Publications

Please also find my publications on Google Scholar ( ).

Preprints

• HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens [PDF] [arXiv] [GitHub]
  Yi Zhou, Haohao Qu, Yunqing Liu, Shanru Lin, Le Song, Wenqi Fan

• Computational Protein Science in the Era of Large Language Models (LLMs) [PDF] [arXiv]
  Wenqi Fan, Yi Zhou, Shijie Wang, Yuyao Yan, Hui Liu, Qian Zhao, Le Song, Qing Li

Publications

• LDAformer: Predicting LncRNA-Disease Associations based on Topological Feature Extraction and Transformer Encoder [PDF] [DOI] [GitHub]
  Yi Zhou, Xinyi Wang, Lin Yao, Min Zhu
  Briefings in Bioinformatics (BIB), 2022

• Timely-MDA: A Benchmark for Generalizable MiRNA-Disease Association Prediction [PDF] [DOI] [Github]
  Yi Zhou, Xian Guan, Meixuan Wu, Chengzhou Ouyang, Min Zhu
  International Conference on Bioinformatics and Biomedicine (BIBM), 2024

• Enhancing Molecular Property Predictions by Learning from Bond Modelling and Interactions [OpenReview] [GitHub]
  Yunqing Liu, Yi Zhou, Wenqi Fan
  International Conference on Learning Representations (ICLR), 2026

• PLHGMDA: Pre-trained Language Model and Heterogeneous Graph Neural Network for MiRNA-Disease Association Prediction [DOI]
  Meixuan Wu, Yizhou Yang, Yi Zhou, Kai Wang, Junqi Bai, Min Zhu
  International Conference on Intelligent Computing (ICIC), 2025, Oral

• Protein-binding RNA Prediction Based on Integrated Sequence-Structure-Function Pre-training [PDF] [DOI] [Github]
  Lin Gan, Xinyi Wang, Yi Zhou, Min Zhu
  IEEE Transactions on Computational Biology and Bioinformatics (TCBB), 2025

• Dowsing: A Task-Driven Approach for Multiple-View Visualizations Dynamic Recommendation [PDF] [DOI] [Webpage] [Online Demo]
  Jiamin Zhu, Meixuan Wu, Yi Zhou, Haotian Zhu, Min Zhu
  Journal of Visualization (JoV), 2024

• GBDT4CTRVis: Visual Analytics of Gradient Boosting Decision Tree for Advertisement Click-Through Rate Prediction [PDF] [DOI] [Video] [Slide]
  Wenwen Gao, Shangsong Liu, Yi Zhou, Fengjie Wang, Feng Zhou, Min Zhu
  Journal of Visualization (JoV), 2024

Patents

• Method and System for Long Non-coding RNA-Disease Association Prediction Based on Self-Attention Mechanism
  Min Zhu, Yi Zhou, Xinyi Wang, Lin Yao (1st Student Author)
  CN202210818621.5
• A MicroRNA-Disease Association Prediction Method Based on Graph Neural Networks
  Min Zhu, Meixuan Wu, Yi Zhou
  CN202411841640.5
• A Visualization Method for Chromatin Hierarchy Analysis Based on Genetic Data
  Min Zhu, Fuqiu Chen, Chunlin Long, Yi Zhou, Xinyi Wang
  CN202111217034.2
• An Analytical Task Perception Method that Integrates Deep Learning Models and Rules
  Min Zhu, Meixuan Wu, Jiamin Zhu, Yi Zhou, Haotian Zhu
  CN202211104004.5 (Under Substantial Examination)
• A Dynamic Visualization Recommendation Method Based on User Tasks
  Min Zhu, Jiamin Zhu, Meixuan Wu, Yi Zhou, Haotian Zhu
  CN202211610962.X (Under Substantial Examination)
• A Prediction Method for Chromatin Topological Association Domain Boundary Based on Multimodal Fusion
  Min Zhu, Xiyao Li, Chunlin Long, Yi Zhou, Xinyi Wang
  CN202211477002.0 (Under Substantial Examination)
• A Visual Analytics Method for RNA-Disease Associations Based on Density Relational Graphs Min Zhu, Jiamin Zhu, Meixuan Wu, Yi Zhou
  CN202311187212.0 (Under Substantial Examination)

Other Available Works

• Sichuan University - Huawei MindSpore Application Case Implementation Project: Swin Transformer [GitHub]
  Yi Zhou, Xiyao Li, Wanjing Zhang

• DLMV: A Visual Analytic System for LncRNA-Disease Association Prediction [Poster] [Online Demo]
  Yi Zhou, Jiamin Zhu, Meixuan Wu