Long-term engagement in AI for Science research. Addressing the bottlenecks of high difficulty, high cost, and long cycles in molecular design, I conduct AI-driven de novo design of small molecules, peptides, proteins, and nucleic acids. My research focuses on the “Expert Wisdom + General AI + Specialized AI + Wet Lab Robot” four-in-one collaborative molecular design theory, constructing a full-chain dry-wet closed-loop intelligent molecular design platform, aiming to significantly improve the success rate and efficiency of molecular design. Related work has been published in journals such as Nature Machine Intelligence and Advanced Science as the lead author. Current research interests include:
- AI Basic Research: Agents and Swarm Intelligence, Molecular Representation Learning and Generative Design
- AI for Science Research: De novo Design of Small Molecules/Peptides/Proteins/Small Nucleic Acids/Materials, Synthesis Planning, Target Discovery, Smart Plant Protection
Contact: I look forward to connecting with experts and students to exchange new ideas (WeChat: yvquanli).
Call for Papers: Welcome to contact me for submissions to TIDD/Innovation/Exploration/iMeta journals. High-quality manuscripts can be prioritized for review.
Recruiting: Recruiting Master’s/Ph.D. students/Joint Training/Interns. I promise not to steal first authorship, not to be abusive, and not to delay graduation. Introductory training upon enrollment, detailed guidance throughout the process, abundant diverse computing resources. I help every student produce a first-author Q1/A-conference paper, and fully support excellent students in publishing in sub-journals.
🎓 Education
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2019.9 - 2024.6 2015.9 - 2019.6 |
Ph.D. & Master - Lanzhou University, School of Chemistry and Chemical Engineering (Major: Chemoinformatics, Supervisor: Prof. Xiaojun Yao) Bachelor - Qinghai University, School of Computer Science (Major: Computer Science and Technology) |
🧑💻 Work Experience
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2024.10 - Present 2024.10 - Present 2022.7 - 2023.4 2020.8 - 2022.6 |
Guizhou University, State Key Laboratory of Public Big Data / College of Computer Science, Special-term Professor Guizhou University, State Key Laboratory of Green Pesticide, Visiting Researcher Beijing Academy of Artificial Intelligence (BAAI) Jie Fu's Team, Research Intern Tencent Quantum Lab, Joint Training (Co-supervisor: Dr. Changyu Hsieh) |
🏛️ Academic Services
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2026.1 - Present 2025.8 - Present 2025.8 - Present 2024.9 - Present 2024.8 - Present 2026.1 2025.1, 2025.8 |
"The Innovation Drug Discovery" (Targeting IF~20), Founding Committee Member, Executive Editorial Board "The Innovation" (Comprehensive Q1 IF=25.7), Youth Editorial Board "iMeta" (Biology Q1 IF=33.2), Youth Editorial Board "Exploration" (Comprehensive Q1 IF=22.5), Youth Editorial Board, Deputy Director of Plant Division of Youth Committee China-Sri Lanka Belt and Road Joint Laboratory of Tea Green Prevention and Control Technology, Founding Participant The 6th International Conference on Green Plant Protection Innovation, Organizing Committee Guizhou Provincial Big Data Bureau Project Artificial Intelligence Industry Direction Review Expert Group, Leader |
📑 Research Projects
[1] National Data Bureau Dataset Pilot Project, National Crop Pests and Weeds - Pesticide Multimodal Plant Protection Dataset, 2026, Sub-project Host
[2] National Natural Science Foundation of China Regional Project, AI-based Mining of Aphid RNAi Genes in Wheat Fields and RNAi Pesticide Design, 320k, 2026, Host
[3] Guizhou University Talent Introduction Special Post Project, Research on New Methods for Multi-constraint Small Molecule Generative Design, 400k, 2024, Host
👥 Team Members
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Xiao Zhang¹, Ph.D. Candidate '21, Nucleic Acid Pesticide Design Xinyu Dong¹, Ph.D. Candidate '24, Multi-objective Molecular Generation Guangyi Huang¹, Ph.D. Candidate '24, AI Target Discovery Shihang Wang², Ph.D. Candidate '25, Cell Phenotype Learning Mutian He², Ph.D. Candidate '25, Macromolecular Drugs, DEL Daohong Gong², Ph.D. Candidate '25, PROTAC Design Haozhen Guo¹, Ph.D. Candidate '25, Agent Peptide Design Hushuangyin Tang², Ph.D. Candidate '26, Delivery Systems, ADC |
Chaoyang Xie³, Master Student '23, Molecular Property Prediction Jun Zhou¹, Master Student '24, Synthesis Planning Jun Zhang³, Master Student '24, PPI, DDI Prediction Yilun Zhang³, Master Student '24, Enzyme Function Prediction & Design Nanwan Wu¹, Master Student '24, Peptide-Drug Conjugate Design Xixuan Luo¹, Master Student '24, DTI, DDI Prediction Longbiao Zhang¹, Master Student '24, AI Delivery System Design Huiyang Hong, Undergraduate '22, PROTAC |
Yong Zhou, Master Student '25, Nucleic Acid Pesticide Design Lei Zhu⁴, Master Student '25, AI Peptide/Protein Design Yuxuan Jiang, Master Student '25, Smart Breeding Weixun Chen, Master Student '25, Agent Molecular Design Zhanhong Tang³, Master Student '25, Targeted Nucleic Acid Degradation Qing Zhu¹, Master Student '25, Plant Pathogen Interaction |
Close Collaborators (Supervisors): Gefei Hao¹, Xiaojun Yao², Qi Wang³ (In no particular order)
Close Partner: Xiaorui Wang, Postdoc in Prof. Tingjun Hou’s Group at Zhejiang University, Research Direction: AI Synthesis Planning
📝 Selected Publications
[1] Li et al. An adaptive graph learning method for automated molecular interactions and properties predictions. Nature Machine Intelligence IF=23.8▴
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[2] Li et al. Introducing block design in graph neural networks for molecular properties prediction. Chemical Engineering Journal IF=16.7▴
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[3] Li* et al. Spectral decomposition of chemical semantics for activity cliffs-aware molecular property prediction. Advanced Science IF=14.1▴
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[4] Li† et al. TrimNet: learning molecular representation from triplet messages for biomedicine. Briefings in Bioinformatics IF=13.9▴
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[5] Li† et al. TrimNet: learning molecular representation from triplet messages for biomedicine. Briefings in Bioinformatics IF=13.9▴
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*Corresponding Author †Co-first Author ▴IF at Publication
All Publications
2026
- [2026b] Chaoyang Xie, Junhu Xu, Guangyi Huang, Shihang Wang, Mutian He, Xinyu Dong, Huiyang Hong, Xiaojun Yao, Qi Wang*, Yuquan Li*. Spectral decomposition of chemical semantics for activity cliffs-aware molecular property prediction[J].
Advanced Science, 2026. [HTML] [PDF] - [2026a] Huiyang Hong, Xinkai Wu, Hongyu Sun, Chaoyang Xie, Qi Wang*, Yuquan Li*. Learning hierarchical interaction for accurate molecular property prediction[J].
Communications Chemistry,2026. (accept)
2025
- [2025c] Yanan Tian, Ruiqiang Lu, Xiaoqing Gong, Yuquan Li, Wei Zhao, Xiaorui, Wang, Xinming Jia, Qin Li, Yuwei Yang, Henry H. Y. Tong, Joel P. Arrais*, Huanxiang Liu*, Xiaojun Yao*. Enhancing Kinase-Inhibitor Activity and Selectivity Prediction Through Multimodal and Multiscale Contrastive Learning with Attention Consistency[J].
Nature Communications,2025,16:10860. [HTML] [PDF] - [2025b] Xiaorui Wang†, Xiaodan Yin†, Xujun Zhang†, Huifeng Zhao, Shukai Gu, Zhenxing Wu, Odin Zhang, Wenjia Qian, Yuansheng Huang, Yuquan Li, Dejun Jiang, Mingyang Wang, Huanxiang Liu, Xiaojun Yao*, Chang-Yu Hsieh*, Tingjun Hou*. A virtual platform for automated hybrid organic-enzymatic synthesis planning[J].
Nature Communications,2025,16:10929. [HTML] [PDF] - [2025a] Zhenglu Chen, Chunbin Gu*, Shuoyan Tan, Xiaorui Wang, Yuquan Li, Mutian He, Ruiqiang Lu, Shijia Sun, Chang-Yu Hsieh*, Xiaojun Yao*, Huanxiang Liu*, Pheng-Ann Heng. Interpretable PROTAC Degradation Prediction With Structure-Informed Deep Ternary Attention Framework[J].
Advanced Science, 2025. [HTML] [PDF]
2024
- [2024a] Xiaorui Wang, Xiaodan Yin, Dejun Jiang, Huifeng Zhao, Zhenxing Wu, Odin Zhang, Jike Wang, Yuquan Li, Yafeng Deng, Huanxiang Liu, Pei Luo, Yuqiang Han, Tingjun Hou*, Xiaojun Yao*, Chang-Yu Hsieh*. Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites[J].
Nature Communications, 2024, 15(1): 7348. [HTML] [PDF]
2023
- [2023a] Xiaorui Wang†, Chang-Yu Hsieh†, Xiaodan Yin, Jike Wang, Yuquan Li, Yafeng Deng, Dejun Jiang, Zhenxing Wu, Hongyan Du, Hongming Chen, Yun Li, Huanxiang Liu, Yuwei Wang, Pei Luo, Tingjun Hou*, Xiaojun Yao*. Generic Interpretable Reaction Condition Predictions with Open Reaction Condition Datasets and Unsupervised Learning of Reaction Center[J].
Research, 2023, 6: 0231. [HTML] [PDF]
2022
- [2022a] Yuquan Li†, Chang-Yu Hsieh†, Ruiqiang Lu, Xiaoqing Gong, Xiaorui Wang, Pengyong Li, Shuo Liu, Yanan Tian, Dejun Jiang, Jiaxian Yan, Qifeng Bai, Huanxiang Liu, Shengyu Zhang , Xiaojun Yao*. An adaptive graph learning method for automated molecular interactions and properties predictions[J].
Nature Machine Intelligence, 2022, 4(7):645-651. [HTML] [PDF]
2021
- [2021c] Pengyong Li†, Yuquan Li†, Chang-Yu Hsieh, Shengyu Zhang, Xianggen Liu, Huanxiang Liu, Sen Song*, Xiaojun Yao*. TrimNet: learning molecular representation from triplet messages for biomedicine[J].
Briefings in Bioinformatics, 2021, 22(4): bbaa266.[HTML] [PDF] - [2021b] Xiaorui Wang†, Yuquan Li†, Jiezhong Qiu, Guangyong Chen, Huanxiang Liu, Benben Liao*, Chang-Yu Hsieh*, Xiaojun Yao*. RetroPrime: A Diverse, plausible and Transformer-based method for Single-Step retrosynthesis predictions[J].
Chemical Engineering Journal, 2021, 420: 129845. [HTML] [PDF] - [2021a] Yuquan Li, Pengyong Li, Xing Yang, Chang-Yu Hsieh, Shengyu Zhang, Xiaorui Wang, Ruiqiang Lu, Huanxiang Liu, Xiaojun Yao*. Introducing block design in graph neural networks for molecular properties prediction[J].
Chemical Engineering Journal, 2021, 414: 128817. [HTML] [PDF]
🌟 Honors & Awards
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2025.9 2024.10 |
"Exploration" Journal 2025 Outstanding Youth Editorial Board Member Award Guizhou University First-class Discipline Construction Special Talent Introduction |
🏛️ Academic Activities
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2026.1 2025.11 2025.10 2023.3 2023.5-Present 2021.9-Present |
The 6th International Conference on Green Plant Protection Innovation, Talk: AI-driven Essential Gene Mining and dsRNA Design Yangzhou University, Green Agriculture Academic Lecture Hall, Talk: Artificial Intelligence Aided Pesticide Design The 14th National Conference on Bioinformatics and Systems Biology, Talk: Multi-objective Molecular Generation Lanzhou University 15th Graduate Academic Annual Meeting, Talk: Chemistry × AI, Present and Future Reviewer for iMeta, Nature Communications, etc. Professional Member of China Society of Plant Protection, Chinese Association for Artificial Intelligence, China Computer Federation, Chinese Chemical Society |
🙌 Others
ARAM, War3 RPG/RTS, DNF
Owner of 5 Legendary Fire Sticks
I know clearly that the path between people is not replicable, I lie in my own bed.
