Epigenetics is all you need: A transformer to decode chromatin structural compartments from the epigenome
Fig 2
Assessment of TECSAS prediction at 50 kbp and 25kbp resolution for GM12878 and K562 cell lines.
(A) Confusion matrix comparing TECSAS predictions with experimentally derived subcompartment annotations for the GM12878 cell line at 50 kb resolution. The diagonal elements represent the fraction of correctly predicted loci for each subcompartment, highlighting the high accuracy of the model. (B) Confusion matrix for A/B compartment predictions based on the inferred subcompartments in GM12878, demonstrating accurate compartment classification. (C) Distribution of confidence probabilities for each predicted subcompartment in GM12878. B1 and B2 subcompartments exhibit lower average confidence probabilities, reflecting their more complex epigenomic profiles. (D) Confusion matrix comparing TECSAS predictions with subcompartment annotations derived using the SLICE method for the K562 cell line at 25 kb resolution, demonstrating the model’s ability to predict subcompartments at higher resolutions. (E) Overall accuracy of TECSAS in predicting subcompartments for GM12878 and K562, comparing performance for all loci and loci excluding transition regions. The exclusion of transition regions significantly improves prediction accuracy for both cell lines. (F) Fraction of successful and failed predictions within transition regions for GM12878 and K562, highlighting the challenges of predicting subcompartments in these regions with mixed epigenomic signatures.