Abstract: A method for automatically generating an anomaly detection system for a cyber-physical system. A directed graph is obtained from the cyber-physical system's design. The directed graph has nodes representing control components of the cyber-physical system that control physical processes. The directed graph is traversed to determine associated control components from the nodes and edges based on predefined parameters. Invariants are derived from the associated control components based on physical/chemical properties governing them. The invariants define conditions for detecting anomalies of the physical processes and are configured as an executable invariant computer program. Upon execution, the anomalies are detectable in response to determining that measurements from the control components have violated the invariant conditions.