Mufan Qiu
Ph.D. Student, University of North Carolina at Chapel Hill
mufan [AT] cs.unc.edu
Bio
I am a Ph.D. student in Computer Science at the University of North Carolina at Chapel Hill, where I am fortunate to be advised by Prof. Tianlong Chen. Prior to UNC, I received my B.S. in Computational Mathematics from the University of Science and Technology of China (USTC) in 2024. I was also an algorithm engineer intern at Microsoft Research AI for Science, working with Dr. Shuxin Zheng.
My current research interests lie in AI for Science and Efficient ML. Specifically, I am interested in:
- AI for Science: Building foundation models for computational biology, including multi-omics RNA foundation models and multimodal protein language models. I explore the integration of MoE and GNNs for drug discovery applications such as perturbation prediction and drug response prediction.
- Efficient ML: Developing Mixture-of-Experts (MoE) models, with a focus on optimization strategies, representation learning, and computational efficiency.
Publications
Most recent publications on Google Scholar.
* indicates equal contribution.
KeyTAR: Practical Keystroke Timing Attacks and Input Reconstruction
Mufan Qiu*, Lihsuan Chuang*, Dohhyun Kim, Huaizhi Qu, Tianlong Chen, Andrew Kwong
IEEE S&P'26: IEEE Symposium on Security and Privacy. 2026.
Bag of Tricks for Sparse Mixture-of-Experts: A Benchmark Across Reasoning, Efficiency, and Safety
Mufan Qiu*, Zheyu Shen*, Pingzhi Li, Ang Li, Tianlong Chen
Findings of EMNLP'25: Empirical Methods in Natural Language Processing. 2025.
GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models
Mufan Qiu, Xinyu Hu, Fengwei Zhan, Sukwon Yun, Jie Peng, Ruichen Zhang, Bhavya Kailkhura, Jiekun Yang, Tianlong Chen
Findings of ACL'25: Association for Computational Linguistics. 2025.
Advancing MoE Efficiency: A Collaboration-Constrained Routing (C2R) Strategy for Better Expert Parallelism Design
Mohan Zhang*, Pingzhi Li*, Jie Peng, Mufan Qiu, Tianlong Chen
NAACL'25: Annual Conference of the North American Chapter of the Association for Computational Linguistics. 2025. (Senior AC Award)
Single-cell epigenomics and transcriptomics reveals altered circuitry in Alzheimer's disease across multiple brain regions
Zunpeng Liu, Benjamin T. James, Shanshan Zhang, Kyriaki Galani, Riley J. Mangan, Stuart Benjamin Fass, Sukwon Yun, Carles A. Boix, Yena Sung, Xushen Xiong, Na Sun, Lei Hou, Martin Wohlwend, Yosuke Tanigawa, Mufan Qiu, Xikun Han, Lei Xiong, Efthalia Preka, Lei Huang, Li-Lun Ho, Julio Mantero, Hansruedi Mathys, Tianlong Chen, David A. Bennett, Li-Huei Tsai, Manolis Kellis
Cell. 2025.
KeyTAR: Practical Keystroke Timing Attacks and Input Reconstruction
Mufan Qiu*, Lihsuan Chuang*, Dohhyun Kim, Huaizhi Qu, Tianlong Chen, Andrew Kwong
IEEE S&P'26: IEEE Symposium on Security and Privacy. 2026.
Bag of Tricks for Sparse Mixture-of-Experts: A Benchmark Across Reasoning, Efficiency, and Safety
Mufan Qiu*, Zheyu Shen*, Pingzhi Li, Ang Li, Tianlong Chen
Findings of EMNLP'25: Empirical Methods in Natural Language Processing. 2025.
GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models
Mufan Qiu, Xinyu Hu, Fengwei Zhan, Sukwon Yun, Jie Peng, Ruichen Zhang, Bhavya Kailkhura, Jiekun Yang, Tianlong Chen
Findings of ACL'25: Association for Computational Linguistics. 2025.
Advancing MoE Efficiency: A Collaboration-Constrained Routing (C2R) Strategy for Better Expert Parallelism Design
Mohan Zhang*, Pingzhi Li*, Jie Peng, Mufan Qiu, Tianlong Chen
NAACL'25: Annual Conference of the North American Chapter of the Association for Computational Linguistics. 2025. (Senior AC Award)
Single-cell epigenomics and transcriptomics reveals altered circuitry in Alzheimer's disease across multiple brain regions
Zunpeng Liu, Benjamin T. James, Shanshan Zhang, Kyriaki Galani, Riley J. Mangan, Stuart Benjamin Fass, Sukwon Yun, Carles A. Boix, Yena Sung, Xushen Xiong, Na Sun, Lei Hou, Martin Wohlwend, Yosuke Tanigawa, Mufan Qiu, Xikun Han, Lei Xiong, Efthalia Preka, Lei Huang, Li-Lun Ho, Julio Mantero, Hansruedi Mathys, Tianlong Chen, David A. Bennett, Li-Huei Tsai, Manolis Kellis
Cell. 2025.
SPATIA: Multimodal Model for Prediction and Generation of Spatial Cell Phenotypes
Zhenglun Kong*, Mufan Qiu*, John Boesen, Xiang Lin, Sukwon Yun, Tianlong Chen, Manolis Kellis, Marinka Zitnik
Submitted to ICLR'26: International Conference on Learning Representations. 2026.
scPaLM: Pre-training of Single-cell Language Models through Genetic Pathway Learning
Mufan Qiu*, Xuxi Chen*, Sukwon Yun*, Zhangyang Wang, Marinka Zitnik, Manolis Kellis, Tianlong Chen
Submitted to ICLR'26: International Conference on Learning Representations. 2026.
Symbiotic Cooperation for Web Agents: Harnessing Complementary Strengths of Large and Small LLMs
Ruichen Zhang*, Mufan Qiu*, Zhen Tan*, Mohan Zhang, Xiaopeng Lu, Jie Peng, Kaidi Xu, Leandro Z. Agudelo, Peter Zhenghao Qian, Tianlong Chen
Submitted to ICLR'26: International Conference on Learning Representations. 2026.
Vitæ
Full Resume in PDF.
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Amazon May 2025 - nowApplied Scientist Intern
Mentor: Dr. Mostafa Karimi -
UNC Chapel Hill 2024 - nowPh.D. Student
Computer Science
Advisor: Prof. Tianlong Chen -
MSRA AI for Science Oct 2023 - Jul 2024Algorithm Engineer Intern
Mentor: Dr. Shuxin Zheng -
UNC Chapel Hill Feb 2024 - Jun 2024Remote Research Intern
Mentor: Prof. Tianlong Chen -
USTC 2020 - 2024B.S. Student
Computational Mathematics