Application-initiated network traffic is intercepted and analyzed by an application firewall in order to identify streams of traffic for a target application. An application signature generator preprocesses the raw data packets from the intercepted network traffic by tokenizing the data packets and then weighting each token according to its importance for application identification. The weighted features for each data packet are clustered using an unsupervised learning model, and the resulting clusters are iteratively refined and re-clustered using a proximity score between the clusters and feature vectors for key tokens for the target application. The application signature generator generates a signature for the clusters corresponding to the target application which the application firewall implements for filtering network traffic.