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Commissioning of building service systems with associated automation systems is important for functionality verification and performance evaluation. Especially for building HVAC system, a rudimentary commissioning and functioning testwill lead to suboptimal behavior and even faulty equipment. Hence, an automated commissioning methodology is developed. The objective is performing developed procedures upon two representative subsystems and hence validating the methodology regarding feasibility. To automate the main step in the commissioning cycle i.e. functional performance test, a data driven method is adopted. Compared to first principles-based approach, this method requires a minimumof engineering-related information. By means of topdown strategy, a single HVAC subsystem is chosen and a corresponding black-box-likeMulti-Input Single-Output (MISO) model is built. As the output relates to a specific set point variable, inputsconsists of several process variables that might be changeable due to set point variation. Moreover, a multi-layer perceptron is introduced to estimate mathematical cause-effect correlations between involved variables.