Unless stated otherwise, we used the following default parameters in all the BO runs: the GPR model as the surrogate model, the MAP4 fingerprint with a radius of 1 and a dimension of 4096 bits paired with the TS kernel, EI as the acquisition function, and the top-k strategy for selecting batches of 96 peptides for each DMT cycle. The homolog scanning strategy was used as the default initialization strategy to generate the initial batch. Each BO was run for a total of 5 DMT cycles. The standard GA method was used for SOO, and the SMS-EMOA for MOO. For SOO, the SMM PMBEC PSSMs for MHC class I A*0201 were used to obtain the pIC50 of each peptide sequence, covering lengths from 8-to 11-mers. In MOO, the SMM PMBEC PSSMs for MHC class I A*0101 and A*2602 were used, but only for 9-mers peptides.