Publications

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

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

Redefining the Task of Bioactivity Prediction

Published in ICLR 2025, 2025

Yanwen Huang*, Bowen Gao*, Yinjun Jia, Hongbo Ma, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan

Recommended citation: Yanwen Huang*, Bowen Gao*, Yinjun Jia, Hongbo Ma, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan. "Redefining the Task of Bioactivity Prediction." International Conference on Learning Representations (ICLR), 2025. https://openreview.net/pdf?id=S8gbnkCgxZ

SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction

Published in Under Review, 2024

Yanwen Huang*, Bowen Gao*, Yinjun Jia, Hongbo Ma, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan

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Multi-level Interaction Modeling for Protein Mutational Effect Prediction

Published in Under Review, 2024

Yuanle Mo, Xin Hong, Bowen Gao, Yinjun Jia, Yanyan Lan

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Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion

Published in ICML, 2024

Bowen Gao</strong>, Minsi Ren, Yuyan Ni, Yanwen Huang, Bo Qiang, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan

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Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment

Published in ICLR, 2024

Bowen Gao</strong>, Yinjun Jia, Yuanle Mo, Yuyan Ni, Weiying Ma, Zhiming Ma, Yanyan Lan

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Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods

Published in NeurIPS GenBio workshop, 2023

Minsi Ren, Bowen Gao, Bo Qiang, Yanyan Lan

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DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening

Published in NeurIPS, 2023

Bowen Gao</strong>, Bo Qiang, Haichuan Tan, Yinjun Jia, Minsi Ren, Minsi Lu, Jingjing Liu, Wei-Ying Ma, Yanyan Lan

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Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D

Published in ICML, 2023

Bo Qiang, Yuxuan Song, Minkai Xu, Jingjing Gong, Bowen Gao, Hao Zhou, Weiying Ma, Yanyan Lan