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. 2022 Aug 4;14:52. doi: 10.1186/s13321-022-00634-3

Table 3.

Model performance on kinase datasets

Dataset Splitting MPNN AttentiveFP RG-MPNN
MCC AUC MCC AUC MCC AUC
EGFR Random 0.699 ± 0.022 0.923 ± 0.009 0.729 ± 0.017 0.933 ± 0.010 0.738 ± 0.029 0.942 ± 0.008
Scaffold 0.648 ± 0.03 0.901 ± 0.010 0.684 ± 0.029 0.908 ± 0.006 0.706 ± 0.020 0.925 ± 0.007
BRAF Random 0.703 ± 0.052 0.916 ± 0.020 0.753 ± 0.035 0.938 ± 0.006 0.774 ± 0.020 0.915 ± 0.012
Scaffold 0.614 ± 0.040 0.883 ± 0.006 0.685 ± 0.018 0.905 ± 0.008 0.677 ± 0.044 0.915 ± 0.006
PIM1 Random 0.691 ± 0.069 0.933 ± 0.029 0.741 ± 0.026 0.957 ± 0.009 0.758 ± 0.029 0.951 ± 0.013
Scaffold 0.612 ± 0.050 0.881 ± 0.024 0.681 ± 0.021 0.921 ± 0.006 0.710 ± 0.042 0.928 ± 0.007
mTOR Random 0.591 ± 0.037 0.888 ± 0.036 0.641 ± 0.033 0.927 ± 0.010 0.674 ± 0.038 0.921 ± 0.008
Scaffold 0.408 ± 0.060 0.792 ± 0.033 0.588 ± 0.022 0.876 ± 0.011 0.574 ± 0.015 0.886 ± 0.009
AKT1 Random 0.669 ± 0.068 0.905 ± 0.035 0.751 ± 0.038 0.933 ± 0.011 0.771 ± 0.031 0.941 ± 0.014
Scaffold 0.605 ± 0.041 0.883 ± 0.016 0.657 ± 0.029 0.914 ± 0.010 0.649 ± 0.023 0.910 ± 0.008
AURKA Random 0.634 ± 0.061 0.892 ± 0.020 0.665 ± 0.021 0.909 ± 0.010 0.690 ± 0.028 0.917 ± 0.007
Scaffold 0.471 ± 0.031 0.793 ± 0.012 0.475 ± 0.023 0.807 ± 0.008 0.522 ± 0.037 0.836 ± 0.006
BTK Random 0.670 ± 0.065 0.915 ± 0.022 0.748 ± 0.083 0.947 ± 0.017 0.759 ± 0.042 0.954 ± 0.017
Scaffold 0.545 ± 0.044 0.849 ± 0.021 0.626 ± 0.044 0.902 ± 0.014 0.682 ± 0.031 0.893 ± 0.015
CDK2 Random 0.567 ± 0.041 0.865 ± 0.019 0.624 ± 0.074 0.886 ± 0.021 0.652 ± 0.050 0.902 ± 0.013
Scaffold 0.376 ± 0.052 0.752 ± 0.024 0.412 ± 0.026 0.773 ± 0.022 0.495 ± 0.015 0.820 ± 0.008
MAP4K2 Random 0.457 ± 0.131 0.792 ± 0.059 0.484 ± 0.123 0.813 ± 0.041 0.540 ± 0.046 0.863 ± 0.025
Scaffold 0.174 ± 0.039 0.578 ± 0.037 0.277 ± 0.03 0.652 ± 0.033 0.306 ± 0.045 0.706 ± 0.034
CK1 Random 0.156 ± 0.162 0.673 ± 0.111 0.313 ± 0.128 0.751 ± 0.047 0.433 ± 0.090 0.800 ± 0.065
Scaffold − 0.020 ± 0.051 0.576 ± 0.029 0.159 ± 0.084 0.653 ± 0.011 0.333 ± 0.107 0.687 ± 0.033

Note that the best AUC and MCC for each kinase target are in bold