Mufan Qiu

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)

HoloZip: High Hologram Compression via Latent-of-Latent Coding

Huaizhi Qu^*, Yujie Wang^*, Ruichen Zhang, Hengyu Lian, Mufan Qiu, Samarjit Chakraborty, Henry Fuchs, Tianlong Chen, Praneeth Chakravarthula

ICCP'25: IEEE International Conference on Computational Photography. 2025.

Sparse C-AFM: A Deep Learning Method for Fast and Accurate Characterization of MoS2 with Conductive Atomic Force Microscopy

Levi Harris, Md Jayed Hossain, Mufan Qiu, Ruichen Zhang, Pingchuan Ma, Tianlong Chen, Jiaqi Gu, Seth Ariel Tongay, Umberto Celano

SPIE Low-Dimensional Materials and Devices. 2025.

Single-cell multiregion epigenomic rewiring in Alzheimer's disease progression and cognitive resilience

Zunpeng Liu, Shanshan Zhang, Benjamin T. James, Kyriaki Galani, Riley J. Mangan, Stuart Benjamin Fass, Chuqian Liang, Manoj M. Wagle, Carles A. Boix, Yosuke Tanigawa, Sukwon Yun, Yena Sung, Xushen Xiong, Na Sun, Lei Hou, Martin Wohlwend, Mufan Qiu, Xikun Han, Lei Xiong, Efthalia Preka, Lei Huang, William F. Li, Li-Lun Ho, Amy Grayson, Julio Mantero, Alexey Kozlenkov, Hansruedi Mathys, Tianlong Chen, Stella Dracheva, David A. Bennett, Li-Huei Tsai, Manolis Kellis

Cell. 2025.

GatorSC: Multi-Scale Cell and Gene Graphs with Mixture-of-Experts Fusion for Single-Cell Transcriptomics

Yuxi Liu^*, Zhenhao Zhang^*, Mufan Qiu, Song Wang, Flora D. Salim, Jun Shen, Tianlong Chen, Imran Razzak, Fuyi Li, Jiang Bian

Briefings in Bioinformatics. 2025.

Chreode: A Cell World Model for One-Step Temporal Dynamics and Perturbation Prediction

Mufan Qiu, Genhui Zheng, Yinuo Xu, Ruichen Zhang, Ying Ding, Qi Long, Tianlong Chen

arXiv preprint. 2026.

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

ICML'26: International Conference on Machine Learning. 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

CPAL'26: Conference on Parsimony and Learning (Proceedings Track). 2026.

Understanding the Role of Hallucination in Reinforcement Post-Training of Multimodal Reasoning Models

Gengwei Zhang, Jie Peng, Zhen Tan, Mufan Qiu, Hossein Nourkhiz Mahjoub, Vaishnav Tadiparthi, Kwonjoon Lee, Yanyong Zhang, Tianlong Chen

CVPR'26: IEEE/CVF Conference on Computer Vision and Pattern Recognition. 2026.

Investigation of Scaling Laws for Encoder-Decoder Protein Language Models

Mufan Qiu, Sharmi Banerjee, Athanasios Nikolakopoulos, Gherman Uritskiy, Hamid Mohamadi, Huda Khayrallah, Jonah Noh, Jiachen Li, Mostafa Karimi, Tianlong Chen, Bella Dubrov, Shang Shang

ICLR'26 Workshop on Machine Learning for Genomics Explorations. 2026.

CellDuality: Unlocking Biological Reasoning in LLMs with Self-Supervised RLVR

Yuhang Chen, Zhen Tan, Ruichen Zhang, Mufan Qiu, Tianlong Chen

Submitted to ICLR'26: International Conference on Learning Representations. 2026.

Enhancing Biological Insights with Knowledge-Driven Multi-Modal RNA Models

Mufan Qiu^*, Sukwon Yun^*, Ruichen Zhang^*, Joseph Wakim, Jonathan Allen, Jose Manuel Marti, Vinayak Gupta, Brian Bartoldson, Bhavya Kailkhura, Tianlong Chen

Preprint (Lawrence Livermore National Laboratory). 2025.

Beyond Invariance: A Feature-Strength Framework for OOD Generalization

Rana Muhammad Shahroz Khan, Zhen Tan, Mufan Qiu, Charles Fleming, Tianlong Chen

Preprint. 2025.