Fig. 7From: Footprints of antigen processing boost MHC class II natural ligand predictionsPredictive performance on a panel of CD4+ T cell epitopes. The boxplots represent the distribution of AUC values over all epitope evaluation data sets restricted to a given allele comparing the different models. Middle lines in boxes correspond to median values. The height of the box represents 50% of the data. Whiskers represent 1.5 quartile range (QR) of data, and dots represent outliers of 1.5 of QR. P significance is calculated from Wilcoxon test. nsP > 0.05, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001. In both benchmarks, an AUC value was calculated for each epitope/source protein pair by considering peptides identical to the epitope as positives and all other peptides as negatives excluding peptides with an overlap of at least nine amino acids to the epitope. a Comparison of the combined models developed in this study with context information (EL + context) and without context (EL) to current state-of-the-art prediction methods trained on binding affinity data only (NetMHCII-2.3 and NetMHCIIpan-3.2). b Comparison of EL + context and EL in a benchmark where the epitope evaluation set was constructed using the evaluation strategy accounting for ligand preference described in the textBack to article page