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Table 3 The ablation study results obtained by attempting the removal of various components

From: PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models

Method

Test set 1

Test set 2

Combined set

PCC\(\uparrow\)

MAE\(\downarrow\)

PCC\(\uparrow\)

MAE\(\downarrow\)

PCC\(\uparrow\)

MAE\(\downarrow\)

Standard

0.641

1.64

0.625

1.51

0.633

1.57

Without PPI-Graphomer

0.624

1.70

0.586

1.64

0.601

1.71

Without esm2 feature

0.545

1.83

0.521

1.69

0.511

1.91

Without esm-if1 feature

0.608

1.70

0.603

1.63

0.605

1.66