Please also find my publications on Google Scholar ( ).

Preprints

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

• Geometric Flow Matching for Molecular Conformation Generation via Manifold Decomposition [arXiv]
  Yunqing Liu, Yi Zhou, Wenqi Fan

Publications

• Unlocking Multimodal Protein Language Models at Inference Time
  Yi Zhou, Qipeng Wang, Yunqing Liu, Jun Xia, Qing Li, Wenqi Fan
  Conference on Empirical Methods in Natural Language Processing (EMNLP Main), 2026 (CCF-B), to appear

• 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
  International Conference on Knowledge Discovery and Data Mining (KDD), 2026 (CCF-A)

• 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 (CCF-B)

• 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 (JCR-Q1, IF=13.994)

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

• Wavelet-Driven Cross-Domain Consistency for Mixed-Supervised 3D Tumor Segmentation
  Tianzhong Lan, Weili Jiang, Yisong Liu, Yi Zhou, Junqi Bai, Si Yong Yeo, Xulei Yang, Min Zhu
  European Conference on Computer Vision (ECCV), 2026 (CCF-B), to appear

• 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 (JCR-Q1)

• 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

• A MicroRNA-Disease Association Prediction Method Based on Graph Neural Networks
  Min Zhu, Meixuan Wu, Yi Zhou
  CN119763668B, 2024
• 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)
  CN115171780B, 2022
• A Prediction Method for Chromatin Topological Association Domain Boundary Based on Multimodal Fusion
  Min Zhu, Xiyao Li, Chunlin Long, Yi Zhou, Xinyi Wang
  CN115831217B, 2022
• A Dynamic Visualization Recommendation Method Based on User Tasks
  Min Zhu, Jiamin Zhu, Meixuan Wu, Yi Zhou, Haotian Zhu
  CN116204704B, 2022
• An Analytical Task Perception Method that Integrates Deep Learning Models and Rules
  Min Zhu, Meixuan Wu, Jiamin Zhu, Yi Zhou, Haotian Zhu
  CN116303737B, 2022
• A Visualization Method for Chromatin Hierarchy Analysis Based on Genetic Data
  Min Zhu, Fuqiu Chen, Chunlin Long, Yi Zhou, Xinyi Wang
  CN113946730B, 2021