An attention-based neural network basecaller for Oxford Nanopore sequencing data. - Neng Huang; Fan Nie; Peng Ni; Feng Luo 001; Jianxin Wang 001 (BIBM, 2019)

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks. - Neng Huang; Fan Nie; Peng Ni; Feng Luo 001; Xin Gao 001; Jianxin Wang 001 (Bioinform., 2021)

GraphDE: A Generative Framework for Debiased Learning and Out-of-Distribution Detection on Graphs. - Zenan Li; Qitian Wu; Fan Nie; Junchi Yan (NeurIPS, 2022)

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer. - Neng Huang; Fan Nie; Peng Ni; Xin Gao 001; Feng Luo 001; Jianxin Wang 001 (Briefings Bioinform., 2022)

Fec: a fast error correction method based on two-rounds overlapping and caching. - Jun Zhang; Fan Nie; Neng Huang; Peng Ni; Feng Luo 001; Jianxin Wang 001 (Bioinform., 2022)

SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism. - Neng Huang; Fan Nie; Peng Ni; Feng Luo 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Simplifying and Empowering Transformers for Large-Graph Representations. - Qitian Wu; Wentao Zhao; Chenxiao Yang; Hengrui Zhang; Fan Nie; Haitian Jiang; Yatao Bian; Junchi Yan (NeurIPS, 2023)

Advective Diffusion Transformers for Topological Generalization in Graph Learning. - Qitian Wu; Chenxiao Yang; Kaipeng Zeng; Fan Nie; Michael M. Bronstein; Junchi Yan (CoRR, 2023)

NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data. - Neng Huang; Minghua Xu 005; Fan Nie; Peng Ni; Chuan-Le Xiao; Feng Luo 001; Jianxin Wang 001 (Bioinform., 2023)

Why Increase of Heterogeneity Signals Pre-Deterioration During Tumor Progression: A Unified Mathematical Model. - Yuanling Niu; Hao Kang; Pingyang Wang; Chenchen Guo; Fan Nie; Hongbin Ji; Jiarui Wu; Luonan Chen (SIAM J. Appl. Math., 2023)

Uncertainty-Aware Decision Transformer for Stochastic Driving Environments. - Zenan Li; Fan Nie; Qiao Sun; Fang Da; Hang Zhao (CoRL, 2024)

Learning Divergence Fields for Shift-Robust Graph Representations. - Qitian Wu; Fan Nie; Chenxiao Yang; Junchi Yan (ICML, 2024)

Boosting Offline Reinforcement Learning for Autonomous Driving with Hierarchical Latent Skills. - Zenan Li; Fan Nie; Qiao Sun; Fang Da; Hang Zhao (ICRA, 2024)

FRADE: Forgery-aware Audio-distilled Multimodal Learning for Deepfake Detection. - Fan Nie; Jiangqun Ni; Jian Zhang 086; Bin Zhang 048; Weizhe Zhang (ACM Multimedia, 2024)

Graph Out-of-Distribution Generalization via Causal Intervention. - Qitian Wu; Fan Nie; Chenxiao Yang; Tianyi Bao; Junchi Yan (WWW, 2024)

Generalizing Motion Planners with Mixture of Experts for Autonomous Driving. - Qiao Sun; Huimin Wang; Jiahao Zhan; Fan Nie; Xin Wen; Leimeng Xu; Kun Zhan; Peng Jia; Xianpeng Lang; Hang Zhao (CoRR, 2024)

FactTest: Factuality Testing in Large Language Models with Finite-Sample and Distribution-Free Guarantees. - Fan Nie; Xiaotian Hou; Shuhang Lin; James Zou 001; Huaxiu Yao; Linjun Zhang (CoRR, 2024)

TAROT: Targeted Data Selection via Optimal Transport. - Lan Feng; Fan Nie; Yuejiang Liu; Alexandre Alahi (CoRR, 2024)

Ualign: pushing the limit of template-free retrosynthesis prediction with unsupervised SMILES alignment. - Kaipeng Zeng; Bo Yang; Xin Zhao; Yu Zhang; Fan Nie; Xiaokang Yang 001; Yaohui Jin; Yanyan Xu 002 (J. Cheminformatics, 2024)

DSM: Domain Shift Modeling for general deepfake detection. - Jian Zhang 086; Jiangqun Ni; Fan Nie (Signal Process., 2025)

DIP: Diffusion Learning of Inconsistency Pattern for General DeepFake Detection. - Fan Nie; Jiangqun Ni; Jian Zhang 086; Bin Zhang 048; Weizhe Zhang (IEEE Trans. Multim., 2025)

Domain-invariant and Patch-discriminative Feature Learning for General Deepfake Detection. - Jian Zhang 086; Jiangqun Ni; Fan Nie; Jiwu Huang (ACM Trans. Multim. Comput. Commun. Appl., 2025)

Weak-for-Strong: Training Weak Meta-Agent to Harness Strong Executors. - Fan Nie; Lan Feng; Haotian Ye; Weixin Liang; Pan Lu; Huaxiu Yao; Alexandre Alahi; James Zou 001 (CoRR, 2025)

EvoLM: In Search of Lost Language Model Training Dynamics. - Zhenting Qi; Fan Nie; Alexandre Alahi; James Zou 001; Himabindu Lakkaraju; Yilun Du; Eric P. Xing; Sham M. Kakade; Hanlin Zhang 002 (CoRR, 2025)