GraphMI: Extracting Private Graph Data from Graph Neural Networks. - Zaixi Zhang; Qi Liu 003; Zhenya Huang; Hao Wang 076; Chengqiang Lu; Chuanren Liu; Enhong Chen (IJCAI, 2021)

Motif-based Graph Self-Supervised Learning for Molecular Property Prediction. - Zaixi Zhang; Qi Liu 003; Hao Wang 076; Chengqiang Lu; Chee-Kong Lee (NeurIPS, 2021)

Backdoor Attacks to Graph Neural Networks. - Zaixi Zhang; Jinyuan Jia 001; Binghui Wang; Neil Zhenqiang Gong (SACMAT, 2021)

ProtGNN: Towards Self-Explaining Graph Neural Networks. - Zaixi Zhang; Qi Liu 003; Hao Wang 076; Chengqiang Lu; Cheekong Lee (AAAI, 2022)

FLDetector: Defending Federated Learning Against Model Poisoning Attacks via Detecting Malicious Clients. - Zaixi Zhang; Xiaoyu Cao; Jinyuan Jia 001; Neil Zhenqiang Gong (KDD, 2022)

Hierarchical Graph Transformer with Adaptive Node Sampling. - Zaixi Zhang; Qi Liu 003; Qingyong Hu; Chee-Kong Lee (NeurIPS, 2022)

FLCert: Provably Secure Federated Learning Against Poisoning Attacks. - Xiaoyu Cao; Zaixi Zhang; Jinyuan Jia 001; Neil Zhenqiang Gong (IEEE Trans. Inf. Forensics Secur., 2022)

Untargeted Attack against Federated Recommendation Systems via Poisonous Item Embeddings and the Defense. - Yang Yu 001; Qi Liu 003; Likang Wu; Runlong Yu; Sanshi Lei Yu; Zaixi Zhang (AAAI, 2023)

Backdoor Defense via Deconfounded Representation Learning. - Zaixi Zhang; Qi Liu 003; Zhicai Wang; Zepu Lu; Qingyong Hu (CVPR, 2023)

Molecule Generation For Target Protein Binding with Structural Motifs. - Zaixi Zhang; Yaosen Min; Shuxin Zheng; Qi Liu 003 (ICLR, 2023)

Learning Subpocket Prototypes for Generalizable Structure-based Drug Design. - Zaixi Zhang; Qi Liu 003 (ICML, 2023)

Knowledge Distillation for High Dimensional Search Index. - Zepu Lu; Jin Chen 008; Defu Lian; Zaixi Zhang; Yong Ge; Enhong Chen (NeurIPS, 2023)

AdaptSSR: Pre-training User Model with Augmentation-Adaptive Self-Supervised Ranking. - Yang Yu; Qi Liu 003; Kai Zhang 038; Yuren Zhang; Chao Song; Min Hou; Yuqing Yuan; Zhihao Ye; Zaixi Zhang; Sanshi Lei Yu (NeurIPS, 2023)

Full-Atom Protein Pocket Design via Iterative Refinement. - Zaixi Zhang; Zepu Lu; Zhongkai Hao; Marinka Zitnik; Qi Liu 003 (NeurIPS, 2023)

FedRecover: Recovering from Poisoning Attacks in Federated Learning using Historical Information. - Xiaoyu Cao; Jinyuan Jia 001; Zaixi Zhang; Neil Zhenqiang Gong (SP, 2023)

Differentiable Optimized Product Quantization and Beyond. - Zepu Lu; Defu Lian; Jin Zhang 035; Zaixi Zhang; Chao Feng 008; Hao Wang 076; Enhong Chen (WWW, 2023)

An Equivariant Generative Framework for Molecular Graph-Structure Co-Design. - Zaixi Zhang; Qi Liu 003; Chee-Kong Lee; Chang-Yu Hsieh; Enhong Chen (CoRR, 2023)

A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design. - Zaixi Zhang; Jiaxian Yan; Qi Liu 003; Enhong Chen (CoRR, 2023)

Sparse Attention-Based Neural Networks for Code Classification. - Ziyang Xiang; Zaixi Zhang; Qi Liu 003 (CoRR, 2023)

Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking. - Jiaxian Yan; Zaixi Zhang; Kai Zhang 038; Qi Liu 003 (CoRR, 2023)

Model Inversion Attacks Against Graph Neural Networks. - Zaixi Zhang; Qi Liu 003; Zhenya Huang; Hao Wang 076; Chee-Kong Lee; Enhong Chen (IEEE Trans. Knowl. Data Eng., 2023)

Binding-Adaptive Diffusion Models for Structure-Based Drug Design. - Zhilin Huang; Ling Yang 006; Zaixi Zhang; Xiangxin Zhou; Yu Bao; Xiawu Zheng; Yuwei Yang; Yu Wang; Wenming Yang (AAAI, 2024)

What Improves the Generalization of Graph Transformers? A Theoretical Dive into the Self-attention and Positional Encoding. - Hongkang Li; Meng Wang 003; Tengfei Ma 001; Sijia Liu 001; Zaixi Zhang; Pin-Yu Chen (ICML, 2024)

DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking. - Jiaxian Yan; Zaixi Zhang; Jintao Zhu; Kai Zhang 038; Jianfeng Pei; Qi Liu 003 (NeurIPS, 2024)

FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling. - Zaixi Zhang; Mengdi Wang; Qi Liu (NeurIPS, 2024)

Generalized Protein Pocket Generation with Prior-Informed Flow Matching. - Zaixi Zhang; Marinka Zitnik; Qi Liu 003 (NeurIPS, 2024)

Towards Few-Shot Self-explaining Graph Neural Networks. - Jingyu Peng; Qi Liu 003; Linan Yue; Zaixi Zhang; Kai Zhang 038; Yunhao Sha (ECML/PKDD (6), 2024)

FedGT: Federated Node Classification with Scalable Graph Transformer. - Zaixi Zhang; Qingyong Hu; Yang Yu; Weibo Gao; Qi Liu 003 (CoRR, 2024)

Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. - Odin Zhang; Yufei Huang 002; Shichen Cheng; Mengyao Yu; Xujun Zhang; Haitao Lin; Yundian Zeng; Mingyang Wang 004; Zhenxing Wu; Huifeng Zhao; Zaixi Zhang; Chenqing Hua; et al. (CoRR, 2024)

Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate? - Kangyu Zheng; Yingzhou Lu; Zaixi Zhang; Zhongwei Wan; Yao Ma; Marinka Zitnik; Tianfan Fu (CoRR, 2024)

Model Inversion Attacks Through Target-Specific Conditional Diffusion Models. - Ouxiang Li; Yanbin Hao; Zhicai Wang; Bin Zhu 006; Shuo Wang 008; Zaixi Zhang; Fuli Feng (CoRR, 2024)

FoldMark: Protecting Protein Generative Models with Watermarking. - Zaixi Zhang; Ruofan Jin; Kaidi Fu; Le Cong; Marinka Zitnik; Mengdi Wang (CoRR, 2024)

Efficient generation of protein pockets with PocketGen. - Zaixi Zhang; Wan Xiang Shen; Qi Liu 003; Marinka Zitnik (Nat. Mac. Intell., 2024)

GraphPrompter: Multi-Stage Adaptive Prompt Optimization for Graph In-Context Learning. - Rui Lv; Zaixi Zhang; Kai Zhang 038; Qi Liu 003; Weibo Gao; Jiawei Liu; Jiaxia Yan; Linan Yue; Fangzhou Yao (ICDE, 2025)

From Understanding to Excelling: Template-Free Algorithm Design through Structural-Functional Co-Evolution. - Zhe Zhao 008; Haibin Wen; Pengkun Wang 001; Ye Wei; Zaixi Zhang; Xi Lin 001; Fei Liu 044; Bo An 001; Hui Xiong 001; Yang Wang 015; Qingfu Zhang 001 (CoRR, 2025)

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking. - Yize Jiang; Xinze Li; Yuanyuan Zhang; Jin Han; Youjun Xu; Ayush Pandit; Zaixi Zhang; Mengdi Wang; Mengyang Wang; Chong Liu; Guang Yang; Yejin Choi 001; et al. (CoRR, 2025)

GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance. - Zaixi Zhang; Zhenghong Zhou; Ruofan Jin; Le Cong; Mengdi Wang (CoRR, 2025)

STELLA: Self-Evolving LLM Agent for Biomedical Research. - Ruofan Jin; Zaixi Zhang; Mengdi Wang; Le Cong (CoRR, 2025)