Extended Data Fig. 8: Geneformer boosted predictions in a diverse panel of downstream tasks.

a, Confusion matrix and F1 score for Geneformer predictions vs. alternative methods (as described in Fig. 2a) for downstream task of distinguishing genome-wide³⁰ bivalent vs. Lys4-only methylated genes with model fine-tuned only on 56 highly conserved loci²⁸. b, ROC curve of Geneformer fine-tuned to distinguish genome-wide bivalent vs. Lys4-only-methylated genes using limited data (about 15K ESCs), compared to alternative methods. c, Confusion matrices and F1 score for Geneformer predictions vs. alternative methods for downstream task of distinguishing genome-wide bivalent vs. non-methylated genes with model fine-tuned on 80% of genome-wide loci and predicting on 20% of out of sample loci. d, Confusion matrices and F1 score for Geneformer predictions vs. alternative methods for downstream task of distinguishing long- vs. short-range transcription factors. e, Confusion matrices and F1 score for Geneformer predictions vs. alternative methods for downstream task of distinguishing central vs. peripheral genes within the N1-dependent network in endothelial cells.