Systems and methods are described for recommending security groups using graph-based learning models. A server can create a network graph that illustrates network flows between devices in a network and security groups that the devices belong to. The network graph can include nodes that represent the devices and security groups. The server can apply a graph-based learning model to learn embeddings of the nodes and create vectors using the embeddings. Using vectors of two nodes, the server can calculate a vector that represents an edge between the two nodes. The server can apply a binary classifier determine whether the edge should exist. A “true” classification between two nodes can indicate that they should be able to communicate, and vice versa. A “true” classification between a device node and a security group node can indicate that the device should be assigned to the security group, and vice versa.