287-scArches: Reference Mapping for Single-Cell Atlases

Paper Talk · Dec 2, 2025 · 16m

The paper introduces scArches, a novel deep learning strategy based on transfer learning (TL) and architectural surgery, designed for efficiently mapping new, or query, single-cell datasets onto existing, large-scale reference atlases. This method addresses the challenges in single-cell genomics of batch effects between datasets, limited computational resources, and data sharing restrictions by only requiring fine-tuning a small subset of the network parameters (adaptors). The scArches pipeline enables decentralized, iterative building and updating of reference models without needing to share…