A method and system for analysis of a facility may include providing an emulation host system, generating a pristine circuit model on the emulation host system, inserting a first hardware trojan model, emulating operation of the golden circuit model, and emulating operation of the first hardware trojan model, and determine a set of machine-learning models, detecting the presence of an unknown trojan as a function of the set of machine learning models and using the same to authenticate the integrity of a GPS signal.