Carbon dioxide concentration in enclosed spaces is an air quality indicator that affects occupants’ well-being. To maintain healthy carbon dioxide levels indoors, enclosed space settings must be adjusted to maximize air quality while minimizing energy consumption. Studying the effect of these settings on carbon dioxide concentration levels is not feasible through physical experimentation and data collection. This problem can be solved by using validated simulation models, generating indoor settings scenarios, simulating those scenarios, and studying results. In previous work, we presented a formal Cellular Discrete Event System Specifications simulation model for studying carbon dioxide dispersion in rooms with various settings. However, designers may need to predict the results of altering large combinations of settings on air quality. Generating and simulating multiple scenarios with different combinations of space settings to test their effect on indoor air quality is time-consuming. In this research, we solve the two problems of the lack of ground truth data and the inefficiency of producing and studying simulation results for many combinations of settings by proposing a novel framework. The framework utilizes a Cellular Discrete Event System Specifications model, simulates different scenarios of enclosed spaces with various settings, and collects simulation results to form a data set to train a deep neural network. Without needing to generate all possible scenarios, the trained deep neural network is used to predict unknown settings of the closed space when other settings are altered. The framework facilitates configuring enclosed spaces to enhance air quality. We illustrate the framework uses through a case study.