Systems and methods are provided for automatically discovering applications/clusters in a network and mapping dependencies between the applications/clusters. A network monitoring system can capture network flow data using sensors executing on physical and/or virtual servers of the network and sensors executing on networking devices connected to the servers. The system can determine a graph including nodes, representing at least the servers, and edges, between pairs of the nodes of the graph indicating the network flow data includes one or more observed flows between pairs of the servers represented by the pairs of the nodes. The system can determine a dependency map, including representations of clusters of the servers and representations of dependencies between the clusters, based on the graph. The system can display a first representation of a first cluster of the dependency map and information indicating a confidence level of identifying the first cluster.