Traditional control methods are inadequate in many deployment settings involving autonomous control of Cyber-Physical Systems (CPS). In such settings, CPS controllers must operate and respond to unpredictable interactions, conditions, or failure modes. Dealing with such unpredictability requires the use of executive and cognitive control functions that allow for planning and reasoning. Motivated by the sport of drone racing, this dissertation addresses these concerns for state-of-the-art flight control by investigating the use of deep artificial neural networks to bring essential elements of higher-level cognition to bear on the design, implementation, deployment, and evaluation of low level (attitude) flight controllers.