Fig 6. The ResNet model fails to learn the correct representation of individual grammars when there are multiple regulatory grammars that can distinguish one heterogenous regulatory class from another.

For this simulation, we created three heterogeneous regulatory sequence classes with no overlap among their grammars (Table 1) and applied our interpretation approach. a) Actual labels of simulated regulatory grammars of the TF binding sites overlaid on t-SNE visualization of TFBS saliency values across neurons. The TFBSs do not separate according to their grammars. b) Sum of saliency values for TFBSs in each regulatory grammar across neurons in the penultimate layer.