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Table 2 Multiple Kernel AUPRC values on gold standard data sets in the pairwise cross-validation setting (maximum values are denoted by bold face (maximum values are denoted by bold face)

From: VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization

Neighbors MrgRbf MrgTan McsRbf McsTan Orig All
Nuclear Receptor (KBMF-MKL: 0.566, KronRLS-MKL: 0.522)
 2 0.749 0.758 0.742 0.735 0.754 0 . 7 7 9
 3 0.744 0.771 0.761 0.734 0.773 0.775
 5 0.732 0.757 0.739 0.724 0.755 0.756
 2+3 0.750 0.765 0.754 0.736 0.757 0.758
 2+3+5 0.760 0.765 0.740 0.738 0.764 0.760
GPCR (KBMF-MKL: 0.622, KronRLS-MKL: 0.696)
 2 0.743 0.759 0.754 0.762 0.764 0.793
 3 0.755 0.774 0.772 0.780 0.777 0 . 8 0 2
 5 0.762 0.787 0.782 0.783 0.787 0.796
 2+3 0.763 0.782 0.781 0.786 0.785 0 . 8 0 2
 2+3+5 0.777 0.798 0.793 0.789 0.796 0.800
Ion Channel (KBMF-MKL: 0.826, KronRLS-MKL: 0.885)
 2 0.909 0.911 0.910 0.911 0.910 0.909
 3 0.911 0.914 0.915 0.914 0.912 0.916
 5 0.915 0.914 0.913 0.916 0.916 0 . 9 1 7
 2+3 0.912 0.914 0.916 0.914 0.913 0.909
 2+3+5 0.912 0.915 0.915 0.915 0.916 0.906
Enzyme (KBMF-MKL: 0.704, KronRLS-MKL: 0.893)
 2 0.885 0.887 0.879 0.883 0.888 0.884
 3 0.885 0.890 0.885 0.882 0.890 0 . 8 9 5
 5 0.883 0.886 0.880 0.881 0.884 0.883
 2+3 0.888 0.889 0.880 0.881 0.888 0.881
 2+3+5 0.887 0.889 0.881 0.878 0.888 0.875
Kinase (KBMF-MKL: 0.846, KronRLS-MKL: 0.561)
Neighbors - 2D 3D ECFP All
 2   0.850 0.849 0.849 0.850
 3   0.850 0.848 0.850 0.851
 5 - 0.850 0.849 0.850 0.851
 2+3   0.850 0.850 0.850 0.853
 2+3+5   0.851 0.851 0.850 0 . 8 5 4
  1. The table headers indicate the best AUPRC values obtained using the KBMF-MKL and KronRLS-MKL tools, utilizing all kernels and a grid search method for parameterization. The table bodies show AUPRC values from the VB-MK-LMF method in a cumulative manner. In particular, rows correspond to the cut-off value of the number of closest neighbors and the combinations of the resulting truncated kernels. Columns correspond to individual kernels. The last column was obtained by combining all kernels