Finding the Stars in the Fireworks: Deep Understanding of Motion Sensor Fingerprint. - Huiqi Liu; Xiangyang Li 001; Lan Zhang 002; Yaochen Xie; Zhenan Wu; Qian Dai; Ge Chen; Chunxiao Wan (INFOCOM, 2018)

Finding the Stars in the Fireworks: Deep Understanding of Motion Sensor Fingerprint. - Xiangyang Li 001; Huiqi Liu; Lan Zhang 002; Zhenan Wu; Yaochen Xie; Ge Chen; Chunxiao Wan; Zhongwei Liang (IEEE/ACM Trans. Netw., 2019)

Noise2Same: Optimizing A Self-Supervised Bound for Image Denoising. - Yaochen Xie; Zhengyang Wang; Shuiwang Ji (NeurIPS, 2020)

Augmented Equivariant Attention Networks for Electron Microscopy Image Super-Resolution. - Yaochen Xie; Yu Ding 002; Shuiwang Ji (CoRR, 2020)

MoleculeKit: Machine Learning Methods for Molecular Property Prediction and Drug Discovery. - Zhengyang Wang; Meng Liu 015; Youzhi Luo; Zhao Xu 005; Yaochen Xie; Limei Wang; Lei Cai; Shuiwang Ji (CoRR, 2020)

zhengyang-wang/GVTNets: Code for "Global Voxel Transformer Networks for Augmented Microscopy". - Zhengyang Wang; Yaochen Xie; Shuiwang Ji (Zenodo, 2020)

Self-Supervised Learning of Graph Neural Networks: A Unified Review. - Yaochen Xie; Zhao Xu 005; Zhengyang Wang; Shuiwang Ji (CoRR, 2021)

Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks. - Meng Liu 015; Cong Fu 003; Xuan Zhang; Limei Wang; Yaochen Xie; Hao Yuan 001; Youzhi Luo; Zhao Xu 005; Shenglong Xu; Shuiwang Ji (CoRR, 2021)

Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs. - Zhao Xu 005; Youzhi Luo; Xuan Zhang; Xinyi Xu; Yaochen Xie; Meng Liu 015; Kaleb Dickerson; Cheng Deng; Maho Nakata; Shuiwang Ji (CoRR, 2021)

DIG: A Turnkey Library for Diving into Graph Deep Learning Research. - Meng Liu 015; Youzhi Luo; Limei Wang; Yaochen Xie; Hao Yuan 001; Shurui Gui; Haiyang Yu 005; Zhao Xu 005; Jingtun Zhang; Yi Liu 059; Keqiang Yan; Haoran Liu; et al. (J. Mach. Learn. Res., 2021)

Global voxel transformer networks for augmented microscopy. - Zhengyang Wang; Yaochen Xie; Shuiwang Ji (Nat. Mach. Intell., 2021)

Self-Supervised Representation Learning via Latent Graph Prediction. - Yaochen Xie; Zhao Xu 005; Shuiwang Ji (ICML, 2022)

Frontiers of Graph Neural Networks with DIG. - Shuiwang Ji; Meng Liu 015; Yi Liu 059; Youzhi Luo; Limei Wang; Yaochen Xie; Zhao Xu 005; Haiyang Yu 005 (KDD, 2022)

Task-Agnostic Graph Explanations. - Yaochen Xie; Sumeet Katariya; Xianfeng Tang; Edward W. Huang; Nikhil Rao 001; Karthik Subbian; Shuiwang Ji (NeurIPS, 2022)

Advanced graph and sequence neural networks for molecular property prediction and drug discovery. - Zhengyang Wang; Meng Liu 015; Youzhi Luo; Zhao Xu 005; Yaochen Xie; Limei Wang; Lei Cai; Qi Qi 006; Zhuoning Yuan; Tianbao Yang; Shuiwang Ji (Bioinform., 2022)

Augmented Equivariant Attention Networks for Microscopy Image Transformation. - Yaochen Xie; Yu Ding 002; Shuiwang Ji (IEEE Trans. Medical Imaging, 2022)

Self-Supervised Learning of Graph Neural Networks: A Unified Review. - Yaochen Xie; Zhao Xu 005; Jingtun Zhang; Zhengyang Wang; Shuiwang Ji (IEEE Trans. Pattern Anal. Mach. Intell., 2023)

Group Contrastive Self-Supervised Learning on Graphs. - Xinyi Xu; Cheng Deng; Yaochen Xie; Shuiwang Ji (IEEE Trans. Pattern Anal. Mach. Intell., 2023)

Exploring Query Understanding for Amazon Product Search. - Chen Luo 003; Xianfeng Tang; Hanqing Lu; Yaochen Xie; Hui Liu 003; Zhenwei Dai; Limeng Cui; Ashutosh Joshi; Sreyashi Nag; Yang Li 055; Zhen Li; Rahul Goutam; et al. (IEEE Big Data, 2024)

SineNet: Learning Temporal Dynamics in Time-Dependent Partial Differential Equations. - Xuan Zhang; Jacob Helwig; Yuchao Lin; Yaochen Xie; Cong Fu 003; Stephan Wojtowytsch; Shuiwang Ji (ICLR, 2024)

3D Molecular Geometry Analysis with 2D Graphs. - Zhao Xu 005; Yaochen Xie; Youzhi Luo; Xuan Zhang; Xinyi Xu; Meng Liu 015; Kaleb Dickerson; Cheng Deng; Maho Nakata; Shuiwang Ji (SDM, 2024)

SimRAG: Self-Improving Retrieval-Augmented Generation for Adapting Large Language Models to Specialized Domains. - Ran Xu 002; Hui Liu 003; Sreyashi Nag; Zhenwei Dai; Yaochen Xie; Xianfeng Tang; Chen Luo 003; Yang Li 055; Joyce C. Ho; Carl Yang 001; Qi He 002 (CoRR, 2024)

Genetic InfoMax: Exploring Mutual Information Maximization in High-Dimensional Imaging Genetics Studies. - Yaochen Xie; Ziqian Xie; Sheikh Muhammad Saiful Islam; Degui Zhi; Shuiwang Ji (Trans. Mach. Learn. Res., 2024)

Reasoning with Graphs: Structuring Implicit Knowledge to Enhance LLMs Reasoning. - Haoyu Han 001; Yaochen Xie; Hui Liu 003; Xianfeng Tang; Sreyashi Nag; William Headden; Yang Li 055; Chen Luo 003; Shuiwang Ji; Qi He 002; Jiliang Tang (ACL (Findings), 2025)

SimRAG: Self-Improving Retrieval-Augmented Generation for Adapting Large Language Models to Specialized Domains. - Ran Xu 002; Hui Liu 031; Sreyashi Nag; Zhenwei Dai; Yaochen Xie; Xianfeng Tang; Chen Luo 003; Yang Li 055; Joyce C. Ho; Carl Yang 001; Qi He 002 (NAACL (Long Papers), 2025)

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. - Xuan Zhang; Limei Wang; Jacob Helwig; Youzhi Luo; Cong Fu 003; Yaochen Xie; Meng Liu 015; Yuchao Lin; Zhao Xu 005; Keqiang Yan; Keir Adams; Maurice Weiler; et al. (Found. Trends Mach. Learn., 2025)

Beyond Believability: Accurate Human Behavior Simulation with Fine-Tuned LLMs. - Yuxuan Lu 003; Jing Huang; Yan Han 001; Bennet Bei; Yaochen Xie; Dakuo Wang; Zheshen Jessie Wang; Qi He 002 (CoRR, 2025)

AgentA/B: Automated and Scalable Web A/BTesting with Interactive LLM Agents. - Dakuo Wang; Ting-Yao Hsu; Yuxuan Lu 003; Hansu Gu; Limeng Cui; Yaochen Xie; William Headean; Bingsheng Yao; Akash Veeragouni; Jiapeng Liu; Sreyashi Nag; Jessie Wang 003 (CoRR, 2025)