Bowen Gao

Bowen Gao

Ph.D. Student @ Tsinghua University | AI for Drug Discovery

Publications

You can also find my articles on my Google Scholar profile.

Drugging the Undruggable: Benchmarking and Modeling Fragment-Based Screening

Published in ICLR 2026, 2026

Haichuan Tan*, Bowen Gao*, Jiaxin Li, Yinjun Jia, Wenyu Zhu, Wenxuan Xie, Yihong Liu, Yanwen Huang, Jianhui Wang, Yuanhuan Mo, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan

Recommended citation: Haichuan Tan*, Bowen Gao*, Jiaxin Li, Yinjun Jia, Wenyu Zhu, Wenxuan Xie, Yihong Liu, Yanwen Huang, Jianhui Wang, Yuanhuan Mo, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan. "Drugging the Undruggable: Benchmarking and Modeling Fragment-Based Screening." International Conference on Learning Representations (ICLR), 2026. #

S²Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening

Published in AAAI 2026, 2026

Bowei He, Bowen Gao, Yankai Chen, Yanyan Lan, Chen Ma, Philip S. Yu, Ya-Qin Zhang, Wei-Ying Ma

Recommended citation: Bowei He, Bowen Gao, Yankai Chen, Yanyan Lan, Chen Ma, Philip S. Yu, Ya-Qin Zhang, Wei-Ying Ma. "S²Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening." AAAI Conference on Artificial Intelligence, 2026. #

Learning Protein–Ligand Binding in Hyperbolic Space

Published in AAAI 2026, 2026

Jianhui Wang, Wenyu Zhu, Bowen Gao*, Xin Hong, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan

Recommended citation: Jianhui Wang*, Wenyu Zhu*, Bowen Gao*, Xin Hong, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan. "Learning Protein–Ligand Binding in Hyperbolic Space." AAAI Conference on Artificial Intelligence, 2026. #

AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation

Published in NeurIPS 2025, 2025

Wenyu Zhu, Jianhui Wang, Bowen Gao*, Yinjun Jia, Haichuan Tan, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan

Recommended citation: Wenyu Zhu*, Jianhui Wang*, Bowen Gao*, Yinjun Jia, Haichuan Tan, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan. "AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation." Advances in Neural Information Processing Systems (NeurIPS), 2025. #

Reframing Structure-Based Drug Design Model Evaluation via Metrics Correlated to Practical Needs

Published in ICLR 2025, 2025

Bowen Gao</strong>, Haichuan Tan, Yanwen Huang, Minsi Ren, Xiao Huang, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan

Recommended citation: Bowen Gao*, Haichuan Tan*, Yanwen Huang, Minsi Ren, Xiao Huang, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan. "Reframing Structure-Based Drug Design Model Evaluation via Metrics Correlated to Practical Needs." International Conference on Learning Representations (ICLR), 2025. https://openreview.net/pdf?id=RyWypcIMiE