Fig. 2
From: Zero-shot evaluation reveals limitations of single-cell foundation models
Performance comparison of scGPT and Geneformer in gene expression reconstruction. A–C Reconstruction of the expression in the Immune (330k) dataset: A scGPT gene expression prediction (GEP) under the masked language modeling (MLM) objective. B scGPT gene expression prediction from cell embeddings (GEPC). C Geneformer MLM output of the predicted expression ranking (y-axis) versus the true input expression ranking (x-axis). D Mean squared error (MSE) comparison for scGPT objectives. Mean and standard deviation range are shown as points and solid lines, respectively, and a median MSE for mean-based reconstruction is shown as a dashed line. E Pearson’s correlation of input and predicted expression ranking for both Geneformer and for average gene rankings. Mean and standard deviation range are shown as points and solid lines, respectively, and a median correlation for average ranking is shown as a dashed line