Learning Local and Global Multi-context Representations for Document Classification. - Yi Liu 059; Hao Yuan 001; Shuiwang Ji (ICDM, 2019)

Global Transformer U-Nets for Label-Free Prediction of Fluorescence Images. - Yi Liu 059; Hao Yuan 001; Zhengyang Wang; Shuiwang Ji (CoRR, 2019)

Deep Learning of High-Order Interactions for Protein Interface Prediction. - Yi Liu 059; Hao Yuan 001; Lei Cai; Shuiwang Ji (KDD, 2020)

Global Pixel Transformers for Virtual Staining of Microscopy Images. - Yi Liu 059; Hao Yuan 001; Zhengyang Wang; Shuiwang Ji (IEEE Trans. Medical Imaging, 2020)

Machine Learning Explanations to Prevent Overtrust in Fake News Detection. - Sina Mohseni; Fan Yang 023; Shiva K. Pentyala; Mengnan Du; Yi Liu 059; Nic Lupfer; Xia Hu 001; Shuiwang Ji; Eric D. Ragan (ICWSM, 2021)

A Multi-Stage Attentive Transfer Learning Framework for Improving COVID-19 Diagnosis. - Yi Liu 059; Shuiwang Ji (CoRR, 2021)

Spherical Message Passing for 3D Graph Networks. - Yi Liu 059; Limei Wang; Meng Liu 015; Xuan Zhang; Bora Oztekin; Shuiwang Ji (CoRR, 2021)

Sent2Matrix: Folding Character Sequences in Serpentine Manifolds for Two-Dimensional Sentence. - Hongyang Gao; Yi Liu 059; Xuan Zhang; 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)

Topology-Aware Graph Pooling Networks. - Hongyang Gao; Yi Liu 059; Shuiwang Ji (IEEE Trans. Pattern Anal. Mach. Intell., 2021)

CleftNet: Augmented Deep Learning for Synaptic Cleft Detection From Brain Electron Microscopy. - Yi Liu 059; Shuiwang Ji (IEEE Trans. Medical Imaging, 2021)

Spherical Message Passing for 3D Molecular Graphs. - Yi Liu 059; Limei Wang; Meng Liu 015; Yuchao Lin; Xuan Zhang; Bora Oztekin; Shuiwang Ji (ICLR, 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)

ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs. - Limei Wang; Yi Liu 059; Yuchao Lin; Haoran Liu; Shuiwang Ji (NeurIPS, 2022)

Periodic Graph Transformers for Crystal Material Property Prediction. - Keqiang Yan; Yi Liu 059; Yuchao Lin; Shuiwang Ji (NeurIPS, 2022)

Learning Protein Representations via Complete 3D Graph Networks. - Limei Wang; Haoran Liu; Yi Liu 059; Jerry Kurtin; Shuiwang Ji (CoRR, 2022)

Learning Hierarchical Protein Representations via Complete 3D Graph Networks. - Limei Wang; Haoran Liu; Yi Liu 059; Jerry Kurtin; Shuiwang Ji (ICLR, 2023)

Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction. - Yuchao Lin; Keqiang Yan; Youzhi Luo; Yi Liu 059; Xiaoning Qian; Shuiwang Ji (ICML, 2023)

Empowering Active Learning for 3D Molecular Graphs with Geometric Graph Isomorphism. - Ronast Subedi; Lu Wei; Wenhan Gao 002; Shayok Chakraborty; Yi Liu 059 (NeurIPS, 2024)

A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models. - Gongbo Zhang; Zihan Xu; Qiao Jin 001; Fangyi Chen; Yilu Fang; Yi Liu 059; Justin F. Rousseau; Ziyang Xu; Zhiyong Lu; Chunhua Weng; Yifan Peng 002 (CoRR, 2024)

Coordinate Transform Fourier Neural Operators for Symmetries in Physical Modelings. - Wenhan Gao; Ruichen Xu; Hong Wang; Yi Liu 059 (Trans. Mach. Learn. Res., 2024)

Discretization-invariance? On the Discretization Mismatch Errors in Neural Operators. - Wenhan Gao; Ruichen Xu; Yuefan Deng; Yi Liu 059 (ICLR, 2025)

3DGraphX: Explaining 3D Molecular Graph Models via Incorporating Chemical Priors. - Xufeng Liu; Dongsheng Luo; Wenhan Gao; Yi Liu 059 (KDD (1), 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)

Leveraging long context in retrieval augmented language models for medical question answering. - Gongbo Zhang; Zihan Xu; Qiao Jin 001; Fangyi Chen; Yilu Fang; Yi Liu 059; Justin F. Rousseau; Ziyang Xu; Zhiyong Lu; Chunhua Weng; Yifan Peng 002 (npj Digit. Medicine, 2025)

Dynamic Schwartz-Fourier Neural Operator for Enhanced Expressive Power. - Wenhan Gao; Jian Luo; Ruichen Xu; Yi Liu 059 (Trans. Mach. Learn. Res., 2025)

A foundation model for human-AI collaboration in medical literature mining. - Zifeng Wang 008; Lang Cao; Qiao Jin 001; Joey Chan; Nicholas Wan; Behdad Afzali; Hyunjin Cho; Changin Choi; Mehdi Emamverdi; Manjot K. Gill; Sun-Hyung Kim; Yijia Li; et al. (CoRR, 2025)

MedReason: Eliciting Factual Medical Reasoning Steps in LLMs via Knowledge Graphs. - Juncheng Wu; Wenlong Deng; Xingxuan Li; Sheng Liu; Taomian Mi; Yifan Peng 002; Ziyang Xu; Yi Liu 059; Hyunjin Cho; Changin Choi; Yihan Cao; Hui Ren 001; et al. (CoRR, 2025)