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The advancement in technology has transformed Cyber Physical Systems and their interface with IoT into a more sophisticated and challenging paradigm. As a result, vulnerabilities and potential attacks manifest themselves considerably more than before, forcing researchers to rethink the conventional strategies that are currently in place to secure such physical systems. This manuscript studies the complex interweaving of sensor networks and physical systems and suggests a foundational innovation in the field. In sharp contrast with the existing IDS and IPS solutions, in this paper, a preventive and proactive method is employed to stay ahead of attacks by constantly monitoring network data patterns and identifying threats that are imminent. Here, by capitalizing on the significant progress in processing power (e.g. petascale computing) and storage capacity of computer systems, we propose a deep learning approach to predict and identify various security breaches that are about to occur. The learning process takes place by collecting a large number of files of different types and running tests on them to classify them as benign or malicious. The prediction model obtained as such can then be used to identify attacks. Our project articulates a new framework for interactions between physical systems and sensor networks, where malicious packets are repeatedly learned over time while the system continually operates with respect to imperfect security mechanisms.