scBatchProx: Federated-Inspired Refinement for Stable Cell-Type Discriminability under Heterogeneous Batch Compositions

ArXi:2602.00423v3 Announce Type: replace Single-cell integration workflows often construct low-dimensional cell embeddings and then refine them with post-hoc methods to reduce batch effects. This refinement process can become unstable when cell-type compositions vary across batches, with some populations underrepresented or absent in particular batches. The problem becomes consequential in dynamic single-cell data systems, where newly acquired batches can change both technical conditions and cell-type composition.