cancerAlign: Stratifying tumors by unsupervised alignment across cancer types
Bowen Gao, Yunan Luo, Jianzhu Ma, Sheng Wang
Preprint, 2020
Education
- B.S. in Computer Engineering, University of Toronto, 2019
- M.S. in Electrical Engineering, Caltech, 2021
- Ph.D in Computer Science, Tsinghua University, 2027 (expected)
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
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, 2023DrugCLIP: 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, 2023Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods
Minsi Ren, Bowen Gao, Bo Qiang, Yanyan Lan
NeurIPS GenBio workshop, 2023Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment
Bowen Gao*, Yinjun Jia*, Yuanle Mo, Yuyan Ni, Weiying Ma, Zhiming Ma, Yanyan Lan
ICLR, 2024Rethinking 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, 2024Multi-level Interaction Modeling for Protein Mutational Effect Prediction
Yuanle Mo, Xin Hong, Bowen Gao, Yinjun Jia, Yanyan Lan
Under Review, 2024From 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
Under Review, 2024SIU: 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
Under Review, 2024