publications

Selected Publications

(* equal contribution)

Figure 2: comparison of single-agent and multi-agent context flow and relay compression.

When Do Multi-Agent Systems Help? An Information Bottleneck Perspective

Wendi Yu^*, Lianhao Zhou^*, Xiangjue Dong, Sai Sudarshan Barath, Declan Staunton, Byung-Jun Yoon, Xiaoning Qian, James Caverlee, Shuiwang Ji

NeurIPS, 2026

arXiv

Spherical harmonics and spin-weighted spherical harmonics

Spin-Weighted Spherical Harmonics Enable Complete and Scalable E(3)-Equivariant Networks

Chenxing Liang, Yuchao Lin, Andrii Kryvenko, Wendi Yu, Chuan Li, Jianwen Xie, Xiaofeng Qian, Shuiwang Ji

NeurIPS, 2026

arXiv

AMEvo framework: individual agent summaries, memory synthesis, and asymmetric updates to shared and private memory.

Multi-Agent Asymmetric Memory Evolution for Algorithm Design

Lianhao Zhou, Wendi Yu, Brady Nguyen, Declan Staunton, Sai Sudarshan Barath, Shuiwang Ji

Manuscript, 2026

Autonomous agents for scientific discovery: orchestration of scientists, language, code, and physics.

Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics

Lianhao Zhou, Hongyi Ling, Cong Fu, Yepeng Huang, Michael Sun, Wendi Yu, Xiaoxuan Wang, Xiner Li, Xingyu Su, Junkai Zhang, Xiusi Chen, Chenxing Liang, Xiaofeng Qian, Heng Ji, Wei Wang, Marinka Zitnik, Shuiwang Ji

Preprint, arXiv:2510.09901, 2025

arXiv

Algorithm 1: Auto-Polynomial Learning Algorithm.

Automated Polynomial Filter Learning for Graph Neural Networks

Wendi Yu, Zhichao Hou, Xiaorui Liu

IEEE BigData, 2024

arXiv

Model Developmental Safety: A Safety-Centric Method and Applications in Vision-Language Models

Gang Li, Wendi Yu, Yao Yao, Wei Tong, Yingbin Liang, Qihang Lin, Tianbao Yang

NeurIPS AFM Workshop, 2024

OpenReview

Other Publications

2026

EvoAntigen: An Evolving Agent for Antigen Design

Lianhao Zhou, Raj S Roy, Zachary Krueger, Wendi Yu, Byung-Jun Yoon, Xiaoning Qian, Shuiwang Ji

NeurIPS AgenticLS Workshop, 2026

2026

Generative Artificial Intelligence for Biology: Toward Unifying Models, Algorithms, and Modalities

Xiner Li, Xingyu Su, Yuchao Lin, Chenyu Wang, Yijia Xiao, Tianyu Liu, Chi Han, Michael Sun, Montgomery Bohde, Anna Hart, Wendi Yu, Masatoshi Uehara, Gabriele Scalia, Xiao Luo, Carl Edwards, Wengong Jin, Jianwen Xie, Ehsan Hajiramezanali, Edward De Brouwer, Qing Sun, Byung-Jun Yoon, Xiaoning Qian, Marinka Zitnik, Heng Ji, Hongyu Zhao, Wei Wang, Shuiwang Ji

ChemRxiv preprint, 2026

Paper

2025

Deep learning analyses of splicing variants identify the link of PCP4 with amyotrophic lateral sclerosis

Xuelin Tang, Yan Chen, Yongfei Ren, Wanli Yang, Wendi Yu, Yu Zhou, Jingyan Guo, Jiali Hu, Xi Chen, Yuqi Gu, Chuyi Wang, Yi Dong, Hong Yang, Christine Sato, Ji He, Dongsheng Fan, Linya You, Lorne Zinman, Ekaterina Rogaeva, Yelin Chen, Ming Zhang

Brain, 2025

Paper

2025

A Benchmark for Quantum Chemistry Relaxations via Machine Learning Interatomic Potentials

Cong Fu, Yuchao Lin, Zachary Krueger, Wendi Yu, Xiaoning Qian, Byung-Jun Yoon, Raymundo Arróyave, Xiaofeng Qian, Toshiyuki Maeda, Maho Nakata, Shuiwang Ji

Preprint, arXiv:2506.23008, 2025

arXiv