AI-enabled Cyber-Physical Systems (CPS) are highly vulnerable to adversarial and anomalous inputs, where small perturbations can induce cascading errors and unsafe control actions. Existing approaches, such as rule-based filtering, training-time regularization, or diffusion-based reconstruction, either operate outside the model or lack mechanisms to incorporate formal security specifications into the prediction process. In this paper, we take the first step toward embedding security properties directly into AI-enabled CPS, enabling predictive models to enforce system-level constraints during inference rather than relying on external defenses. We introduce a logic-conditioned bi-stage diffusion framework that integrates Signal Temporal Logic (STL) specifications into forecasting. STL serves as a first-class conditioning signal that guides both an input repair stage and an output refinement stage, allowing the model to jointly mitigate adversarial perturbations and enforce desired temporal behaviors to satisfy security-critical properties. We evaluate our approach on two real-world multivariate CPS forecasting datasets under a diverse set of physical sensor and cyber attacks. Across sensor faults, gradient-based attacks, adaptive attacks, and varying attack strengths, our method consistently improves robustness and specification compliance, degrades more gracefully as attack strength increases, and generalizes better to unseen attacks. Ablation studies on specification coverage and quality further show that embedding logical security properties yields gains unattainable by reconstruction-based methods alone, highlighting a new direction for integrating formal methods with generative models in secure CPS.

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