Universal Cell Embedding (UCE)

Universal Cell Embedding (UCE) is a transformer that represents each cell through ESM2 protein embeddings of the genes it expresses, so genes from different species map into the same space and no retraining is needed for a new organism. Developed at Stanford with the Chan Zuckerberg Initiative and described in a 2023 bioRxiv preprint, it was trained on 36M cells across 8 species and enables zero-shot cell type mapping, placing a new cell into a universal atlas without labels. It is useful for cross-species comparison, for example relating mouse tumour models to human samples. Its embeddings are coarse for fine perturbation effects, so it is a mapping tool rather than a model of how cells respond to drugs. For a newcomer: UCE puts every cell from any species onto one shared map.