* denotes first authorship; multiple starred authors indicate equal contribution.
Xinyou Wang*, Cheng-Yen Hsieh*, Daiheng Zhang, Dongyu Xue, Fei Ye, Shujian Huang, Zaixiang Zheng, and Quanquan Gu. (2025). "Elucidating the Design Space of Multimodal Protein Language Models." Proceedings of the 42nd International Conference on Machine Learning, 24156-24175.
Keywords: multimodal protein language models, structure tokenization, geometric representation learning, protein folding
Fei Ye, Zaixiang Zheng, Dongyu Xue, Yuning Shen, Lihao Wang, Yiming Ma, Yan Wang, Xinyou Wang, Xiangxin Zhou, and Quanquan Gu. (2025). "ProteinBench: A Holistic Evaluation of Protein Foundation Models." International Conference on Learning Representations.
Keywords: protein foundation models, holistic evaluation
Xinyou Wang*, Zaixiang Zheng, Fei Ye, Dongyu Xue, Shujian Huang, and Quanquan Gu. (2025). "DPLM-2: A Multimodal Diffusion Protein Language Model." International Conference on Learning Representations.
Keywords: multimodal protein language models, discrete diffusion, structure tokenization, sequence-structure co-generation
Xinyou Wang*, Zaixiang Zheng*, Fei Ye, Dongyu Xue, Shujian Huang, and Quanquan Gu. (2024). "Diffusion Language Models Are Versatile Protein Learners." Proceedings of the 41st International Conference on Machine Learning, 52309-52333.
Keywords: diffusion protein language models, protein sequence generation, protein representation learning, controllable protein design
Xinyou Wang*, Zaixiang Zheng, and Shujian Huang. (2022). "Helping the Weak Makes You Strong: Simple Multi-Task Learning Improves Non-Autoregressive Translators." Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, 5513-5519.
Keywords: non-autoregressive generation, neural machine translation, multi-task learning
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