Fast Flow-based Random Walk with Restart in a Multi-query Setting. - Yujun Yan; Mark Heimann; Di Jin 003; Danai Koutra (SDM, 2018)

GroupINN: Grouping-based Interpretable Neural Network for Classification of Limited, Noisy Brain Data. - Yujun Yan; Jiong Zhu; Marlena Duda; Eric Solarz; Chandra Sekhar Sripada; Danai Koutra (KDD, 2019)

Neural Execution Engines: Learning to Execute Subroutines. - Yujun Yan; Kevin Swersky; Danai Koutra; Parthasarathy Ranganathan; Milad Hashemi (NeurIPS, 2020)

Beyond Homophily in Graph Neural Networks: Current Limitations and Effective Designs. - Jiong Zhu; Yujun Yan; Lingxiao Zhao; Mark Heimann; Leman Akoglu; Danai Koutra (NeurIPS, 2020)

Generalizing Graph Neural Networks Beyond Homophily. - Jiong Zhu; Yujun Yan; Lingxiao Zhao; Mark Heimann; Leman Akoglu; Danai Koutra (CoRR, 2020)

Benchmarking Semi-supervised Federated Learning. - Zhengming Zhang 001; Zhewei Yao; Yaoqing Yang; Yujun Yan; Joseph E. Gonzalez; Michael W. Mahoney (CoRR, 2020)

A Dataset-Dispersion Perspective on Reconstruction Versus Recognition in Single-View 3D Reconstruction Networks. - Yefan Zhou; Yiru Shen; Yujun Yan; Chen Feng 002; Yaoqing Yang (3DV, 2021)

Improving Semi-supervised Federated Learning by Reducing the Gradient Diversity of Models. - Zhengming Zhang 001; Yaoqing Yang; Zhewei Yao; Yujun Yan; Joseph E. Gonzalez; Kannan Ramchandran; Michael W. Mahoney (IEEE BigData, 2021)

Two Sides of the Same Coin: Heterophily and Oversmoothing in Graph Convolutional Neural Networks. - Yujun Yan; Milad Hashemi; Kevin Swersky; Yaoqing Yang; Danai Koutra (ICDM, 2022)

Augmentations in Graph Contrastive Learning: Current Methodological Flaws & Towards Better Practices. - Puja Trivedi; Ekdeep Singh Lubana; Yujun Yan; Yaoqing Yang; Danai Koutra (WWW, 2022)

Towards Generalizable Neural Networks for Graph Applications - Yujun Yan (2022)

Interpretable Sparsification of Brain Graphs: Better Practices and Effective Designs for Graph Neural Networks. - Gaotang Li; Marlena Duda; Xiang Zhang 012; Danai Koutra; Yujun Yan (KDD, 2023)

Size Generalizability of Graph Neural Networks on Biological Data: Insights and Practices from the Spectral Perspective. - Yujun Yan; Gaotang Li; Danai Koutra (CoRR, 2023)

Heterophily and Graph Neural Networks: Past, Present and Future. - Jiong Zhu; Yujun Yan; Mark Heimann; Lingxiao Zhao; Leman Akoglu; Danai Koutra (IEEE Data Eng. Bull., 2023)

GraphScale: A Framework to Enable Machine Learning over Billion-node Graphs. - Vipul Gupta; Xin Chen 084; Ruoyun Huang; Fanlong Meng; Jianjun Chen 001; Yujun Yan (CIKM, 2024)

Enhancing Size Generalization in Graph Neural Networks through Disentangled Representation Learning. - Zheng Huang; Qihui Yang; Dawei Zhou 003; Yujun Yan (ICML, 2024)

EvoluNet: Advancing Dynamic Non-IID Transfer Learning on Graphs. - Haohui Wang; Yuzhen Mao; Yujun Yan; Yaoqing Yang; Jianhui Sun; Kevin Choi; Balaji Veeramani; Alison Hu; Edward Bowen; Tyler Cody; Dawei Zhou 003 (ICML, 2024)

Exploring Consistency in Graph Representations: from Graph Kernels to Graph Neural Networks. - Xuyuan Liu; Yinghao Cai; Qihui Yang; Yujun Yan (NeurIPS, 2024)

Sharpness-diversity tradeoff: improving flat ensembles with SharpBalance. - Haiquan Lu; Xiaotian Liu; Yefan Zhou; Qunli Li; Kurt Keutzer; Michael W. Mahoney; Yujun Yan; Huanrui Yang; Yaoqing Yang (NeurIPS, 2024)

Medformer: A Multi-Granularity Patching Transformer for Medical Time-Series Classification. - Yihe Wang; Nan Huang 004; Taida Li; Yujun Yan; Xiang Zhang 012 (NeurIPS, 2024)

Firmware Vulnerability Detection Algorithm Based on Matching Pattern-Specific Numerical Features With Structural Features. - Peng Liu; Yasu Cao; Yujun Yan; Yong Wang (IEEE Access, 2024)

How to evaluate your medical time series classification? - Yihe Wang; Taida Li; Yujun Yan; Wenzhan Song 001; Xiang Zhang 012 (CoRR, 2024)

Exploring Consistency in Graph Representations:from Graph Kernels to Graph Neural Networks. - Xuyuan Liu; Yinghao Cai; Qihui Yang; Yujun Yan (CoRR, 2024)

Spectral Insights into Data-Oblivious Critical Layers in Large Language Models. - Xuyuan Liu; Lei Hsiung; Yaoqing Yang; Yujun Yan (ACL (Findings), 2025)

Towards Agentic AI for Science: Hypothesis Generation, Comprehension, Quantification, and Validation. - Lifu Huang; Danai Koutra; Adithya Kulkarni; Temiloluwa Prioleau; Qingyun Wu; Yujun Yan; Yaoqing Yang; James Zou 001; Dawei Zhou 003 (WWW (Companion Volume), 2025)

MindLLM: A Subject-Agnostic and Versatile Model for fMRI-to-Text Decoding. - Weikang Qiu; Zheng Huang; Haoyu Hu; Aosong Feng; Yujun Yan; Rex Ying (CoRR, 2025)

Transfer Faster, Price Smarter: Minimax Dynamic Pricing under Cross-Market Preference Shift. - Yi Zhang; Elynn Chen; Yujun Yan (CoRR, 2025)

Judging with Many Minds: Do More Perspectives Mean Less Prejudice? - Chiyu Ma; Enpei Zhang; Yilun Zhao 001; Wenjun Liu; Yaning Jia; Peijun Qing; Lin Shi; Arman Cohan; Yujun Yan; Soroush Vosoughi (CoRR, 2025)

Non-exchangeable Conformal Prediction for Temporal Graph Neural Networks. - Tuo Wang; Jian Kang 008; Yujun Yan; Adithya Kulkarni; Dawei Zhou 003 (CoRR, 2025)