Siyuan Chen

Welcome to you, and also welcome to me!

I’m a CS Ph.D. student at the University of British Columbia, advised by Prof. Peter Yichen Chen.

My research develops AI foundation models for protein structure, interaction, and dynamics, combining geometric deep learning, physics-grounded priors, and large-scale molecular dynamics data. I am particularly interested in (i) physically valid biomolecular generation, (ii) scalable protein–protein interaction discovery, and (iii) Transformer-based neural simulators that learn protein conformational dynamics from MD trajectories. More broadly, I work on neural surrogate models for physical dynamics, at the intersection of computer graphics, scientific computing, and machine learning.

I graduated from Shanghai Jiao Tong University with a B.S. degree in Physics and a minor in Computer Science.

Before starting my Ph.D., I interned at SJTU DA Lab, where I worked with Prof. Xubo Yang and Ph.D. student Hui Wang, and also collaborated remotely with Bo Zhu. I also worked at DMCV with Prof. Ran Yi. From September 2024 to December 2024, I was an exchange student at the University of Toronto, where I worked with Zhecheng and Prof. Eitan Grinspun.

news


Sep 27, 2026	WorldAgent preprint is out on arXiv !
Sep 23, 2026	WorldContact preprint is out on arXiv !
Sep 1, 2026	WorldParticle has been accepted to SIGGRAPH Asia 2026 (Conference Track) !
Jul 8, 2026	My advisor Prof. Peter Yichen Chen received the Early Career Researcher Award at SCA 2026 !
Jul 8, 2026	Presented Closing Trajectories at SCA 2026 in Barcelona !
May 22, 2026	Closing Trajectories preprint is out on arXiv !
May 1, 2026	WorldParticle preprint is out on arXiv !
Mar 1, 2026	Factorized Neural Implicit DMD preprint is out on arXiv !
Jan 26, 2026	One paper has been accepted to ICLR 2026 !
Jan 16, 2026	SG-Splatting has been accepted to ICASSP 2026 !
Apr 1, 2025	One paper has been conditionally accepted to Siggraph 2025 !
Mar 27, 2025	Start journey as a Ph.D. student in Computer Science at the University of British Columbia !

selected publications

WorldParticle: Unified World Simulation of Lagrangian Particle Dynamics via Transformer

Caoliwen Wang ^* , Minghao Guo ^* ^† , Siyuan Chen ^* , Heng Zhang , Mengdi Wang , Xingyu Ni , Hanson Sun , Kunyi Wang , Zherong Pan , Kui Wu , Lingjie Liu , Yin Yang , Chenfanfu Jiang , Taku Komura , Wojciech Matusik , Peter Yichen Chen ^†

SIGGRAPH Asia (Conference Track) 2026

^* Co-first authors. ^† Corresponding authors.

PDF Website
WorldAgent: Verification-Guided Agentic Physical World Construction

Caoliwen Wang ^* , Mengdi Wang ^* ^† , Yige Chen ^* , Zejia Wu , Bowen Huang , Siyuan Chen , Guanxiong Chen , Lifu Wei , Heng Zhang , Qinghai Zhang , Yin Yang , Guandao Yang , Shiying Xiong , Peng Wang , Chenfanfu Jiang , Peter Yichen Chen

Preprint, arXiv:2609.33208 2026

^* Co-first authors. ^† Corresponding author.

PDF
WorldContact: A Contact-Centric World Model for Scalable Robot Learning

Caoliwen Wang ^* , Mengdi Wang ^* ^† , Heng Zhang , Shixun Huang , Siyuan Chen , Chao Liu , Anpei Chen , Zhendong Wang , Peter Yichen Chen ^† , Huamin Wang

Preprint, arXiv:2609.19600 2026

^* Co-first authors. ^† Corresponding authors.

PDF
Closing Trajectories: Equation-Free Cyclic Animation via Koopman Surrogates

Shixun Huang ^* , Siyuan Chen ^* ^† , Yue Chang , Zhecheng Wang , Peter Yichen Chen ^†

ACM SIGGRAPH/Eurographics Symposium on Computer Animation (SCA), Computer Graphics Forum 2026

^* Co-first authors. ^† Corresponding authors.

Project Webpage PDF
Physically Valid Biomolecular Interaction Modeling with Gauss-Seidel Projection

Siyuan Chen ^* , Minghao Guo ^* ^† , Caoliwen Wang , Anka He Chen , Yikun Zhang , Jingjing Chai , Yin Yang , Wojciech Matusik , Peter Yichen Chen ^†

International Conference on Learning Representations (ICLR) 2026

^* Co-first authors. ^† Corresponding authors.

PDF
Factorized Neural Implicit DMD for Parametric Dynamics

Siyuan Chen ^* , Zhecheng Wang ^* ^† , Yixin Chen , Yue Chang , Peter Yichen Chen , Eitan Grinspun , Jonathan Panuelos

Preprint, arXiv:2603.10995 2026

^* Co-first authors. ^† Corresponding author.

PDF
Fast Subspace Fluid Simulation with a Temporally-Aware Basis

Siyuan Chen , Yixin Chen , Jonathan Panuelos , Otman Benchekroun , Yue Chang , Eitan Grinspun , Zhecheng Wang ^†

ACM Transactions on Graphics (Proceedings of SIGGRAPH) 2025

^† Corresponding author.

Project Webpage PDF