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Table 4 Independent evaluation of eluted ligand data set in terms of AUC 0.1

From: Footprints of antigen processing boost MHC class II natural ligand predictions

Training set Eval set BA single BA combined EL single EL combined NetMHCIIpan NetMHCII
BA EL
DR1 BA DR1 Ph DR1 Pm 0.57 0.644 0.839 0.849 0.562 0.585
DR1 Sm 0.573 0.648 0.81 0.813 0.576 0.578
DR1 Pm DR1 Ph 0.498 0.557 0.757 0.754 0.478 0.469
DR1 Sm 0.514 0.549 0.665 0.669 0.519 0.511
DR1 Sm DR1 Ph 0.506 0.556 0.704 0.707 0.481 0.478
DR1 Pm 0.568 0.636 0.824 0.835 0.54 0.57
DR15 BA DR15 Ph DR15 Pm 0.584 0.672 0.869 0.869 0.427 0.58
DR15 Pm DR15 Ph 0.615 0.71 0.888 0.889 0.459 0.583
  1. “Training set” refers to the data sets used to train the given model (BA indicates binding affinity and EL eluted ligand data). For references on the training sets names and compositions, refer to Table 1. Cross-validated performance values are reported as AUC 0.1. “Eval set” refers to the independent eluted ligand data set from the same allotype used for evaluation. “BA single” or “EL single” refers to model trained on single data types (BA or EL respectively). “BA combined” or “EL combined” refers to the eluted ligand prediction output or binding affinity output of models trained on both data types. NetMHCIIpan or NetMHCII refers to predictions made using the NetMHCIIpan 3.2 [36], and NetMHCII 2.3 [36] publicly available prediction methods