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Table 1 Terms and Notations

From: GNE: a deep learning framework for gene network inference by aggregating biological information

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
\(\textbf {v}_{i}^{(s)}\) Topological representation of gene vi
\(\textbf {v}_{i}^{(a)}\) Attribute representation of gene vi
\(\widetilde {\textbf {v}}_{i}\) 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