About Me

I am currently a researcher at Anew Labs. Before that, I received my Ph.D. from the Department of Computer Science and Technology at Tsinghua University, where I was advised by Prof. Yang Liu. I was also affiliated with THUNLP and AIR, Tsinghua University. In addition, I have been fortunate to work closely with Prof. Wenbing Huang at Gaoling School of Artificial Intelligence, Renmin University of China. During my Ph.D., I was also fortunate to spend research internships at Microsoft Research Cambridge, Alibaba DAMO Academy, and Alibaba Tongyi Lab.

My research interests lie in generative models and agentic systems for scientific discovery, with a focus on materials and biomolecules. More broadly, I believe that stronger scientific systems will emerge from the interplay between systematic agent frameworks and reliable, user-friendly scientific tools tailored to specific domains. Along this line, I work on geometric and generative AI methods for molecular representation learning, material/biomolecular design, and scientific discovery workflows. I am always happy to discuss research ideas and potential academic collaborations.

News

  1. I received my Ph.D. degree from the Department of Computer Science and Technology, Tsinghua University, and was honored as a Tsinghua Outstanding Graduate with an Outstanding Doctoral Dissertation Award.

  2. One paper was accepted to KDD 2026.

  3. Our work on Elements was released as a preprint, where we use a general foundation model as a tool and combine it with an agent workflow to discover four low-temperature superconducting materials.

  4. Our paper, "Siamese Foundation Models for Crystal Structure Prediction", was published in Nature Communications.

  5. We released AnewOmni, a programmable all-atom generative framework that unifies peptide, antibody, and small-molecule binder design with graph-prompt-based control, with multiple designs experimentally validated in wet-lab assays.

  6. Our paper, "An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning", was published in Nature Communications.

  7. One paper was accepted to ICLR 2026.

  8. Our paper, "Peptide Design through Binding Interface Mimicry with PepMimic", was published in Nature Biomedical Engineering.

  9. Two papers were accepted to NeurIPS 2025.

  10. Our paper, "Powder Diffraction Crystal Structure Determination Using Generative Models", was published in Nature Communications.

  11. Two papers were accepted to ICML 2025.

  12. Our survey paper, "A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications", was published in Frontiers of Computer Science.

  13. One paper was accepted to ICLR 2025.

  14. Two papers were accepted to NeurIPS 2024.

  15. One paper was accepted to ICML 2024.

  16. One paper was accepted to ICLR 2024.

  17. One paper was accepted to NeurIPS 2023.

  18. One paper was accepted to AAAI 2023.

  19. I received my B.E. degree from the Department of Computer Science and Technology, Tsinghua University, and was honored as a Beijing Outstanding Graduate.

  20. One paper was accepted to KDD 2021.

  21. One paper was accepted to Findings of ACL-IJCNLP 2021.

Selected Publications

Full List
DrugTrail overview

Interpretable Drug Discovery via Structured Reasoning and Druggability-Tailored Preference Optimization

Yurou Liu, Mingyang Li, Xinyuan Zhu, Rui Jiao, Yiming Dong, Xinyu Tang, Yang Liu, Jieping Ye, Bing Su, Zheng Wang

ICLR 2026

Elements overview

Agentic Fusion of Large Atomic and Language Models to Accelerate Superconductor Discovery

Mingze Li, Yu Rong, Songyou Li, Lihong Wang, Jiacheng Cen, Liming Wu, Anyi Li, Zongzhao Li, Qiuliang Liu, Rui Jiao, Tian Bian, Pengju Wang, Hao Sun, Jianfeng Zhang, Ji-Rong Wen, Deli Zhao, Shifeng Jin, Tingyang Xu, Wenbing Huang

Preprint 2026

EPT overview

An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning

Rui Jiao*, Xiangzhe Kong*, Li Zhang*, Ziyang Yu, Fangyuan Ren, Wenjuan Tan, Wenbing Huang, Yang Liu

Nature Communications 2026

DAO overview

Siamese Foundation Models for Crystal Structure Prediction

Liming Wu, Wenbing Huang, Rui Jiao, Jianxing Huang, Liwei Liu, Yipeng Zhou, Hao Sun, Yang Liu, Fuchun Sun, Yuxiang Ren, Ji-Rong Wen

Nature Communications 2026

MOF-BFN overview

MOF-BFN: Metal-Organic Frameworks Structure Prediction via Bayesian Flow Networks

Rui Jiao, Hanlin Wu, Wenbing Huang, Yuxuan Song, Yawen Ouyang, Yu Rong, Tingyang Xu, Pengju Wang, Hao Zhou, Wei-Ying Ma, Jingjing Liu, Yang Liu

NeurIPS 2025

AniDS overview

Learning 3D Anisotropic Noise Distributions Improves Molecular Force Fields

Xixian Liu*, Rui Jiao*, Zhiyuan Liu, Yurou Liu, Yang Liu, Ziheng Lu, Wenbing Huang, Yang Zhang, Yixin Cao

NeurIPS 2025

PXRDGen overview

Powder Diffraction Crystal Structure Determination Using Generative Models

Qi Li*, Rui Jiao*, Liming Wu, Tiannian Zhu, Wenbing Huang, Shifeng Jin, Yang Liu, Hongming Weng, Xiaolong Chen

Nature Communications 2025

UniMoMo overview

UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design

Xiangzhe Kong, Zishen Zhang, Ziting Zhang, Rui Jiao, Jianzhu Ma, Kai Liu, Wenbing Huang, Yang Liu

ICML 2025

FlowDPO overview

3D Structure Prediction of Atomic Systems with Flow-based Direct Preference Optimization

Rui Jiao, Xiangzhe Kong, Wenbing Huang, Yang Liu

NeurIPS 2024

DiffCSP++ overview

Space Group Constrained Crystal Generation

Rui Jiao, Wenbing Huang, Yu Liu, Deli Zhao, Yang Liu

ICLR 2024

DiffCSP overview

Crystal Structure Prediction by Joint Equivariant Diffusion

Rui Jiao, Wenbing Huang, Peijia Lin, Jiaqi Han, Pin Chen, Yutong Lu, Yang Liu

NeurIPS 2023

3D-EMGP overview

Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs

Rui Jiao, Jiaqi Han, Wenbing Huang, Yu Rong, Yang Liu

AAAI 2023

Education Experience

Ph.D. in Computer Science and Technology, Tsinghua University

B.E. in Computer Science and Technology, Tsinghua University

Research Experience

Researcher, Anew Labs

Research Intern, Microsoft Research Cambridge

Research Intern, Alibaba DAMO Lab

Research Intern, Alibaba Tongyi Lab

Personal

Outside research, I enjoy board games and spending time with cats. If you are nearby, feel free to find me offline for a board game or a casual chat :)