CellMSA: Context Modeling for Single-Cell Representation Learning

Excerpt

arXiv:2609.38908v1 Announce Type: cross Abstract: Single-cell transcriptomics enables profiling of cellular states at unprecedented resolution, but its high dimensionality, sparsity, and technical batch effects pose significant challenges for representation learning. Existing single-cell foundation models typically encode each cell independently or only model cells from the same batch for denoising, thereby underutilizing the rich relational information across batches and cell types to model gen