ML Anthology

Xia, Jun

40 publications

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
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 2025 EDBench: Large-Scale Electron Density Data for Molecular Modeling Hongxin Xiang, Ke Li, Mingquan Liu, Zhixiang Cheng, Bin Yao, Wenjie Du, Jun Xia, Li Zeng, Xin Jin, Xiangxiang Zeng
IJCAI 2025 Electron Density-Enhanced Molecular Geometry Learning Hongxin Xiang, Jun Xia, Xin Jin, Wenjie Du, Li Zeng, Xiangxiang Zeng
IJCAI 2025 GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype Changxi Chi, Jun Xia, Jingbo Zhou, Jiabei Cheng, Chang Yu, Stan Z. Li
ICLRW 2025 GuardReasoner: Towards Reasoning-Based LLM Safeguards Yue Liu, Hongcheng Gao, Shengfang Zhai, Jun Xia, Tianyi Wu, Zhiwei Xue, Yulin Chen, Kenji Kawaguchi, Jiaheng Zhang, Bryan Hooi
IJCAI 2025 MTGIB-UNet: A Multi-Task Graph Information Bottleneck and Uncertainty Weighted Network for ADMET Prediction Xuqiang Li, Wenjie Du, Jun Xia, Jianmin Wang, Xiaoqi Wang, Yang Yang, Yang Wang
ICLR 2025 MeToken: Uniform Micro-Environment Token Boosts Post-Translational Modification Prediction Cheng Tan, Zhenxiao Cao, Zhangyang Gao, Lirong Wu, Siyuan Li, Yufei Huang, Jun Xia, Bozhen Hu, Stan Z. Li
NeurIPS 2025 PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation Jiabei Cheng, Changxi Chi, Jingbo Zhou, Hongyi Xin, Jun Xia
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
ICML 2024 A Graph Is Worth $k$ Words: Euclideanizing Graph Using Pure Transformer Zhangyang Gao, Daize Dong, Cheng Tan, Jun Xia, Bozhen Hu, Stan Z. Li
NeurIPS 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
IJCAI 2024 An Image-Enhanced Molecular Graph Representation Learning Framework Hongxin Xiang, Shuting Jin, Jun Xia, Man Zhou, Jianmin Wang, Li Zeng, Xiangxiang Zeng
NeurIPSW 2024 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
AAAI 2024 Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer Cheng Tan, Zhangyang Gao, Lirong Wu, Jun Xia, Jiangbin Zheng, Xihong Yang, Yue Liu, Bozhen Hu, Stan Z. Li
ICML 2024 Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective Cheng Tan, Zhangyang Gao, Hanqun Cao, Xingran Chen, Ge Wang, Lirong Wu, Jun Xia, Jiangbin Zheng, 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 End-to-End Learnable Clustering for Intent Learning in Recommendation Yue Liu, Shihao Zhu, Jun Xia, Yingwei Ma, Jian Ma, Xinwang Liu, Shengju Yu, Kejun Zhang, Wenliang Zhong
NeurIPS 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
NeurIPSW 2024 GeneGench: Systematic Evaluation of Genomic Foundation Models and Beyond Zicheng Liu, Jiahui Li, Lei Xin, Siyuan Li, Chang Yu, Zelin Zang, Cheng Tan, Yufei Huang, Yajingbai, Jun Xia, Stan Z. Li
ICLR 2024 KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement Zhangyang Gao, Cheng Tan, Xingran Chen, Yijie Zhang, Jun Xia, Siyuan Li, Stan Z. Li
NeurIPS 2024 Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure Bozhen Hu, Cheng Tan, Jun Xia, Yue Liu, Lirong Wu, Jiangbin Zheng, Yongjie Xu, Yufei Huang, Stan Z. Li
IJCAI 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
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 ProtGO: Function-Guided Protein Modeling for Unified Representation Learning Bozhen Hu, Cheng Tan, Yongjie Xu, Zhangyang Gao, Jun Xia, Lirong Wu, Stan Z. Li
NeurIPS 2024 WaveAttack: Asymmetric Frequency Obfuscation-Based Backdoor Attacks Against Deep Neural Networks Jun Xia, Zhihao Yue, Yingbo Zhou, Zhiwei Ling, Yiyu Shi, Xian Wei, Mingsong Chen
IJCAI 2023 A Systematic Survey of Chemical Pre-Trained Models Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li
CVPR 2023 CVT-SLR: Contrastive Visual-Textual Transformation for Sign Language Recognition with Variational Alignment Jiangbin Zheng, Yile Wang, Cheng Tan, Siyuan Li, Ge Wang, Jun Xia, Yidong Chen, Stan Z. Li
ECML-PKDD 2023 Co-Supervised Pre-Training of Pocket and Ligand Zhangyang Gao, Cheng Tan, Jun Xia, Stan Z. Li
ICML 2023 Dink-Net: Neural Clustering on Large Graphs Yue Liu, Ke Liang, Jun Xia, Sihang Zhou, Xihong Yang, Xinwang Liu, Stan Z. Li
ICLR 2023 Mole-BERT: Rethinking Pre-Training Graph Neural Networks for Molecules Jun Xia, Chengshuai Zhao, Bozhen Hu, Zhangyang Gao, Cheng Tan, Yue Liu, Siyuan Li, Stan Z. Li
CVPR 2023 Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning Cheng Tan, Zhangyang Gao, Lirong Wu, Yongjie Xu, Jun Xia, Siyuan Li, Stan Z. Li
NeurIPS 2023 Understanding the Limitations of Deep Models for Molecular Property Prediction: Insights and Solutions Jun Xia, Lecheng Zhang, Xiao Zhu, Yue Liu, Zhangyang Gao, Bozhen Hu, Cheng Tan, Jiangbin Zheng, Siyuan Li, Stan Z. Li
ICMLW 2023 Why Deep Models Often Cannot Beat Non-Deep Counterparts on Molecular Property Prediction? Jun Xia, Lecheng Zhang, Xiao Zhu, Stan Z. Li
IJCAI 2022 Eliminating Backdoor Triggers for Deep Neural Networks Using Attention Relation Graph Distillation Jun Xia, Ting Wang, Jiepin Ding, Xian Wei, Mingsong Chen
WACV 2022 Generalized Clustering and Multi-Manifold Learning with Geometric Structure Preservation Lirong Wu, Zicheng Liu, Jun Xia, Zelin Zang, Siyuan Li, Stan Z. Li
ECML-PKDD 2022 GraphMixup: Improving Class-Imbalanced Node Classification by Reinforcement Mixup and Self-Supervised Context Prediction Lirong Wu, Jun Xia, Zhangyang Gao, Haitao Lin, Cheng Tan, Stan Z. Li
ICMLW 2022 Pre-Training Graph Neural Networks for Molecular Representations: Retrospect and Prospect Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li
ICML 2022 ProGCL: Rethinking Hard Negative Mining in Graph Contrastive Learning Jun Xia, Lirong Wu, Ge Wang, Jintao Chen, Stan Z. Li
ECML-PKDD 2021 Invertible Manifold Learning for Dimension Reduction Siyuan Li, Haitao Lin, Zelin Zang, Lirong Wu, Jun Xia, Stan Z. Li