DeepPep: Deep proteome inference from peptide profiles
Fig 2
Input peptide constructs the n set of input sequences where n is the number of all proteins and the position of the input peptide is marked in binary mode. For example, the input peptide (TRPAY) marks ones where it has matches in each of protein sequences, otherwise zeros. The input sequence is processed in four sequential convolution layers where a pooling layer and dropout are applied between each. Fully connected layer is applied after the fourth convolution layer, which produces the output value of predicted peptide probability. ReLU function was used for all transformations.