EP-pair (AKA gene regulation modeling): gene regulation leads to the creation of different cell types that possess different gene expression profiles from the same genome sequence in multicellular organisms. The process is essential for cellular differentiation, morphogenesis, and normal functioning of tissues. Despite increasing experimental data indicating gene regulation activities, we are still unaware of the fundamental rules driving temporal-spatial gene regulation programs, partially due to the missing of appropriate tools. Wherefore, we try to leverage computational power and deep learning techniques to decrypt the secret of gene regulation from the accumulating biological data.