Comparison results of the proposed MGraphDTA and baselines on the Metz dataset (regression).

Model	Proteins	Compounds	MSE	CI	r m 2 index
DeepDTA	CNN	CNN	0.286 (0.001)	0.815 (0.001)	0.678 (0.003)
GraphDTA	CNN	GCN	0.282 (0.007)	0.815 (0.002)	0.679 (0.008)
GraphDTA	CNN	GAT	0.323 (0.003)	0.800 (0.001)	0.625 (0.010)
GraphDTA	CNN	GIN	0.313 (0.002)	0.803 (0.001)	0.632 (0.001)
GraphDTA	CNN	GAT–GCN	0.282 (0.011)	0.816 (0.004)	0.681 (0.026)
RF	ECFP	PSC	0.351 (0.002)	0.793 (0.001)	0.565 (0.001)
SVM	ECFP	PSC	0.361 (0.001)	0.794 (0.000)	0.590 (0.001)
FNN	ECFP	PSC	0.316 (0.001)	0.805 (0.001)	0.660 (0.003)
MGraphDTA	MCNN	MGNN	0.265 (0.002)	0.822 (0.001)	0.701 (0.001)