Papers by Jiekun Yang
GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models (2025.findings-acl)
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Mufan Qiu, Xinyu Hu, Fengwei Zhan, Sukwon Yun, Jie Peng, Ruichen Zhang, Bhavya Kailkhura, Jiekun Yang, Tianlong Chen
| Challenge: | Foundation models for single-cell RNA sequencing ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals. |
| Approach: | They propose a framework that integrates multi-scale gene regulatory networks into RNA foundation model training. |
| Outcome: | The proposed framework improves on state-of-the-art models on three downstream tasks . it integrates multi-scale gene regulatory networks (GRNs) from multi-omics data into training . |