Table 3.

Layer ablation study. The AUROC values for a link prediction task compared across different graph layers and different GNN models. Best performances are indicated in bold.

Graph layers	GDRnet	GraphSAGE	GCN	GAT
Drugs, Diseases	$0.61\pm 0.02$	$0.707\pm 0.02$	$0.692\pm 0.02$	$0.655\pm 0.01$
Drugs, Diseases, Anatomies	$0.652\pm 0.01$	$0.75\pm 0.01$	$0.728\pm 0.02$	$0.722\pm 0.01$
Drugs, Diseases, Genes	$0.845\pm 0.02$	$\mathbf{0.881 \pm 0.02}$	$0.833\pm 0.01$	$0.84\pm 0.01$
Drugs, Diseases, Genes, Anatomies	$\mathbf{0.855 \pm 0.02}$	$0.874\pm 0.01$	$\mathbf{0.842 \pm 0.02}$	$\mathbf{0.863 \pm 0.01}$