Table 1.

Terms and Notations

Symbol	Definitions
M	Total number of genes in gene network
E	Number of expression values for each gene
N i	Set of the neighbor genes of gene vi
${\mathbf{\text{v}}}_i^{\left(s\right)}$	Topological representation of gene vi
${\mathbf{\text{v}}}_i^{\left(a\right)}$	Attribute representation of gene vi
${\widetilde{\mathbf{\text{v}}}}_i$	Neighborhood representation of gene vi
v i	Concatenated representation of topological properties and expression data
k	Number of hidden layers to transform concatenated representation into embedding space
h ( k)	Output of kth hidden layer
W k	Weight matrix for kth hidden layer
W id	Weight matrix for topological structure embedding
W att	Weight matrix for attribute embedding
W out	Weight matrix for output layer