Fig. 1. Overview of the EpiGePT model for multiple epigenomic signals prediction.

The model consists of four modules, namely the Sequence module, the TF module, the Transformer module, and the Multi-task module. The sequence module comprises multiple layers of convolution applied to the one-hot encoded DNA sequence input. The input sequence length consists of 1000 genomic bins of 128bp for the prediction of multiple signals and 50 bins of 200bp for the prediction of DNase signal alone. The TF module encompasses the binding status and expression of 711 transcription factors. The Transformer module consists of a series of consecutive transformer encoders, while the multi-task module is composed of a fully connected layer.