Zheng, Shuangjia

18 publications

NeurIPS 2025 Accurately Predicting Protein Mutational Effects via a Hierarchical Many-Body Attention Network Dahao Xu, Jiahua Rao, Mingming Zhu, Jixian Zhang, Wei Lu, Shuangjia Zheng, Yuedong Yang

CVPR 2025 Multi-Modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery Jiahua Rao, Hanjing Lin, Leyu Chen, Jiancong Xie, Shuangjia Zheng, Yuedong Yang

NeurIPS 2025 Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-Design Nianzu Yang, Songlin Jiang, Jian Ma, Huaijin Wu, Shuangjia Zheng, Wengong Jin, Junchi Yan

ICLRW 2025 Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-Design Nianzu Yang, Jian Ma, Songlin Jiang, Huaijin Wu, Shuangjia Zheng, Wengong Jin, Junchi Yan

ICLR 2025 Retrieval Augmented Diffusion Model for Structure-Informed Antibody Design and Optimization Zichen Wang, Yaokun Ji, Jianing Tian, Shuangjia Zheng

NeurIPS 2025 RiboFlow: Conditional De Novo RNA Co-Design via Synergistic Flow Matching Runze Ma, Zhongyue Zhang, Zichen Wang, Will Hua, Jiahua Rao, Zhuomin Zhou, Shuangjia Zheng

NeurIPSW 2024 AlphaFold3, a Secret Sauce for Predicting Mutational Effects on Protein-Protein Interactions Wei Lu, Jixian Zhang, Jiahua Rao, Zhongyue Zhang, Shuangjia Zheng

NeurIPSW 2024 BindingGYM: A Large-Scale Mutational Dataset Toward Deciphering Protein-Protein Interactions Wei Lu, Jixian Zhang, Ming Gu, Shuangjia Zheng

NeurIPSW 2024 Effective Protein-Protein Interaction Exploration with PPIretrieval Chenqing Hua, Connor W. Coley, Guy Wolf, Doina Precup, Shuangjia Zheng

NeurIPSW 2024 EnzymeFlow: Generating Reaction-Specific Enzyme Catalytic Pockets Through Flow Matching and Co-Evolutionary Dynamics Chenqing Hua, Yong Liu, Dinghuai Zhang, Odin Zhang, Sitao Luan, Kevin K Yang, Guy Wolf, Doina Precup, Shuangjia Zheng

NeurIPS 2024 ReactZyme: A Benchmark for Enzyme-Reaction Prediction Chenqing Hua, Bozitao Zhong, Sitao Luan, Liang Hong, Guy Wolf, Doina Precup, Shuangjia Zheng

NeurIPSW 2023 DynamicBind: Predicting Ligand-Specific Protein-Ligand Complex Structure with a Deep Equivariant Generative Model Wei Lu, Jixian Zhang, Huang Weifeng, Ziqiao Zhang, Chengtao Li, Shuangjia Zheng

IJCAI 2022 Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang

NeurIPS 2022 TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction Wei Lu, Qifeng Wu, Jixian Zhang, Jiahua Rao, Chengtao Li, Shuangjia Zheng

AAAI 2021 Communicative Message Passing for Inductive Relation Reasoning Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu

IJCAI 2021 Learning Attributed Graph Representation with Communicative Message Passing Transformer Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang

IJCAI 2020 Communicative Representation Learning on Attributed Molecular Graphs Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang

NeurIPS 2020 RetroXpert: Decompose Retrosynthesis Prediction like a Chemist Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang