Immunogenicity ligandome

Instead of trying to model the space of immunogenic epitope strings directly, instead let's model immunogenicity by only keeping track of which patterns *can't* be recognized by T-cells. These are epitopes which overlap with the set of "self" peptides used for negative selection in the thymus. 
So you're taking the scored epitopes from binding prediction and re-scoring them, right? I found the overloading of the variable "scored_epitopes" a bit confusing in that regard.