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Table 1 Performances of kernels utilizing sequential structure and/or AA properties on three MHC alleles

From: Exploiting physico-chemical properties in string kernels

KERNEL A*2301 B*5801 A*0201
  auROC (std) auROC (std) auROC (std)
WD 0.7307 (0.0900) 0.9314 (0.0279) 0.9485 (0.0076)
Poly (pca) 0.8363 (0.0808) 0.9428 (0.0336) 0.9354 (0.0111)
Poly (zscale) 0.7964 (0.0727) 0.8778 (0.0637) 0.9052 (0.0070)
Poly (blosum50) 0.8220 (0.0442) 0.4948 (0.0560) 0.4729 (0.0246)
RBF (pca) 0.8277 (0.0904) 0.9396 (0.0303) 0.9345 (0.0114)
RBF (zscale) 0.7847 (0.0787) 0.9235 (0.0347) 0.9157 (0.0072)
RBF (blosum50) 0.8204 (0.0864) 0.9509 (0.0317) 0.9520 (0.0072)
WD-Poly (pca) 0.7879* (0.0858) 0.9406* (0.0319) 0.9495* (0.0084)
WD-Poly (zscale) 0.7983* (0.0902) 0.9499* (0.0348) 0.9483 (0.0073)
WD-Poly (blosum50) 0.8307* (0.1077) 0.9491* (0.0224) 0.9490* (0.0070)
WD-RBF (pca) 0.8133* (0.0806) 0.9510* (0.0265) 0.9486* (0.0051)
WD-RBF (zscale) 0.7782* (0.1222) 0.9487* (0.0434) 0.9500* (0.0074)
WD-RBF (blosum50) 0.8312* (0.0993) 0.9571* (0.0265) 0.9503* (0.0067)
  1. auROCs and standard deviation were determined in two times nested 5-fold cross-validation. Best (bold) and second-best (underlined) performances per MHC allele are highlighted. An asterisk marks performance improvement due to the proposed modifications.