Fig. 1.

ISM (a) given an input sequence, ISM proceeds by running the CNN forward propagation on all possible mutations of the input and recording the output. In practice, the mutated sequences are run through the model in a batched fashion; (b) an example of ISM using the DeepSEA Beluga model (Zhou et al., 2018) at hg38 chr3:138863109–138863254 for the small intestine DNase-seq output task. Differences from reference output are visualized in the matrix, while reference nucleotides are scaled by the L2-norm of the differences. The ISM scores highlight AP1 and HNF4 motifs at the locus