Author

Wei‐Ying Ma

Tsinghua UniversityORCID 0000-0002-7384-0735Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 4 Research Focus:benchmarking· 3 Approach:contrastive learning· 3 Research Focus:drug response / drug discovery· 2 Organism:human· 2 Assay:protein structure· 2 Research Focus:software / tool· 2 Research Focus:database / resource· 1

Frequent Co-Authors

Kangjie ZhengiD· 2 shared Siyu LongiD· 2 shared Xinyu DaiiD· 2 shared Zaiqing NieiD· 2 shared Bowen GaoiD· 1 shared Chuangye YaniD· 1 shared Haichuan Tan· 1 shared Hao ZhouiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersBioinformatics

Kangjie ZhengORCID

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Author profile →

4 papers

Recent·Most cited

Deep contrastive learning enables genome-wide virtual screening

Yinjun Jia, Bowen Gao, Jiaxin Tan, Jiqing Zheng, Xin Hong, Wenyu Zhu, Haichuan Tan, Yuan Xiao, Liping Tan, Hongyi Cai, Yanwen Huang, Zhiheng Deng, Xiangwei Wu, Yue Jin, Yafei Yuan, , Yanyan Lan

DrugCLIP, a contrastive dense-retrieval model for pockets and molecules, beats docking on DUD-E and LIT-PCBA and screened about 10,000 human AlphaFold2 proteins in 24 hours.

Science · Jan 8, 2026Peer-reviewedBioinformatics✦ In-depth digest

Peptide Design through Binding Interface Mimicry

Xiangzhe Kong, Rui Jiao, Haowei Lin, Ruihan Guo, Wenbing Huang, Wei‐Ying Ma, Zihua Wang, Yang Liu, Jianzhu Ma

PepMimic, an all-atom latent diffusion model guided by a contrastive interface encoder, designs peptides mimicking known binders; 8% of tested peptides across five targets reached 10^-8M KD.

Nature Biomedical Engineering · Oct 1, 2025Peer-reviewedBiochemistry✦ In-depth digest

MOL-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective

Junwei Yang, Kangjie Zheng, Siyu Long, Zaiqing Nie, Ming Zhang, Xinyu Dai, Wei‐Ying Ma, Hao Zhou

The paper introduces a 3D molecular auto-encoder with a new training objective, achieving better performance than existing methods.

bioRxiv · Apr 13, 2024 · PreprintBioinformatics

ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling

Kangjie Zheng, Siyu Long, Tianyu Lu, Junwei Yang, Xinyu Dai, Ming Zhang, Zaiqing Nie, Wei‐Ying Ma, Hao Zhou

This paper introduces ESM-AA, a protein language model that operates at both atom and residue scales, outperforming previous methods in protein-molecule tasks.

bioRxiv · Mar 4, 2024 · PreprintBioinformatics