Wenjie Du

According to our database, Wenjie Du authored at least 12 papers between 2023 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

Soft causal learning for generalized molecule property prediction: An environment perspective.

Limin Li, Kuo Yang, Wenjie Du, Pengkun Wang, Zhengyang Zhou, Yang Wang

CoRR, May, 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, Yang Wang

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide Sequencing.

Shaorong Chen, Jun Xia, Jingbo Zhou, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan, Wenjie Du, Stan Z. Li

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

2024

Text-guided Diffusion Model for 3D Molecule Generation.

Yanchen Luo, Junfeng Fang, Sihang Li, Zhiyuan Liu, Jiancan Wu, An Zhang, Wenjie Du, Xiang Wang

CoRR, 2024

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics.

Jingbo Zhou, Shaorong Chen, Jun Xia, Sizhe Liu, Tianze Ling, Wenjie Du, Yue Liu, Jianwei Yin, Stan Z. Li

CoRR, 2024

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information.

Jun Xia, Shaorong Chen, Jingbo Zhou, Tianze Ling, Wenjie Du, Sizhe Liu, Stan Z. Li

CoRR, 2024

NovoBench: Benchmarking Deep Learning-based \emph{De Novo} Sequencing Methods in Proteomics.

Jingbo Zhou, Shaorong Chen, Jun Xia, Sizhe Liu, Tianze Ling, Wenjie Du, Yue Liu, Jianwei Yin, Stan Z. Li

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning.

Sizhe Liu, Jun Xia, Lecheng Zhang, Yuchen Liu, Yue Liu, Wenjie Du, Zhangyang Gao, Bozhen Hu, Cheng Tan, Hongxin Xiang, Stan Z. Li

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics against Data Biases.

Jun Xia, Shaorong Chen, Jingbo Zhou, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan, Bozhen Hu, Jiangbin Zheng, Stan Z. Li

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

MMGNN: A Molecular Merged Graph Neural Network for Explainable Solvation Free Energy Prediction.

Wenjie Du, Shuai Zhang, Di Wu, Jun Xia, Ziyuan Zhao, Junfeng Fang, Yang Wang

Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence, 2024

MolTC: Towards Molecular Relational Modeling In Language Models.

Junfeng Fang, Shuai Zhang, Chang Wu, Zhengyi Yang, Zhiyuan Liu, Sihang Li, Kun Wang, Wenjie Du, Xiang Wang

Proceedings of the Findings of the Association for Computational Linguistics, 2024

2023

Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers.

Wenjie Du, Xiaoting Yang, Di Wu, Fenfen Ma, Baicheng Zhang, Chaochao Bao, Yaoyuan Huo, Jun Jiang, Xin Chen, Yang Wang

Briefings Bioinform., January, 2023