Systems and methods analyze input files to automatically determine malware signatures. A set of input files known to contain a particular type of malware can be provided to a file analyzer. The file analyzer can analyze the file using a sliding window to create vectors from values that are provided by multiple filters that process each window. The vectors created for a file define a response matrix. The response matrices for a set of input files can be analyzed by a classifier to determine useful vector components that can define a signature for the malware.