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An increasing number of software applications incorporate runtime Deep Neural Networks (DNNs) to process sensor data and return inference results to humans. Effective deployment of DNNs in these interactive scenarios requires meeting latency and accuracy constraints while minimizing energy, a problem exacerbated by common system dynamics. %nature of computation resources and the accuracy, latency, or energy constraints. Prior approaches handle dynamics through either (1) system-oblivious DNN adaptation, which adjusts DNN latency/accuracy tradeoffs, or (2) application-oblivious system adaptation, which adjusts resources to change latency/energy tradeoffs. In contrast, this paper improves on the state-of-the-art by coordinating application- and system-level adaptation. ALERT, our runtime scheduler, uses a probabilistic model to detect environmental volatility and then simultaneously select both a DNN and a system resource configuration to meet latency, accuracy, and energy constraints. We evaluate ALERT on CPU and GPU platforms for image and speech tasks in dynamic environments. ALERT's holistic approach achieves more than 13% energy reduction, and 27% error reduction over prior approaches that adapt solely at the application or system level. Furthermore, ALERT incurs only 3% more energy consumption and 2% higher DNN-inference error than an oracle scheme with perfect application and system knowledge.