Benchmarking results across six data sets. (A) The label transfer accuracy and F1-score of scNym, Portal, Concerto, scGCN, Seurat, scJoint, scBridge, scNCL, and scSHEFT on six data sets. (B) UMAP visualizations of the scATAC-seq cell embeddings generated by different methods on the T cell bone marrow data set, with cells colored by type. (C) Label transfer matrix comparing predicted labels with ground-truth annotations, where a clearer diagonal indicates better label transfer performance.