Rui Jiao - Full Publication List

2026

Scalable Peptide Design via Memory-Efficient Equivariant Transformer

Preprint, 2026 Paper Code

Rui Jiao, Xiangzhe Kong, Yinjun Jia, Yijia Zhang, Ziyi Yang, Yang Liu, Jianzhu Ma

Programming Biomolecular Interactions with All-Atom Generative Model

Preprint, 2026 Paper Code

Xiangzhe Kong, Junwei Chen, Ziting Zhang, Gaodeng Li, Qingyuan Zhu, Lei Wei, Mingyu Li, Yan Shi, Weiyang Dai, Zishen Zhang, Wenjuan Tan, Rui Jiao, Xiaolun Wang, Jiqing Zheng, Ziyang Yu, Qilong Wu, Zhiye Guo, Li Zhang, Wentao Li, Qiaojing Huang, Tian Zhu, Xiaowo Wang, Wenbing Huang, Yuli She, Jian Zhang, Yang Liu, Kai Liu, Jianzhu Ma

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

Preprint, 2026 Paper Homepage

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

Experimental Powder X-ray Diffraction Crystal Structure Determination with RealPXRD-Solver

Preprint, 2026 Paper Code

Qi Li, Mingyu Guo, Rui Jiao, Jing Gao, Fanjie Xu, Haonan Xue, Weixiong Zhang, Wenbing Huang, Junchi Yan, Linfeng Zhang, Cheng Wang, Zhuang Yan, Guolin Ke, Weinan E, Zhiyong Tang, Shifeng Jin, Lin Yao

DMFlow: Disordered Materials Generation by Flow Matching

KDD 2026 Paper Code

Liming Wu, Rui Jiao, Qi Li, Mingze Li, Songyou Li, Shifeng Jin, Wenbing Huang

Siamese Foundation Models for Crystal Structure Prediction

Nature Communications, 2026 Paper Code

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

An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning

Nature Communications, 2026 Paper Code

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

HBDrug3D: A Dataset and Benchmark for AI-Driven Heterobifunctional Molecule Design

Preprint, 2026 Paper

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

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

ICLR 2026 Paper

Yuxuan Liu, Xinyuan Zhu, Yudong Huang, Yuzheng Wu, Rui Jiao, Zhongyi Liu, Wenhao Gao, Shengyu Zhang, Yang Liu, Wenbing Huang

2025

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

NeurIPS 2025 Paper Code

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

Peptide Design through Binding Interface Mimicry with PepMimic

Nature Biomedical Engineering, 2025 Paper Code

Xiangzhe Kong, Rui Jiao, Haowei Lin, Ruihan Guo, Wenbing Huang, Wei-Ying Ma, Zihua Wang, Yang Liu, Jianzhu Ma

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

ICML 2025 Paper Code

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

Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints

ICML 2025 Paper Code

Dapeng Jiang, Xiangzhe Kong, Jiaqi Han, Mingyu Li, Rui Jiao, Wenbing Huang, Stefano Ermon, Jianzhu Ma, Yang Liu

Powder Diffraction Crystal Structure Determination Using Generative Models

Nature Communications, 2025 Paper

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

DenoiseVAE: Learning Molecule-Adaptive Noise Distributions for Denoising-based 3D Molecular Pre-training

ICLR 2025 Paper Code

Yurou Liu, Jiahao Chen, Rui Jiao, Jiangmeng Li, Wenbing Huang, Bing Su

Materials Generation in the Era of Artificial Intelligence: A Comprehensive Survey

Preprint, 2025 Paper Code

Zhixun Li, Bin Cao, Rui Jiao, Liang Wang, Ding Wang, Yang Liu, Dingshuo Chen, Jia Li, Qiang Liu, Yu Rong, Liang Wang, Tong-yi Zhang, Jeffrey Xu Yu

Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling

NeurIPS 2025 Paper Code

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

A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications

Frontiers of Computer Science, 2025 Paper Code

Jiaqi Han, Jiacheng Cen, Liming Wu, Zongzhao Li, Xiangzhe Kong, Rui Jiao, Ziyang Yu, Tingyang Xu, Fandi Wu, Zihe Wang, Hongteng Xu, Zhewei Wei, Yang Liu, Yu Rong, Wenbing Huang

2024

Equivariant Diffusion for Crystal Structure Prediction

ICML 2024 Paper Code

Peijia Lin, Pin Chen, Rui Jiao, Qing Mo, Jianhuan Cen, Wenbing Huang, Yang Liu, Dan Huang, Yutong Lu

Space Group Constrained Crystal Generation

ICLR 2024 Paper Code

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

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

NeurIPS 2024 Paper Code

Rui Jiao, Xiangzhe Kong, Wenbing Huang, Yang Liu

Learning Superconductivity from Ordered and Disordered Material Structures

NeurIPS 2024 Paper Code 1 Code 2

Pin Chen, Luoxuan Peng, Rui Jiao, Qing Mo, Zhen Wang, Wenbing Huang, Yang Liu, Yutong Lu

2023

Crystal Structure Prediction by Joint Equivariant Diffusion

NeurIPS 2023 Paper Code

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

Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs

AAAI 2023 Paper Code

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

2022

Interpretable Graph Transformer Network for Predicting Adsorption Isotherms of Metal-Organic Frameworks

Journal of Chemical Information and Modeling, 2022 Paper Code

Pin Chen, Rui Jiao, Jinyu Liu, Yang Liu, Yutong Lu

2021

Alternated Training with Synthetic and Authentic Data for Neural Machine Translation

Findings of ACL-IJCNLP 2021 Paper

Rui Jiao, Zonghan Yang, Maosong Sun, Yang Liu

Practical Root Cause Localization for Microservice Systems via Trace Analysis

IWQoS 2021 Paper

Zeyan Li, Junjie Chen, Rui Jiao, Nengwen Zhao, Zhijun Wang, Shuwei Zhang, Yanjun Wu, Long Jiang, Leiqin Yan, Zikai Wang, Zhekang Chen, Wenchi Zhang, Xiaohui Nie, Kaixin Sui, Dan Pei

Multivariate Time Series Anomaly Detection and Interpretation using Hierarchical Inter-Metric and Temporal Embedding

KDD 2021 Paper Code

Zhihan Li, Youjian Zhao, Jiaqi Han, Ya Su, Rui Jiao, Xidao Wen, Dan Pei

2020

Unsupervised Detection of Microservice Trace Anomalies through Service-Level Deep Bayesian Networks

ISSRE 2020 Paper Code

Ping Liu, Haowen Xu, Qianyu Ouyang, Rui Jiao, Zhekang Chen, Shenglin Zhang, Jiahai Yang, Linlin Mo, Jice Zeng, Wenman Xue, Dan Pei