A method for identifying similarity between query samples and stored samples in an efficiently maintained reference library may include receiving a binary query sample and processing the binary query sample via operations including producing a query sample fingerprint from the binary query sample, scoring the query sample fingerprint with each previously stored fingerprint in the reference library to produce a matching score, and for each previously stored fingerprint for which the matching score meets or exceeds a predetermined threshold, reporting a corresponding reference sample unique identifier associated with the previously stored fingerprint and the matching score. Each previously stored fingerprint in the reference library has been determined, prior to storage, as not being duplicative of another fingerprint in the reference library.