Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers. - Wenjie Du 003; Xiaoting Yang; Di Wu 057; Fenfen Ma; Baicheng Zhang; Chaochao Bao; Yaoyuan Huo; Jun Jiang; Xin Chen; Yang Wang 015 (Briefings Bioinform., 2023)

MolTC: Towards Molecular Relational Modeling In Language Models. - Junfeng Fang; Shuai Zhang; Chang Wu 003; Zhengyi Yang 007; Zhiyuan Liu 001; Sihang Li 002; Kun Wang 056; Wenjie Du 003; Xiang Wang 010 (ACL (Findings), 2024)

MMGNN: A Molecular Merged Graph Neural Network for Explainable Solvation Free Energy Prediction. - Wenjie Du 003; Shuai Zhang; Di Wu 057; Jun Xia 001; Ziyuan Zhao; Junfeng Fang; Yang Wang 015 (IJCAI, 2024)

AdaNovo: Towards Robust emph{De Novo} Peptide Sequencing in Proteomics against Data Biases. - Jun Xia 001; Shaorong Chen; Jingbo Zhou; Xiaojun Shan; Wenjie Du 003; Zhangyang Gao; Cheng Tan 012; Bozhen Hu; Jiangbin Zheng 002; Stan Z. Li (NeurIPS, 2024)

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning. - Sizhe Liu; Jun Xia 001; Lecheng Zhang; Yuchen Liu; Yue Liu 008; Wenjie Du 003; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Hongxin Xiang; Stan Z. Li (NeurIPS, 2024)

NovoBench: Benchmarking Deep Learning-based emph{De Novo} Sequencing Methods in Proteomics. - Jingbo Zhou; Shaorong Chen; Jun Xia 001; Sizhe Liu; Tianze Ling; Wenjie Du 003; Yue Liu 008; Jianwei Yin; Stan Z. Li (NeurIPS, 2024)

AdaNovo: Adaptive emph{De Novo} Peptide Sequencing with Conditional Mutual Information. - Jun Xia 001; Shaorong Chen; Jingbo Zhou; Tianze Ling; Wenjie Du 003; Sizhe Liu; Stan Z. Li (CoRR, 2024)

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics. - Jingbo Zhou; Shaorong Chen; Jun Xia 001; Sizhe Liu; Tianze Ling; Wenjie Du 003; Yue Liu 008; Jianwei Yin; Stan Z. Li (CoRR, 2024)

Text-guided Diffusion Model for 3D Molecule Generation. - Yanchen Luo; Junfeng Fang; Sihang Li 002; Zhiyuan Liu 001; Jiancan Wu; An Zhang 003; Wenjie Du 003; Xiang Wang 010 (CoRR, 2024)

ReNovo: Retrieval-Based emph{De Novo} Mass Spectrometry Peptide Sequencing. - Shaorong Chen; Jun Xia 001; Jingbo Zhou; Lecheng Zhang; Zhangyang Gao; Bozhen Hu; Cheng Tan 012; Wenjie Du 003; Stan Z. Li (ICLR, 2025)

Iterative Substructure Extraction for Molecular Relational Learning with Interactive Graph Information Bottleneck. - Shuai Zhang; Junfeng Fang; Xuqiang Li; Hongxin Xiang; Alan Xia; Ye Wei; Wenjie Du 003; Yang Wang 015 (ICLR, 2025)

Soft causal learning for generalized molecule property prediction: An environment perspective. - Limin Li; Kuo Yang; Wenjie Du 003; Pengkun Wang 001; Zhengyang Zhou; Yang Wang 015 (CoRR, 2025)