2025/04/07 by Y. Mao, Mao, Yuren, Yu Mi +8 · 11 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · #Cell Image Analysis Techniques #Computation and Language (cs.CL) #Domain Adaptation and Few-Shot Learning #FOS: Computer and information sciences #Single-cell and spatial transcriptomics
paper · pdf · doi:10.48550/arxiv.2504.04698
openalex publication_date 2025/04/07 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Cell type annotation is critical for understanding cellular heterogeneity. Based on single-cell RNA-seq data and deep learning models, good progress has been made in annotating a fixed number of cell types within a specific tissue. However, universal cell annotation, which can generalize across tissues, discover novel cell types, and extend to novel cell types, remains less explored. To fill this gap, this paper proposes scAgent, a universal cell annotation framework based on Large Language Models (LLMs). scAgent can identify cell types and discover novel cell types in diverse tissues; furthermore, it is data efficient to learn novel cell types. Experimental studies in 160 cell types and 35 tissues demonstrate the superior performance of scAgent in general cell-type annotation, novel cell discovery, and extensibility to novel cell type.