Papers by Mufan Qiu
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 . |
Advancing MoE Efficiency: A Collaboration-Constrained Routing (C2R) Strategy for Better Expert Parallelism Design (2025.naacl-long)
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| Challenge: | Using Mixture-of-Experts, researchers have found that efficient MoE is difficult to achieve due to two key reasons: imbalanced expert activation and massive communication overhead. |
| Approach: | They propose a collaboration-constrained routing strategy that encourages more specialized expert groups and leverages expert specialization. |
| Outcome: | The proposed approach achieves an average performance improvement of 0.51% and 0.33% on LLaMA-MoE and Qwen-MaE respectively. |
Bag of Tricks for Sparse Mixture-of-Experts: A Benchmark Across Reasoning, Efficiency, and Safety (2025.findings-emnlp)
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| Challenge: | Existing benchmarks focus on isolated aspects of MoE, with conflicting conclusions . a lack of consensus on optimal design choices is limiting to specific aspects of the model. |
| Approach: | They propose to evaluate two popular MoE backbones across four dimensions of design choices . they find token-level routing and z-loss regularization improve reasoning performance . |
| Outcome: | The proposed framework evaluates two popular MoE backbones on over eight metrics. |