Recent progress in building large-scale quantum devices for exploring quantum computing and simulation has relied upon effective tools for achieving and maintaining good experimental parameters, i.e., tuning up devices. In many cases, including quantum dot-based architectures, the parameter space grows substantially with the number of qubits, and may become a limit to scalability. Fortunately, machine learning techniques for pattern recognition and image classification, using so-called deep neural networks, have shown surprising successes for computer-aided understanding of complex systems. We propose a new paradigm for fully automated experimental initialization through a closed-loop system relying on machine learning and optimization techniques. We use deep convolutional neural networks to characterize states and charge configurations of semiconductor quantum dot arrays when only measurements of a current-voltage characteristic of transport are available. For simplicity, we model a semiconductor nanowire connected to leads and capacitively coupled to depletion gates using the Thomas-Fermi approximation and Coulomb blockade physics. We then generate labeled training data for the neural networks, and find at least 90 % accuracy for charge and state identification for single and double dots. Using these characterization networks, we can then optimize the parameter space to achieve a desired configuration of the array, a technique we call "auto-tuning". Finally, we show how such techniques can be implemented in an experimental setting by applying our approach to an experimental dataset, and outline further problems in this domain, from using charge sensing data to extensions to full one-and two-dimensional arrays, that can be tackled with machine learning.