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 assistant in Gerstein Lab at Yale University from 2024 to 2025. My research interests focus on solving scientific problems with AI, with particular emphasis on biomolecule design and large language models. My broader research interests also include human factors in AI, including reliability and the connections between AI and social science.
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. ✉ represents corresponding author.
FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization
Qingchuan Zhang, He Cao, Hao Li, Daniel Shao, Zhiyuan Liu, Shihang Wang, Shufang Xie, Shenghua Gao, Xinwu Ye✉.
Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization
Xinwu Ye*, He Cao*, Hao Li, Bin Feng, Zijing Liu, Xiangru Tang, Yu Li, Shenghua Gao.
VidAnimator: User-Guided Stylized 3D Character Animation from Human Videos
Xinwu Ye*, Jun-Hsiang Yao*, Jielin Feng, Shuhong Mei, Xingyu Lan, Siming Chen.
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.
Tower of Babel in Cross-Cultural Communication: A Case Study of #Give Me a Chinese Name# Dialogues During the “TikTok Refugees” Event
Jielin Feng, Zhibo Yang, Jingyi Zhao, Yujia Li, Xinwu Ye, Xingyu Lan, Siming Chen.
InfoAlign: A Human–AI Co-Creation System for Storytelling with Infographics
Jielin Feng, Xinwu Ye, Qianhui Li, Verena Ingrid Prantl, Jun-Hsiang Yao, Yuheng Zhao, Yun Wang, Siming Chen.
BC-Design: A Biochemistry-Aware Framework for Inverse Protein Design
Xiangru Tang*, Xinwu Ye*, Fang Wu*, Yimeng Liu, Anna Su, Antonia Panescu, Guanlue Li, Daniel Shao, Dong Xu, Mark Gerstein.
MMSciBench: Benchmarking Language Models on Chinese Multimodal Scientific Problems
Xinwu Ye, Chengfan Li, Siming Chen, Wei Wei, Xiangru Tang.
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).
Professional Service
Reviewer
Journal
IEEE TIP, IEEE TCE, IEEE TCSVT, IEEE SPL, IEEE JBHI, TMLR, JMIR, IEEE TAES, APIN
Conference
ICML 2026, ICLR 2026, NeurIPS 2026, PacificVis 2026
Workshop
AAMAS 2026 ASI, ICML 2026 Pluralistic-Alignment, ICML 2026 GenBio, ICML 2026 GlobalSouthML, ICML 2026 Human-AI Co-Creativity, ICML 2025 AI4MATH, COLM 2025 SoLaR, NeurIPS 2025 LXAI