Publications

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^* denotes first authorship; multiple starred authors indicate equal contribution.

Conference Papers

Elucidating the Design Space of Multimodal Protein Language Models

Published in ICML, 2025

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

Keywords: multimodal protein language models, structure tokenization, geometric representation learning, protein folding

Recommended citation: 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.
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ProteinBench: A Holistic Evaluation of Protein Foundation Models

Published in ICLR, 2025

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

Keywords: protein foundation models, holistic evaluation

Recommended citation: 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.
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DPLM-2: A Multimodal Diffusion Protein Language Model

Published in ICLR, 2025

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

Keywords: multimodal protein language models, discrete diffusion, structure tokenization, sequence-structure co-generation

Recommended citation: 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.
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Diffusion Language Models Are Versatile Protein Learners

Published in ICML, 2024

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

Keywords: diffusion protein language models, protein sequence generation, protein representation learning, controllable protein design

Recommended citation: 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.
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Helping the Weak Makes You Strong: Simple Multi-Task Learning Improves Non-Autoregressive Translators

Published in EMNLP, 2022

Xinyou Wang^*, Zaixiang Zheng, and Shujian Huang

Keywords: non-autoregressive generation, neural machine translation, multi-task learning

Recommended citation: 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.
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