Speciesformer: Learning Conserved Cellular States for Cross-Species Generative Virtual Cell Modeling
This work presents Speciesformer, a cross-species generative single-cell foundation model pretrained on SpeciesCorpus (about 131 million cells from 11 species, 154 tissues, and more than 923 cell types) that maps species-specific genes into a shared evolution-informed gene space via a macrogene vocabulary, whose encoder learns transferable cell and gene representations and whose unified generative decoder supports bidirectional generation between transcriptomic states and biological text as well as prediction of post-perturbation transcriptomes from initial cell states and intervention descriptions, reporting performance above existing baselines across multiple benchmarks.