I am an Associate Professor at the School of Automation Science and Engineering, Xi’an Jiaotong University (XJTU), and a graduate supervisor in Control Science and Engineering. I co-lead the AI4Bread Lab, where we develop artificial intelligence for science (AI4S) methods and platforms at the intersection of life sciences, agriculture, and data-driven systems.
My research spans bioinformatics, graph machine learning, and foundation models for science. Current interests include single-cell and multi-omics analysis, AI-enabled biomedicine, crop genomics and intelligent breeding, and trustworthy data-driven modelling for complex systems.
Research
- AI for biomedicine and bioinformatics: single-cell and multi-omics analysis, medical image analysis, disease-association modelling, drug-target virtual screening, and domain-specific foundation models.
- AI for genomics and smart breeding: crop genomics, telomere-to-telomere (T2T) genome analysis, intelligent breeding, agricultural foundation models, and research platforms for smart agriculture.
- Data-driven systems: graph learning and large-scale data modelling for complex systems, with selected applications in intelligent industry.
I welcome enquiries from motivated undergraduate and graduate students who are interested in interdisciplinary AI4S research. Please contact me by email with a brief introduction and your CV.
News
- 2026-08 — UFold-X: An Enhanced Dual & Dynamic U-Mamba Model for Long-Range RNA Secondary Structure Prediction was accepted for publication in Nucleic Acids Research and is now in press. Congrats to the team! 🥂
- 2026-05 — A paper on biased multi-view contrastive learning with attentive masking for spatial transcriptomic analysis was published in Briefings in Bioinformatics.
- 2026-01 — The S3RL framework for separable spatial single-cell transcriptome representation learning was officially published in Advanced Science.
- 2025-11 — The AI4Bread team published a Multi-level Interactive Siamese-Filtering Enhancement and Restoration (MISFR) network for low-light architectural mural imaging in Frontiers of Architectural Research.
- 2025-08 — A dual-balanced augmented topological framework for non-coding RNA–disease association prediction was published in Briefings in Bioinformatics.
- 2025-03 — A multi-receptive-field strategy for enhancing and restoring mural images under low-light and defective conditions was published in npj Heritage Science.
- 2025-03 — The Parallel Seeds framework, which connects foundation models with foundation intelligence for agricultural sustainability, was published in IEEE/CAA Journal of Automatica Sinica.
Earlier updates are available in the AI4BREAD news archive.
Selected Publications
Selected publications are listed chronologically, from newest to oldest. For a complete and up-to-date list, please visit my Google Scholar profile.
UFold-X: An Enhanced Dual & Dynamic U-Mamba Model for Long-Range RNA Secondary Structure Prediction
Laiyi Fu, Jiachun Li, Ruiqi Wang, Hequan Sun* and Danyang Wu*. Nucleic Acids Research (2026, in press).
Biased Multi-view Contrastive Learning with Attentive Masking for Spatial Transcriptomic Analysis
Laiyi Fu, Wenkai Cui, Yifan Chen, Danyang Wu* and Hequan Sun*. Briefings in Bioinformatics (2026).
S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning
Laiyi Fu†, Penglei Wang†, Gaoyuan Xu†, Jitao Lu, Qinke Peng, Danyang Wu* and Hequan Sun*. Advanced Science (2026).
Laiyi Fu, Yangyi Zhou, Hongqiang Lyu* and Hequan Sun*. Briefings in Bioinformatics (2025).
Code · Data · Web server
Parallel Seeds: From Foundation Models to Foundation Intelligence for Agricultural Sustainability
Laiyi Fu, Shunkang Ling, Danyang Wu*, Mengzhen Kang, Fei-Yue Wang and Hequan Sun*. IEEE/CAA Journal of Automatica Sinica (2025).
Predicting Transcription Factor Binding in Single Cells Through Deep Learning
Laiyi Fu, Lihua Zhang, Emmanuel Dollinger, Qinke Peng, Qing Nie* and Xiaohui Xie*. Science Advances (2020).
† Co-first authors; * corresponding authors.
More publications and graphical abstracts
UFold: Fast and Accurate RNA Secondary Structure Prediction with Deep Learning
Laiyi Fu†, Yingxin Cao†, Jie Wu, Qinke Peng, Qing Nie and Xiaohui Xie*. Nucleic Acids Research (2022).
Integrated Analysis of Multimodal Single-Cell Data with Structural Similarity
Yingxin Cao†, Laiyi Fu†, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang* and Xiaohui Xie*. Nucleic Acids Research (2022).
Appointments & Education
- 2026.04–present — Associate Professor, School of Automation Science and Engineering, Xi’an Jiaotong University.
- 2022.04–2026.04 — Assistant Professor, School of Automation Science and Engineering, Xi’an Jiaotong University.
- 2021.04–2022.03 — Assistant Researcher, School of Automation Science and Engineering, Xi’an Jiaotong University.
- 2018.10–2020.03 — Visiting doctoral researcher in Computer Science, University of California, Irvine.
- 2014.09–2021.03 — M.S.–Ph.D. programme in Control Science and Engineering, Xi’an Jiaotong University.
- 2010.09–2014.06 — B.E. in Automation, Xi’an Jiaotong University.
Honors & Service
- Selected for the Xi’an Jiaotong University Young Outstanding Talent Program (Category A).
- Principal Scientist of a Shaanxi Province “Scientist + Engineer” Team.
- Selected for the Xi’an Association for Science and Technology Young Talent Support Program.
- Researcher appointments at the Institute of Intelligent Control and Industrial Big Data, XJTU; the State Key Laboratory of Astronautics Dynamics; and the National Engineering Research Center for Visual Information and Applications.
- Member of the Biomedical Intelligent Computing Committee, Shaanxi Computer Society, and the Artificial Intelligence Committee, Zhejiang Society of Bioinformatics.