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The success of model-based ECU-functions relies on precise and efficient modeling of the behavior of combustion engines. Due to the limited computing power, usually a combination of physical models and calibration parameters is preferred for engine modeling in ECU. The parameters can be scalars, 1 or 2-dimensional empirical models, such as look-up table for volumetric efficiency and effective area of the exhaust gas recirculation (EGR). A novel algorithm is proposed to automatically calibrate the look-up tables characterizing stationary functional relationships in ECU-function of the air system of a diesel engine with minimum calibration cost. The algorithm runs in the framework of online design of experiment (DoE), in which Gaussian process model (GPM) is adopted to approximate the relationships of interest.