Wang, Zaixiang Zheng, Fei Ye, Dongyu Xue, Shujian Huang, Quanquan Gu

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

2023

Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer.

Gongchen Zhang, Chenyu Zhu, Xiaohan Chen, Jifang Yan, Dongyu Xue, Zixuan Wei, Guohui Chuai, Qi Liu

Genom. Proteom. Bioinform., 2023

Structure-informed Language Models Are Protein Designers.

Zaixiang Zheng, Yifan Deng, Dongyu Xue, Yi Zhou, Fei Ye, Quanquan Gu

Proceedings of the International Conference on Machine Learning, 2023

2021

FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery.

Shaoqi Chen, Dongyu Xue, Guohui Chuai, Qiang Yang, Qi Liu

Bioinform., 2021