📃 Publications †Equal Contribution NeurIPS 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 NeurIPS 2024 Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptative Residual Module Jingbo Zhou†, Yixuan Du†, Ruqiong Zhang†, Jun Xia, Zhizhi Yu, Zelin Zang, Di Jin, Carl Yang, Rui Zhang, Stan Z. Li NeurIPS 2024 AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information Jun Xia†, Shaorong Chen†, Jingbo Zhou†, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan, Bozhen Hu, Jiangbin Zheng, Stan Z. Li ICLR 2025 Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo Jun Xia†, Sizhe Liu†, Jingbo Zhou†, Shaorong Chen, hongxin xiang, Zicheng Liu, Yue Liu, Stan Z. Li 🔥 NeurIPS 2024 AIDrugX Spotlight ICLR 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 IJCAI 2025 A comprehensive and systematic review for deep learning-based de novo peptide sequencing Jun Xia†, Jingbo Zhou†, Shaorong Chen†, Tianze Ling†, Stan Z. Li IJCAI 2025 GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype Changxi Chi, Xia Jun, Jingbo Zhou, Jiabei Cheng, Chang Yu, Stan Z. Li Preprint NodeReg: Mitigating the Imbalance and Distribution Shift Effects in Semi-Supervised Node Classification via Norm Consistency Shenzhi Yang, Jun Xia, Jingbo Zhou, Xingkai Yao, Xiaofang Zhang
