GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models. - Mufan Qiu; Xinyu Hu; Fengwei Zhan; Sukwon Yun; Jie Peng 002; Ruichen Zhang; Bhavya Kailkhura; Jiekun Yang; Tianlong Chen 001 (ACL (Findings), 2025)

Advancing MoE Efficiency: A Collaboration-Constrained Routing (C2R) Strategy for Better Expert Parallelism Design. - Mohan Zhang; Pingzhi Li; Jie Peng 002; Mufan Qiu; Tianlong Chen 001 (NAACL (Long Papers), 2025)

Symbiotic Cooperation for Web Agents: Harnessing Complementary Strengths of Large and Small LLMs. - Ruichen Zhang; Mufan Qiu; Zhen Tan 001; Mohan Zhang; Vincent Lu; Jie Peng 002; Kaidi Xu; Leandro Z. Agudelo; Peter Qian; Tianlong Chen 001 (CoRR, 2025)

SPATIA: Multimodal Model for Prediction and Generation of Spatial Cell Phenotypes. - Zhenglun Kong; Mufan Qiu; John Boesen; Xiang Li 001; Sukwon Yun; Tianlong Chen 001; Manolis Kellis; Marinka Zitnik (CoRR, 2025)

SparseC-AFM: a deep learning method for fast and accurate characterization of MoS2 with C-AFM. - Levi Harris; Md Jayed Hossain; Mufan Qiu; Ruichen Zhang; Pingchuan Ma 012; Tianlong Chen 001; Jiaqi Gu 002; Seth Ariel Tongay; Umberto Celano (CoRR, 2025)