Zhiwei Nie - RankMe

14 papers A* 3Journal 11

Year	Rank	Type	Title / Venue / Authors
2026	A*	`conf`	BiHiTo: Biomolecular Hierarchy-inspired Tokenization. AAAI Ruochong Zheng, Yutian Liu, Yian Zhao, Zhiwei Nie, Xuehan Hou, Chang Liu, Siwei Ma, Youdong Mao, Jie Chen
2026	A*	`conf`	ProAR: Probabilistic Autoregressive Modeling for Molecular Dynamics. AAAI Kaiwen Cheng, Yutian Liu, Zhiwei Nie, Mujie Lin, Yanzhen Hou, Yiheng Tao, Chang Liu, Jie Chen, Youdong Mao, Yonghong Tian
2026	J	`jnl`	Pseudodata-guided Invariant Representation Learning Boosts the Out-of-Distribution Generalization in Enzymatic Kinetic Parameter Prediction. CoRR Haomin Wu, Zhiwei Nie, Hongyu Zhang, Zhixiang Ren
2025	J	`jnl`	A Unified Peptide Generative Framework via a Weakly Order-Dependent Autoregressive Language Model and Lifelong Learning. J. Chem. Inf. Model. Zhiwei Nie, Daixi Li, Yutian Liu, Fan Xu, Hongyu Zhang, Xiansong Huang, Xudong Liu, Zhennan Wang, Yiming Ma, Yuxin Ye, Feng Yin, Wen-Bin Zhang, Zhixiang Ren, Zhihong Liu, Zigang Li, Jie Chen
2025	J	`jnl`	A unified evolution-driven deep learning framework for virus variation driver prediction. Nat. Mac. Intell. Zhiwei Nie, Xudong Liu, Jie Chen, Zhennan Wang, Yutian Liu, Haorui Si, Tianyi Dong, Fan Xu, Guoli Song, Yu Wang, Peng Zhou, Wen Gao, Yonghong Tian
2025	J	`jnl`	Aligning sequence and structure representations leveraging protein domains for function prediction. Expert Syst. Appl. Mingqing Wang, Zhiwei Nie, Yonghong He, Athanasios V. Vasilakos, Zhixiang Ren
2025	J	`jnl`	Deep learning methods for protein representation and function prediction: A comprehensive overview. Eng. Appl. Artif. Intell. Mingqing Wang, Zhiwei Nie, Yonghong He, Athanasios V. Vasilakos, Qiang Shawn Cheng, Zhixiang Ren
2025	J	`jnl`	Generative prediction of real-world prevalent SARS-CoV-2 mutation with Briefings Bioinform. Xudong Liu, Zhiwei Nie, Haorui Si, Xurui Shen, Yutian Liu, Xiansong Huang, Tianyi Dong, Fan Xu, Zhixiang Ren, Peng Zhou, Jie Chen
2025	A*	`conf`	MTPNet: Multi-Grained Target Perception for Unified Activity Cliff Prediction. IJCAI Zishan Shu, Yufan Deng, Hongyu Zhang, Zhiwei Nie, Jie Chen
2025	J	`jnl`	MTPNet: Multi-Grained Target Perception for Unified Activity Cliff Prediction. CoRR Zishan Shu, Yufan Deng, Hongyu Zhang, Zhiwei Nie, Jie Chen
2025	J	`jnl`	OmniESI: A unified framework for enzyme-substrate interaction prediction with progressive conditional deep learning. CoRR Zhiwei Nie, Hongyu Zhang, Hao Jiang, Yutian Liu, Xiansong Huang, Fan Xu, Jie Fu, Zhixiang Ren, Yonghong Tian, Wen-Bin Zhang, Jie Chen
2025	J	`jnl`	Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence. Briefings Bioinform. Zhiwei Nie, Yiming Ma, Yutian Liu, Xiansong Huang, Zhihong Liu, Peng Yang, Fan Xu, Feng Yin, Zigang Li, Jie Fu, Zhixiang Ren, Wen-Bin Zhang, Jie Chen
2024	J	`jnl`	ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception. CoRR Mingqing Wang, Zhiwei Nie, Yonghong He, Zhixiang Ren
2023	J	`jnl`	Running ahead of evolution - AI-based simulation for predicting future high-risk SARS-CoV-2 variants. Int. J. High Perform. Comput. Appl. Jie Chen, Zhiwei Nie, Yu Wang, Kai Wang, Fan Xu, Zhiheng Hu, Bing Zheng, Zhennan Wang, Guoli Song, Jingyi Zhang, Jie Fu, Xiansong Huang, Zhongqi Wang, Zhixiang Ren, Qiankun Wang, Daixi Li, Dongqing Wei, Bin Zhou, Chao Yang, Yonghong Tian