I am a Computer Science PhD student at Tsinghua University , supervised by Professor Ya-Qin Zhang and Professor Yanyan Lan. My research focuses on AI for Drug Discovery, particularly deep learning models for small molecule and protein representation and generation.

Before beginning my PhD, I worked as a Research Engineer at Tsinghua AIR from September 2022 to August 2024. Prior to that, I worked as a Machine Learning Engineer at Bytedance from June 2021 to September 2022, where I specialized in Recommendation Systems.

I hold a Bachelor’s degree in Computer Engineering from the University of Toronto (2019) and a Master’s degree in Electrical Engineering from Caltech (2021).

Check our Drug-The-Whole-Genome Project at ATOM Lab

Education

• PhD in Computer science and technology, Tsinghua University, 2024 - Present
• M.S. in Electrical Engineering, Caltech, 2019 - 2021
• B.S. in Computer Engineering, University of Toronto, 2014- 2019

Work experience

• 2022.09 - Present: Research Engineer
  • Tsinghua University
  • Worked on AI for Drug Discovery
• 2021.07 - 2022.09: Machine Learning Engineer
  • Bytedance
  • Worked on Recommendation System for Douyin, Tiktok

Preprints (* euqal contribution)

• Deep contrastive learning enables genome-wide virtual screening.
  Yinjun Jia*, Bowen Gao*, Jiaxin Tan*, Xin Hong*, Wenyu Zhu, Haichuan Tan, Yuan Xiao, Yanwen Huang, Yue Jin, Yafei Yuan, Jiekang Tian, Weiying Ma, Yaqin Zhang, Chuangye Yan, Wei Zhang, Yanyan Lan
  In biorxiv preprint
• SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction.
  Yanwen Huang*, Bowen Gao*, Yinjun Jia, Hongbo Ma, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
  In arXiv preprint arXiv:2406.08961
• From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics.
  Bowen Gao*, Haichuan Tan*, Yanwen Huang, Minsi Ren, Xiao Huang, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
  In arXiv preprint arXiv:2406.08980
• Multi-level Interaction Modeling for Protein Mutational Effect Prediction.
  Yuanle Mo*, Xin Hong*, Bowen Gao, Yinjun Jia, Yanyan Lan
  In arXiv preprint arXiv:2405.17802

Publications (* euqal contribution)

• Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion.
  Bowen Gao*, Minsi Ren*, Yuyan Ni, Yanwen Huang, Bo Qiang, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan
  In International Conference on Machine Learning (ICML) 2024.
• Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment.
  Bowen Gao*, Yinjun Jia*, Yuanle Mo, Yuyan Ni, Weiying Ma, Zhiming Ma, Yanyan Lan
  In International Conference on Learning Representations (ICLR) 2024.
• Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods.
  Minsi Ren, Bowen Gao, Bo Qiang, Yanyan Lan
  In GenBio workshop NeurIPS 2023.
• DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening.
  Bowen Gao*, Bo Qiang*, Haichuan Tan, Yinjun Jia, Minsi Ren, Minsi Lu, Jingjing Liu, Wei-Ying Ma, Yanyan Lan
  In Neural Information Processing Systems (NeurIPS) 2023.
• Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D.
  Bo Qiang*, Yuxuan Song*, Minkai Xu, Jingjing Gong, Bowen Gao, Hao Zhou, Weiying Ma, Yanyan Lan
  In International Conference on Machine Learning (ICML) 2023.