Systems and methods for identifying similarities in program binaries, including extracting program binary features from one or more input program binaries to generate corresponding hybrid features. The hybrid features include a reference feature, a resource feature, an abstract control flow feature, and a structural feature. Combinations of a plurality of pairs of binaries are generated from the extracted hybrid features, and a similarity score is determined for each of the pairs of binaries. A hybrid difference score is generated based on the similarity score for each of the binaries combined with input hybrid feature parameters. A likelihood of malware in the input program is identified based on the hybrid difference score.