Table 2.

Configurations of baseline models on omics, graph structure, gnn layers, and regularizaiton modules

Model	Omics			Graph		GNN Layer		Module
	mRNA	CNV	miRNA	Intra-omic	Inter-omic	GCN	GAT	Decoder	Parallel
GCN (Original) [23]	$✓$	–	–	$✓$	–	$✓$	–	–	–
GCN (Modified)	$✓$	$✓$	$✓$	$✓$	–	$✓$	–	–	–
Multi-omics GCN (Original) [1]	$✓$	$✓$	–	$✓$	–	$✓$	–	$✓$	$✓$
Multi-omics GCN (Modified)	$✓$	$✓$	$✓$	$✓$	–	$✓$	–	$✓$	$✓$
GrAMME (Modified) [25]	$✓$	$✓$	$✓$	–	$✓$	–	$✓$	–	–
Multi-omics GAT (Original) [7]	$✓$	–	$✓$	$✓$	–	–	$✓$	–	–
Multi-omics GAT (Modified)	$✓$	$✓$	$✓$	$✓$	–	–	$✓$	–	–