Table 2.

Performance evaluation on eluted ligand test NetMHCpan-4.1, [34] dataset including 77,053 peptides (lengths 8-14) across 36 distinct HLA-I molecules.

	RNN(no ambig.)	RNN	CNN(no ambig.)	CNN	NetMHCpan-4.1	NetMHCpan-4.0	MHCflurry	MixMHCpred
Mean ROC AUC	0.9657	0.9639	0.9615	0.9610	0.9498	0.9462	0.9335	0.9324
Mean PPV @ 0.95 * n_pos	0.8237	0.8038	0.8651	0.8446	0.8162	0.786	0.7255	0.7705

Our system identifies situations where predictions are ambiguous; columns with the “(no ambig.)” label do not include ambiguous data; this is in contrast to a forced decision in all cases for columns labeled only RNN or CNN. For consistency with referenced study methodology, PPV for each HLA was evaluated considering only a fraction of ranked predictions equal to 0.95 times the number of true positives. See methods for more detail. The mean of these metrics across HLAs is labeled “Mean PPV @ 0.95 * n_pos”.