Are there ways to handle paired inputs in the deep neural network (DNN)? First, I will describe my problem, and then I will describe an equivalent problem in the image.
We have many protein sequences (each distinct but equal length), and we don't know their functions (we know the function of some). To determine the function we need to determine the similarity between them, but we don't know how to define similarity. We want to use DNN to learn similarity/distance for two protein sequence. So input is two protein sequence and output is protein similarity/distance score.
The equivalent problem in images will be: There are images of multiple people in multiple backgrounds/angle, and we need to determine whether any two picture is the same person or not.