Zaixi Zhang - RankMe

65 papers A* 21C 1Journal 42Unranked 1

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Beyond Affinity: A Benchmark of 1D, 2D, and 3D Methods Reveals Critical Trade-offs in Structure-Based Drug Design. CoRR Kangyu Zheng, Kai Zhang, Jiale Tan, Xuehan Chen, Yingzhou Lu, Zaixi Zhang, Lichao Sun, Marinka Zitnik, Tianfan Fu, Zhiding Liang
2026	J	`jnl`	Beyond Affinity: A Benchmark of 1D, 2D, and 3D Methods Reveals Critical Trade-offs in Structure-Based Drug Design. Trans. Mach. Learn. Res. Kangyu Zheng, Kai Zhang, Jiale Tan, Xuehan Chen, Yingzhou Lu, Zaixi Zhang, Lichao Sun, Marinka Zitnik, Tianfan Fu, Zhiding Liang
2026	A*	`conf`	DAWN: Distributed LLM Multi-Agent Workflow Synthesis. AAAI Guancheng Wan, Mo Zhou, Ziyi Wang, Xiaoran Shang, Eric Hanchen Jiang, Guibin Zhang, Jinhe Bi, Yunpu Ma, Zaixi Zhang, Ke Liang, Wenke Huang
2026	J	`jnl`	Structure-Based Drug Design with Geometric Deep Learning: A Comprehensive Survey. ACM Comput. Surv. Zaixi Zhang, Jiaxian Yan, Yining Huang, Qi Liu, Enhong Chen, Mengdi Wang, Marinka Zitnik
2025	J	`jnl`	A Biosecurity Agent for Lifecycle LLM Biosecurity Alignment. CoRR Meiyin Meng, Zaixi Zhang
2025	J	`jnl`	Evolution without an Oracle: Driving Effective Evolution with LLM Judges. CoRR Zhe Zhao, Yuheng Yang, Haibin Wen, Xiaojie Qiu, Zaixi Zhang, Qingfu Zhang
2025	J	`jnl`	From Understanding to Excelling: Template-Free Algorithm Design through Structural-Functional Co-Evolution. CoRR Zhe Zhao, Haibin Wen, Pengkun Wang, Ye Wei, Zaixi Zhang, Xi Lin, Fei Liu, Bo An, Hui Xiong, Yang Wang, Qingfu Zhang
2025	J	`jnl`	GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance. CoRR Zaixi Zhang, Zhenghong Zhou, Ruofan Jin, Le Cong, Mengdi Wang
2025	J	`jnl`	Generative AI for Biosciences: Emerging Threats and Roadmap to Biosecurity. CoRR Zaixi Zhang, Souradip Chakraborty, Amrit Singh Bedi, Emilin Mathew, Varsha Saravanan, Le Cong, Alvaro Velasquez, Sheng Lin-Gibson, Megan Blewett, Dan Hendrycs, Alex John London, Ellen Zhong, Ben Raphael, Jian Ma, Eric Xing, Russ Altman, George Church, Mengdi Wang
2025	A*	`conf`	GraphPrompter: Multi-Stage Adaptive Prompt Optimization for Graph In-Context Learning. ICDE Rui Lv, Zaixi Zhang, Kai Zhang, Qi Liu, Weibo Gao, Jiawei Liu, Jiaxia Yan, Linan Yue, Fangzhou Yao
2025	J	`jnl`	GraphPrompter: Multi-stage Adaptive Prompt Optimization for Graph In-Context Learning. CoRR Rui Lv, Zaixi Zhang, Kai Zhang, Qi Liu, Weibo Gao, Jiawei Liu, Jiaxia Yan, Linan Yue, Fangzhou Yao
2025	J	`jnl`	LabOS: The AI-XR Co-Scientist That Sees and Works With Humans. CoRR Le Cong, Zaixi Zhang, Xiaotong Wang, Yin Di, Ruofan Jin, Michal Gerasimiuk, Yinkai Wang, Ravi K. Dinesh, David Smerkous, Alex Smerkous, Xuekun Wu, Shilong Liu, Peishan Li, Yi Zhu, Simran Serrao, Ning Zhao, Imran A. Mohammad, John B. Sunwoo, Joseph C. Wu, Mengdi Wang
2025	J	`jnl`	PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking. CoRR Yize Jiang, Xinze Li, Yuanyuan Zhang, Jin Han, Youjun Xu, Ayush Pandit, Zaixi Zhang, Mengdi Wang, Mengyang Wang, Chong Liu, Guang Yang, Yejin Choi, Wu-Jun Li, Tianfan Fu, Fang Wu, Junhong Liu
2025	J	`jnl`	STELLA: Self-Evolving LLM Agent for Biomedical Research. CoRR Ruofan Jin, Zaixi Zhang, Mengdi Wang, Le Cong
2025	J	`jnl`	SafeProtein: Red-Teaming Framework and Benchmark for Protein Foundation Models. CoRR Jigang Fan, Zhenghong Zhou, Ruofan Jin, Le Cong, Mengdi Wang, Zaixi Zhang
2024	A*	`conf`	Binding-Adaptive Diffusion Models for Structure-Based Drug Design. AAAI Zhilin Huang, Ling Yang, Zaixi Zhang, Xiangxin Zhou, Yu Bao, Xiawu Zheng, Yuwei Yang, Yu Wang, Wenming Yang
2024	J	`jnl`	Binding-Adaptive Diffusion Models for Structure-Based Drug Design. CoRR Zhilin Huang, Ling Yang, Zaixi Zhang, Xiangxin Zhou, Yu Bao, Xiawu Zheng, Yuwei Yang, Yu Wang, Wenming Yang
2024	J	`jnl`	Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. CoRR Odin Zhang, Yufei Huang, Shichen Cheng, Mengyao Yu, Xujun Zhang, Haitao Lin, Yundian Zeng, Mingyang Wang, Zhenxing Wu, Huifeng Zhao, Zaixi Zhang, Chenqing Hua, Yu Kang, Sunliang Cui, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou
2024	A*	`conf`	DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking. NeurIPS Jiaxian Yan, Zaixi Zhang, Jintao Zhu, Kai Zhang, Jianfeng Pei, Qi Liu
2024	J	`jnl`	DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking. CoRR Jiaxian Yan, Zaixi Zhang, Jintao Zhu, Kai Zhang, Jianfeng Pei, Qi Liu
2024	J	`jnl`	Efficient generation of protein pockets with PocketGen. Nat. Mac. Intell. Zaixi Zhang, Wan Xiang Shen, Qi Liu, Marinka Zitnik
2024	J	`jnl`	FedGT: Federated Node Classification with Scalable Graph Transformer. CoRR Zaixi Zhang, Qingyong Hu, Yang Yu, Weibo Gao, Qi Liu
2024	A*	`conf`	FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling. NeurIPS Zaixi Zhang, Mengdi Wang, Qi Liu
2024	J	`jnl`	FoldMark: Protecting Protein Generative Models with Watermarking. CoRR Zaixi Zhang, Ruofan Jin, Kaidi Fu, Le Cong, Marinka Zitnik, Mengdi Wang
2024	A*	`conf`	Generalized Protein Pocket Generation with Prior-Informed Flow Matching. NeurIPS Zaixi Zhang, Marinka Zitnik, Qi Liu
2024	J	`jnl`	Model Inversion Attacks Through Target-Specific Conditional Diffusion Models. CoRR Ouxiang Li, Yanbin Hao, Zhicai Wang, Bin Zhu, Shuo Wang, Zaixi Zhang, Fuli Feng
2024	J	`jnl`	Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate? CoRR Kangyu Zheng, Yingzhou Lu, Zaixi Zhang, Zhongwei Wan, Yao Ma, Marinka Zitnik, Tianfan Fu
2024	—	`conf`	Towards Few-Shot Self-explaining Graph Neural Networks. ECML/PKDD (6) Jingyu Peng, Qi Liu, Linan Yue, Zaixi Zhang, Kai Zhang, Yunhao Sha
2024	J	`jnl`	Towards Few-shot Self-explaining Graph Neural Networks. CoRR Jingyu Peng, Qi Liu, Linan Yue, Zaixi Zhang, Kai Zhang, Yunhao Sha
2024	A*	`conf`	What Improves the Generalization of Graph Transformers? A Theoretical Dive into the Self-attention and Positional Encoding. ICML Hongkang Li, Meng Wang, Tengfei Ma, Sijia Liu, Zaixi Zhang, Pin-Yu Chen
2024	J	`jnl`	What Improves the Generalization of Graph Transformers? A Theoretical Dive into the Self-attention and Positional Encoding. CoRR Hongkang Li, Meng Wang, Tengfei Ma, Sijia Liu, Zaixi Zhang, Pin-Yu Chen
2023	J	`jnl`	A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design. CoRR Zaixi Zhang, Jiaxian Yan, Qi Liu, Enhong Chen
2023	A*	`conf`	AdaptSSR: Pre-training User Model with Augmentation-Adaptive Self-Supervised Ranking. NeurIPS Yang Yu, Qi Liu, Kai Zhang, Yuren Zhang, Chao Song, Min Hou, Yuqing Yuan, Zhihao Ye, Zaixi Zhang, Sanshi Lei Yu
2023	J	`jnl`	AdaptSSR: Pre-training User Model with Augmentation-Adaptive Self-Supervised Ranking. CoRR Yang Yu, Qi Liu, Kai Zhang, Yuren Zhang, Chao Song, Min Hou, Yuqing Yuan, Zhihao Ye, Zaixi Zhang, Sanshi Lei Yu
2023	J	`jnl`	An Equivariant Generative Framework for Molecular Graph-Structure Co-Design. CoRR Zaixi Zhang, Qi Liu, Chee-Kong Lee, Chang-Yu Hsieh, Enhong Chen
2023	A*	`conf`	Backdoor Defense via Deconfounded Representation Learning. CVPR Zaixi Zhang, Qi Liu, Zhicai Wang, Zepu Lu, Qingyong Hu
2023	J	`jnl`	Backdoor Defense via Deconfounded Representation Learning. CoRR Zaixi Zhang, Qi Liu, Zhicai Wang, Zepu Lu, Qingyong Hu
2023	A*	`conf`	Differentiable Optimized Product Quantization and Beyond. WWW Zepu Lu, Defu Lian, Jin Zhang, Zaixi Zhang, Chao Feng, Hao Wang, Enhong Chen
2023	A*	`conf`	FedRecover: Recovering from Poisoning Attacks in Federated Learning using Historical Information. SP Xiaoyu Cao, Jinyuan Jia, Zaixi Zhang, Neil Zhenqiang Gong
2023	A*	`conf`	Full-Atom Protein Pocket Design via Iterative Refinement. NeurIPS Zaixi Zhang, Zepu Lu, Zhongkai Hao, Marinka Zitnik, Qi Liu
2023	A*	`conf`	Knowledge Distillation for High Dimensional Search Index. NeurIPS Zepu Lu, Jin Chen, Defu Lian, Zaixi Zhang, Yong Ge, Enhong Chen
2023	A*	`conf`	Learning Subpocket Prototypes for Generalizable Structure-based Drug Design. ICML Zaixi Zhang, Qi Liu
2023	J	`jnl`	Learning Subpocket Prototypes for Generalizable Structure-based Drug Design. CoRR Zaixi Zhang, Qi Liu
2023	J	`jnl`	Model Inversion Attacks Against Graph Neural Networks. IEEE Trans. Knowl. Data Eng. Zaixi Zhang, Qi Liu, Zhenya Huang, Hao Wang, Chee-Kong Lee, Enhong Chen
2023	A*	`conf`	Molecule Generation For Target Protein Binding with Structural Motifs. ICLR Zaixi Zhang, Yaosen Min, Shuxin Zheng, Qi Liu
2023	J	`jnl`	Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking. CoRR Jiaxian Yan, Zaixi Zhang, Kai Zhang, Qi Liu
2023	J	`jnl`	Sparse Attention-Based Neural Networks for Code Classification. CoRR Ziyang Xiang, Zaixi Zhang, Qi Liu
2023	A*	`conf`	Untargeted Attack against Federated Recommendation Systems via Poisonous Item Embeddings and the Defense. AAAI Yang Yu, Qi Liu, Likang Wu, Runlong Yu, Sanshi Lei Yu, Zaixi Zhang
2022	J	`jnl`	FLCert: Provably Secure Federated Learning Against Poisoning Attacks. IEEE Trans. Inf. Forensics Secur. Xiaoyu Cao, Zaixi Zhang, Jinyuan Jia, Neil Zhenqiang Gong
2022	J	`jnl`	FLCert: Provably Secure Federated Learning against Poisoning Attacks. CoRR Xiaoyu Cao, Zaixi Zhang, Jinyuan Jia, Neil Zhenqiang Gong
2022	A*	`conf`	FLDetector: Defending Federated Learning Against Model Poisoning Attacks via Detecting Malicious Clients. KDD Zaixi Zhang, Xiaoyu Cao, Jinyuan Jia, Neil Zhenqiang Gong
2022	J	`jnl`	FLDetector: Defending Federated Learning Against Model Poisoning Attacks via Detecting Malicious Clients. CoRR Zaixi Zhang, Xiaoyu Cao, Jinyuan Jia, Neil Zhenqiang Gong
2022	J	`jnl`	FedRecover: Recovering from Poisoning Attacks in Federated Learning using Historical Information. CoRR Xiaoyu Cao, Jinyuan Jia, Zaixi Zhang, Neil Zhenqiang Gong
2022	A*	`conf`	Hierarchical Graph Transformer with Adaptive Node Sampling. NeurIPS Zaixi Zhang, Qi Liu, Qingyong Hu, Chee-Kong Lee
2022	J	`jnl`	Hierarchical Graph Transformer with Adaptive Node Sampling. CoRR Zaixi Zhang, Qi Liu, Qingyong Hu, Chee-Kong Lee
2022	J	`jnl`	Model Inversion Attacks against Graph Neural Networks. CoRR Zaixi Zhang, Qi Liu, Zhenya Huang, Hao Wang, Chee-Kong Lee, Enhong Chen
2022	A*	`conf`	ProtGNN: Towards Self-Explaining Graph Neural Networks. AAAI Zaixi Zhang, Qi Liu, Hao Wang, Chengqiang Lu, Cheekong Lee
2022	J	`jnl`	Untargeted Attack against Federated Recommendation Systems via Poisonous Item Embeddings and the Defense. CoRR Yang Yu, Qi Liu, Likang Wu, Runlong Yu, Sanshi Lei Yu, Zaixi Zhang
2021	C	`conf`	Backdoor Attacks to Graph Neural Networks. SACMAT Zaixi Zhang, Jinyuan Jia, Binghui Wang, Neil Zhenqiang Gong
2021	A*	`conf`	GraphMI: Extracting Private Graph Data from Graph Neural Networks. IJCAI Zaixi Zhang, Qi Liu, Zhenya Huang, Hao Wang, Chengqiang Lu, Chuanren Liu, Enhong Chen
2021	J	`jnl`	GraphMI: Extracting Private Graph Data from Graph Neural Networks. CoRR Zaixi Zhang, Qi Liu, Zhenya Huang, Hao Wang, Chengqiang Lu, Chuanren Liu, Enhong Chen
2021	A*	`conf`	Motif-based Graph Self-Supervised Learning for Molecular Property Prediction. NeurIPS Zaixi Zhang, Qi Liu, Hao Wang, Chengqiang Lu, Chee-Kong Lee
2021	J	`jnl`	Motif-based Graph Self-Supervised Learning for Molecular Property Prediction. CoRR Zaixi Zhang, Qi Liu, Hao Wang, Chengqiang Lu, Cheekong Lee
2021	J	`jnl`	ProtGNN: Towards Self-Explaining Graph Neural Networks. CoRR Zaixi Zhang, Qi Liu, Hao Wang, Chengqiang Lu, Cheekong Lee
2020	J	`jnl`	Backdoor Attacks to Graph Neural Networks. CoRR Zaixi Zhang, Jinyuan Jia, Binghui Wang, Neil Zhenqiang Gong