Fig. 1
From: Zero-shot evaluation reveals limitations of single-cell foundation models
Evaluation of the cell embedding space generated by the models. A Overview of the evaluation setup. We compare Geneformer and scGPT to scVI, Harmony, and the selection of highly variable genes (HVG) on five diverse datasets. B Average BIO score for HVG and embeddings from Harmony, scVI, scGPT, and Geneformer. C, D Visualization of the UMAP projections of the Pancreas (16k) dataset using the cell embedding space generated by the models. Cells are color-coded by cell type (C) and batch (D). E Average batch score for HVG and embeddings from Harmony, scVI, scGPT, and Geneformer. Dashed line in B and E signifies the median calculated across the datasets