Xinwu Ye headshot

I am a PhD student at Department of Computer Science in The University of Hong Kong, advised by Shenghua Gao, and co-advised by Liangyi Chen. I worked as a research assitant at Gerstein Lab in Yale University from 2024 to 2025. My research interests focus on solving scientific problems with artificial intelligence, with particular emphasis on biomolecule deisgn and large language models.

I am always seeking new research collaborations to tackle challenging problems. Additionally, I am open to discussing technology commercialization and co-founding opportunities. If you see a potential for us to work together, please drop me an email.

Publications

* represents equal contribution and co-first authorship.

BC-Design: A Biochemistry-Aware Framework for Highly Accurate Inverse Protein Folding

Xiangru Tang*, Xinwu Ye*, Fang Wu*, Daniel Shao, Yin Fang, Siming Chen, Dong Xu, Mark Gerstein.

ICML 2025 Workshop GenBio.

paper code data

MMSciBench: Benchmarking Language Models on Chinese Multimodal Scientific Problems

Xinwu Ye, Chengfan Li, Siming Chen, Wei Wei, Xiangru Tang.

ACL 2025 Findings.

paper code data

GNNFairViz: Visual Analysis for Graph Neural Network Fairness

Xinwu Ye, Jielin Feng, Erasmo Purificato, Ludovico Boratto, Michael Kamp, Zengfeng Huang, Siming Chen.

IEEE Transactions on Visualization and Computer Graphics (2025).

paper code video

Preprints

* represents equal contribution and co-first authorship.

LatentChem: From Textual CoT to Latent Thinking in Chemical Reasoning

Xinwu Ye*, Yicheng Mao*, Jia Zhang, Yimeng Liu, Li Hao, Fang Wu, Zhiwei Li, Yuxuan Liao, Zehong Wang, Zhiyuan Liu, Zhenfei Yin, Li Yuan, Philip Torr, Huan Sun, Xiangxiang Zeng, Mengdi Wang, Le Cong, Shenghua Gao, Xiangru Tang.

arXiv (2026).

paper code

VidAnimator: User-Guided Stylized 3D Character Animation from Human Videos

Xinwu Ye*, Jun-Hsiang Yao*, Jielin Feng, Shuhong Mei, Xingyu Lan, Siming Chen.

arXiv (2025).

paper

Education

PhD in Computer Science

The University of Hong Kong

2025-present | Hong Kong, China

Master of Science

Fudan University

2023-2025 | Shanghai, China

Bachelor of Science & Bachelor of Engineering

Shanghai University of Finance and Economics

2019-2023 | Shanghai, China

Professional Service

Reviewer

Journal

IEEE Transactions on Image Processing (TIP)

IEEE Signal Processing Letters (SPL)

IEEE Journal of Biomedical and Health Informatics (JBHI)

Transactions on Machine Learning Research (TMLR)

Journal of Medical Internet Research (JMIR)

IEEE Transactions on Aerospace and Electronic Systems (TAES)

Applied Intelligence (APIN)

Conference

ICLR 2026

PacificVis 2026

Workshop

ICML 2025 Workshop AI4MATH

COLM 2025 Workshop SoLaR

NeurIPS 2025 Workshop LXAI