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With the proliferation of autonomous safety-critical cyber-physical systems (CPS) in our daily life, their security is becoming ever more important. Remote attestation is a powerful mechanism to enable remote verification of system integrity. While recent developments have made it possible to efficiently attest IoT operations, autonomous systems that are built on top of real-time cyber-physical control loops and execute missions independently present new unique challenges. In this paper, we formulate a new security property, Real-time Mission Execution Integrity (RMEI) to provide proof of correct and timely execution of the missions. While it is an attractive property, measuring it can incur prohibitive overhead for the real-time autonomous system. To tackle this challenge, we propose policy-based attestation of compartments to enable a trade-off between the level of details in measurement and runtime overhead. To further minimize the impact on real-time responsiveness, multiple techniques were developed to improve the performance, including customized software instrumentation and timing recovery through re-execution. We implemented a prototype of ARI and evaluated its performance on five CPS platforms. A user study involving 21 developers with different skill sets was conducted to understand the usability of our solution.