Cyber-physical systems (CPS) consist of sensors, actuators, and controllers all communicating over a network; if any subset becomes compromised, an attacker could cause significant damage. With access to data logs and a model of the CPS, the physical effects of an attack could potentially be detected before any damage is done. Manually building a model that is accurate enough in practice, however, is extremely difficult. In this paper, we propose a novel approach for constructing models of CPS automatically, by applying supervised machine learning to data traces obtained after systematically seeding their software components with faults ("mutants"). We demonstrate the efficacy of this approach on the simulator of a real-world water purification plant, presenting a framework that automatically generates mutants, collects data traces, and learns an SVM-based model. Using cross-validation and statistical model checking, we show that the learnt model characterises an invariant physical property of the system. Furthermore, we demonstrate the usefulness of the invariant by subjecting the system to 55 network and code-modification attacks, and showing that it can detect 85% of them from the data logs generated at runtime.