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Table 2 Classification result of peptide-encoding schemes

From: EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information

Method

# of features

10-fold cross validation on training dataset only

Holdout method using training dataset and testing dataset

sens

spec

F1

ACC

AUC

sens

spec

F1

ACC

AUC

EpicCapo

360

0.883 ± 0.005

0.792 ± 0.006

0.886 ± 0.003

0.841 ± 0.004

0.915 ± 0.001

0.883

0.744

0.831

0.815

0.882

EpicCapo(3 AAPPs*)

27

0.876 ± 0.005

0.821 ± 0.005

0.862 ± 0.003

0.848 ± 0.003

0.916 ± 0.001

0.855

0.777

0.828

0.817

0.878

DPPS

90

0.865 ± 0.005

0.760 ± 0.007

0.834 ± 0.004

0.816 ± 0.004

0.888 ± 0.001

0.868

0.697

0.807

0.785

0.878

FASGAI

54

0.847 ± 0.004

0.761 ± 0.004

0.825 ± 0.003

0.801 ± 0.003

0.882 ± 0.001

0.840

0.730

0.803

0.787

0.874

z-scale

45

0.847 ± 0.005

0.732 ± 0.005

0.815 ± 0.004

0.793 ± 0.004

0.873 ± 0.002

0.848

0.676

0.788

0.765

0.858

ISA/ECI

18

0.799 ± 0.005

0.652 ± 0.005

0.760 ± 0.003

0.731 ± 0.003

0.797 ± 0.001

0.829

0.643

0.766

0.739

0.796

Binary encoding

180

0.883 ± 0.005

0.721 ± 0.006

0.831 ± 0.003

0.807 ± 0.003

0.883 ± 0.002

0.887

0.705

0.820

0.799

0.879

  1. Means and standard deviations were calculated by 20 iterations of 10-fold cross validation.
  2. Underlined values represent the highest performance.
  3. sens = sensitivity; spec = specificity; F1 = F-score; ACC = accuracy; AUC = area under the curve.
  4. *These three top-ranked AAPPs were MICC010101, SIMK990101, and SIMK990105 (see Additional file1).