Fig. 3. Application of self-attention mechanism in EpiGePT for long-range chromatin interaction identification.

(A) The performance (auPRC) of attention score of EpiGePT in distinguishing enhancer-gene pairs at different distance ranges on two different datasets. (B) The performance (auROC and auPRC) of attention score of EpiGePT in distinguishing silencer-gene pairs at different distance ranges based on the data from SilencerDB²⁵. (C) Heatmap of the self-attention matrix of each attention head centered at the TSS of the CHD4 gene, the (i, j) element in the matrix denotes the average attention score between the ith genomic bin and the jth genomic bin across all layers. (D) Attention scores centered at the TSS of the CHD4 gene, and putative enhancer regions in its vicinity. (E) The performance (auROC and auPRC) of attention score of EpiGePT in distinguishing HiChIP loops of H3K27ac at different distance ranges on K562 cell line and GM12878 cell line.