Traditional network-based computational methods have shown good results in drug analysis
and prediction. However, these methods are time-consuming and lack universality, and it is difficult to
exploit the auxiliary information of nodes and edges. Network embedding provides a promising way
for alleviating the above problems by transforming the network into a low-dimensional space while
preserving network structure and auxiliary information. This thus facilitates the application of machine
learning algorithms for subsequent processing. Network embedding has been introduced into drug
analysis and prediction in the last few years, and has shown superior performance over traditional
methods. However, there is no systematic review of this issue. This article offers a comprehensive
survey of the primary network embedding methods and their applications in drug analysis and prediction.
The network embedding technologies applied in homogeneous network and heterogeneous network
are investigated and compared, including matrix decomposition, random walk, and deep learning.
Especially, the Graph neural network (GNN) methods in deep learning are highlighted. Furthermore,
the applications of network embedding in drug similarity estimation, drug-target interaction prediction,
adverse drug reactions prediction, protein function and therapeutic peptides prediction are discussed.
Several future potential research directions are also discussed.