Bowen Gao

Bowen Gao

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

About me

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 (AIDD), with a particular emphasis on developing and applying deep learning models for the representation and generation of small molecules and proteins. I aim to build data-centric methods to address the data scarcity problem in the AIDD domain.

Before beginning my PhD in August 2024, I worked as a Research Engineer at Tsinghua AIR from September 2022 to August 2024, where I focused on machine learning techniques for drug discovery research. Prior to that, I worked as a Machine Learning Engineer at ByteDance from July 2021 to September 2022, contributing to core recommendation and advertising models for major platforms including Toutiao, Douyin, and TikTok.

I hold a Bachelor’s degree in Computer Science from the University of Toronto (2019, GPA: 3.85/4.0, Highest Honors) and a Master’s degree in Electrical Engineering from Caltech (2021, GPA: 4.2/4.3).

🔬 Research Highlights

🧬 Drug-The-Whole-Genome Project @ ATOM Lab

💊 Molecule Virtual Screening Platform

Publications (* equal contribution)

📅 2026

Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening
Bowei He, Bowen Gao, Yankai Chen, Yanyan Lan, Chen Ma, Philip S. Yu, Ya-Qin Zhang, Wei-Ying Ma
🤖 AAAI 2026 / Paper

Learning Protein–Ligand Binding in Hyperbolic Space
Jianhui Wang*, Wenyu Zhu*, Bowen Gao*, Xin Hong, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan
🤖 AAAI 2026 / Paper

📅 2025

Deep Contrastive Learning Enables Genome-wide Virtual Screening
Yinjun Jia*, Bowen Gao*, Jiaxin Tan*, Jiqing Zheng*, Xin Hong*, Wenyu Zhu, Haichuan Tan, Yuan Xiao, Yanwen Huang, Yue Jin, Yafei Yuan, et al.
⭐ Science 2025 (Accepted) / Paper

CIDD: Collaborative Intelligence for Structure-Based Drug Design Empowered by LLMs
Bowen Gao*, Yanwen Huang*, Yiqiao Liu, Wenxuan Xie, Bowei He, Haichuan Tan, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
🧠 NeurIPS 2025 / Paper

AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation
Wenyu Zhu*, Jianhui Wang*, Bowen Gao*, Yinjun Jia, Haichuan Tan, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan
🧠 NeurIPS 2025 / Paper

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
🎓 ICLR 2025 / Paper

Reframing Structure-Based Drug Design Model Evaluation via Metrics Correlated to Practical Needs
Bowen Gao*, Haichuan Tan*, Yanwen Huang, Minsi Ren, Xiao Huang, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
🎓 ICLR 2025 / Paper

📅 2024

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
🎯 ICML 2024 / Paper / Code

Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment
Bowen Gao*, Yinjun Jia*, Yuanle Mo, Yuyan Ni, Weiying Ma, Zhiming Ma, Yanyan Lan
🎓 ICLR 2024 / Paper / Code

📅 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
🧠 NeurIPS 2023 / Paper / Code

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
🎯 ICML 2023 / Paper / Code

Preprints (* equal contribution)

PharmAgents: Building a Virtual Pharma with Large Language Model Agents
Bowen Gao*, Yanwen Huang*, Yiqiao Liu*, Wenxuan Xie*, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
📑 arXiv 2025 / Paper

Coder as Editor: Code-driven Interpretable Molecular Optimization
Wenyu Zhu, Chengzhu Li, Xiaohe Tian, Yifan Wang, Yinjun Jia, Jianhui Wang, Bowen Gao, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan
📑 arXiv 2025 / Paper

Multi-level Interaction Modeling for Protein Mutational Effect Prediction
Yuanle Mo, Xin Hong, Bowen Gao, Yinjun Jia, Yanyan Lan
📑 arXiv 2024 / Paper

Education

  • Ph.D. in Computer Science and Technology, Tsinghua University, 2024 - Present
    • Supervised by Professor Ya-Qin Zhang and Professor Yanyan Lan
  • M.S. in Electrical Engineering, California Institute of Technology (Caltech), 2019 - 2021
    • GPA: 4.2/4.3
    • Advised by Professor Yaser Abu-Mostafa and Professor Yisong Yue
  • B.S. in Computer Science, University of Toronto, 2014 - 2019
    • GPA: 3.85/4.0
    • Dean’s Honour List for all academic years
    • Graduated with Highest Honors

Work Experience

  • Research Engineer (September 2022 - August 2024)
    • Institute for AI Industry Research, Tsinghua University (AIR)
    • Focus: AI for Drug Discovery, Deep Learning for Molecular Representation and Generation
  • Machine Learning Engineer (July 2021 - September 2022)
    • ByteDance - Applied Machine Learning (AML)
    • Focus: Recommendation Systems and Advertising Models for Toutiao, Douyin, and TikTok
  • Autonomous Driving Algorithm Intern (June 2020 - September 2020)
    • Uber Advanced Technology Group (ATG)
    • Focus: 3D Object Detection and BEV Perception for Autonomous Vehicles

Academic Services

Conference Reviewer:

  • International Conference on Learning Representation (ICLR) 2025, 2026
  • Neural Information Processing Systems (NeurIPS) 2024, 2025
  • International Conference on Machine Learning (ICML) 2025
  • International Conference on Artificial Intelligence and Statistics (AISTATS) 2025
  • Annual Conference on Artificial Intelligence (AAAI) 2026

Journal Reviewer:

  • IEEE Transactions on Neural Networks and Learning Systems (TNNLS)

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