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Table 2 Comparison of kernels for ℓ-mer content with their AA-property enhanced counterparts.

From: Exploiting physico-chemical properties in string kernels

Method

auROC50

#Wins

Spectrum (ℓ = 5)

15.2%

7/54

Spectrum-RBF (ℓ = 5, σ = 1)

42.1%

45/54

Mismatch (ℓ = 5, m = 1)

42.3%

13/54

Mismatch-RBF (ℓ = 5,m = 1, σ = 1)

43.6%

36/54

Profile (ℓ = 5, τ = 7.5)

82.1%

3/54

Profile-RBF (ℓ = 5,τ = 7.5, σ = 100)

82.2%

10/54

  1. Comparison of the three kernels proposed in [11, 21, 22], with their AA-property enhanced counterparts for remote homology detection of 54 protein families. auROC50 is the average auROC50 score and #Wins the number of families for which each method outperforms its counterpart (Spectrum vs. Spectrum-RBF, Mismatch vs. Mismatch-RBF, Profile vs. Profile-RBF). The kernels taking advantage of AA properties lead to a higher average accuracy in all three cases (p-Values: 6.92 10−8 for spectrum, 0.0045 for mismatch, and 1.0 for profile kernels). For ℓ and τ we use the published parameter settings. For σ we chose the best result among σ = {0.1,1,10,100,1000}.