About me
I am a Research Engineer at Tsinghua AIR, mentored by Professor Yanyan Lan. My focus is on AI for Drug Discovery, particularly deep learning models for small molecule and protein representation and generation.
Previously, I worked as a Machine Learning Engineer at Bytedance(June 2021 - Sep 2022), specializing in Recommendation Systems. My academic credentials include a Bachelor’s in Computer Engineering from the University of Toronto (2019) and a Master’s in Electrical Engineering from Caltech (2021).
Education
- 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
Publications (* euqal contribution)
- 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 - 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. - cancerAlign: Stratifying tumors by unsupervised alignment across cancer types.
Bowen Gao, Yunan Luo, Jianzhu Ma, Sheng Wang
In biorxiv preprint.