Table 3.

The performance of superMHC in comparison with NetMHCII-2.3, NetMHCIIpan-3.2, and their consensus method on the NetMHCIIpan-3.2 dataset in terms of AUC.

MHC Molecules	# of Peptides	NetMHCII-2.3	NetMHCIIpan-3.2	Consensus (Net)	superMHC (AUC)	superMHC (RMSE)
DRB1_0101	10412	0.829	0.832	0.838	0.835	0.197
DRB1_0103	42	0.250	0.678	0.599	0.697	0.178
DRB1_0301	5352	0.816	0.816	0.826	0.831	0.183
DRB1_0401	6317	0.798	0.809	0.813	0.809	0.199
DRB1_0402	53	0.633	0.701	0.649	0.663	0.229
DRB1_0403	59	0.644	0.841	0.787	0.830	0.140
DRB1_0404	3657	0.787	0.812	0.808	0.811	0.189
DRB1_0405	3962	0.839	0.827	0.846	0.836	0.173
DRB1_0701	6325	0.877	0.875	0.885	0.880	0.173
DRB1_0801	937	0.834	0.844	0.854	0.834	0.170
DRB1_0802	4465	0.834	0.834	0.844	0.842	0.182
DRB1_0901	4318	0.832	0.833	0.843	0.831	0.175
DRB1_1001	2066	0.912	0.923	0.924	0.910	0.157
DRB1_1101	6045	0.867	0.864	0.873	0.865	0.175
DRB1_1201	2384	0.891	0.868	0.892	0.883	0.146
DRB1_1301	1034	0.828	0.857	0.856	0.855	0.225
DRB1_1302	4477	0.889	0.885	0.895	0.883	0.184
DRB1_1501	4850	0.833	0.834	0.842	0.842	0.188
DRB1_1602	1699	0.879	0.883	0.888	0.883	0.154
DRB3_0101	4633	0.898	0.888	0.900	0.891	0.160
DRB3_0202	3334	0.887	0.869	0.886	0.873	0.183
DRB3_0301	884	0.824	0.840	0.845	0.818	0.198
DRB4_0101	3961	0.837	0.822	0.844	0.852	0.171
DRB4_0103	846	0.839	0.841	0.861	0.867	0.193
DRB5_0101	5125	0.849	0.849	0.858	0.854	0.192
HLA-DPA10103-DPB10201	787	0.910	0.917	0.921	0.920	0.144
HLA-DPA10103-DPB10301	1563	0.914	0.902	0.916	0.914	0.165
HLA-DPA10103-DPB10401	2725	0.935	0.935	0.939	0.936	0.144
HLA-DPA10103-DPB10402	45	0.497	0.710	0.636	0.515	0.186
HLA-DPA10103-DPB10601	584	0.996	0.995	0.995	0.996	0.105
HLA-DPA10201-DPB10101	2447	0.903	0.903	0.909	0.899	0.145
HLA-DPA10201-DPB10501	2470	0.914	0.911	0.919	0.915	0.153
HLA-DPA10201-DPB11401	2302	0.937	0.930	0.938	0.940	0.151
HLA-DPA10301-DPB10402	2641	0.906	0.904	0.910	0.900	0.158
HLA-DQA10101-DQB10501	2946	0.917	0.900	0.917	0.916	0.144
HLA-DQA10102-DQB10501	833	0.867	0.839	0.874	0.869	0.192
HLA-DQA10102-DQB10502	800	0.850	0.835	0.859	0.868	0.157
HLA-DQA10102-DQB10602	2747	0.905	0.890	0.906	0.893	0.152
HLA-DQA10103-DQB10603	462	0.816	0.861	0.855	0.856	0.186
HLA-DQA10104-DQB10503	883	0.844	0.805	0.844	0.840	0.145
HLA-DQA10201-DQB10202	944	0.851	0.814	0.853	0.838	0.133
HLA-DQA10201-DQB10301	827	0.864	0.849	0.871	0.857	0.195
HLA-DQA10201-DQB10303	761	0.887	0.894	0.899	0.891	0.150
HLA-DQA10201-DQB10402	768	0.858	0.860	0.875	0.857	0.186
HLA-DQA10301-DQB10301	207	0.761	0.839	0.814	0.875	0.183
HLA-DQA10301-DQB10302	3111	0.849	0.810	0.842	0.854	0.125
HLA-DQA10303-DQB10402	567	0.836	0.820	0.855	0.835	0.176
HLA-DQA10401-DQB10402	2890	0.894	0.883	0.897	0.894	0.117
HLA-DQA10501-DQB10201	2897	0.889	0.876	0.888	0.882	0.133
HLA-DQA10501-DQB10301	3585	0.922	0.915	0.924	0.922	0.143
HLA-DQA10501-DQB10302	847	0.831	0.822	0.840	0.824	0.136
HLA-DQA10501-DQB10303	564	0.884	0.876	0.892	0.887	0.132
HLA-DQA10501-DQB10402	749	0.857	0.868	0.876	0.863	0.166
HLA-DQA10601-DQB10402	565	0.845	0.848	0.872	0.859	0.187
Average		0.840	0.854	0.861	0.857	0.167

Consensus (Net) represents the consensus method by averaging the prediction scores from NetMHCII-2.3 and NetMHCIIpan-3.2. The performance of superMHC in terms of RMSE is given in the last column.