Yaoyao Xu

About Me

I am a 2rd-year CS PhD student at the Chinese University of Hong Kong, Shenzhen, where I am fortunate to be advised by Prof. Tianshu Yu. My research focuses on AI4Science.

Before my PhD, I obtained my M.S. in Mechanical Engineering from the Columbia University, and my B.S. in Mechanical Engineering from Sichuang University and University of Pittsburgh.

Research Interests

AI4Science
GNNs

Publications

Conference & Journal Papers

* Equal contribution

TEMPO: Temporal Multi-scale Autoregressive Generation of Protein Conformational Ensembles
Yaoyao Xu, Di Wang, Zihan Zhou, Tianshu Yu, Mingchen Chen
Conference on Neural Information Processing Systems (NeurIPS), 2025

The Underappreciated Power of Vision Models for Graph Structural Understanding
Xinjian Zhao*, Wei Pang*, Zhongkai Xue*, Xiangru Jian*, Lei Zhang, Yaoyao Xu, Xiaozhuang Song, Shu Wu, Tianshu Yu.
Conference on Neural Information Processing Systems (NeurIPS), 2025

Graph Learning with Distributional Edge Layouts
Xinjian Zhao, Chaolong Ying, Yaoyao Xu, Tianshu Yu
ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2025

Rethinking Spectral Augmentation for Contrast-based Graph Self-Supervised Learning
Xiangru Jian*, Xinjian Zhao*, Wei Pang*, Chaolong Ying, Yimu Wang, Yaoyao Xu, Tianshu Yu
Transactions on Machine Learning Research (TMLR), 2025

Boosting Protein Language Models with Negative Sample Mining
Yaoyao Xu*, Xinjian Zhao, Xiaozhuang Song, Benyou Wang, Tianshu Yu
*European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), 2024

Demystify the Secret Function in Protein Sequence via Conditional Diffusion Models
Yaoyao Xu, Xuxi Chen, Tong Wang, Huan He, Tianlong Chen, Manolis Kellis
ICLR Workshop GEM, 2024