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Table 2 Kernel transformations

From: Consistent probabilistic outputs for protein function prediction

Name Linear Normalized linear Linear2 Normalized linear2 RBF Diffusion Parameters
MGI      
OMIM      σ = 1
Inpar      σ = 1
Biomart      σ = 1
Inter      σ = 1
PfamA      σ = 1
PPI     τ {0.1, 1, 10}
Su        
Zhang   σ = 1
SAGE      σ = 1
  1. Each row in the table corresponds to one of the ten data types listed in Table 1. Check marks indicate which kernels were computed for each data set. The kernels are described in the Kernels section in Materials and methods. 'Linear2' and 'Normalized linear2' refer to the squared version of the original kernel matrix, as described in Materials and methods. The three check marks for the PPI data indicate that three diffusion kernels were computed using τ {0.1, 1, 10}. RBF, radial basis function.