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During the development of an Internal Combustion Engine-based powertrain, traditional procedures for control strategies calibration and validation produce huge amount of data, that can be used to develop innovative data-driven applications, such as emission virtual sensing. One of the main criticalities is related to the data quality, that cannot be easily assessed for such a big amount of data. This work focuses on an emission modeling activity, using an enhanced Light Gradient Boosting Regressor and a dedicated data pre-processing pipeline to improve data quality. First thing, a software tool is developed to access a database containing data coming from emissions tests. The tool performs a data cleaning procedure to exclude corrupted data or invalid parts of the test. Moreover, it automatically tunes model hyperparameters, it chooses the best set of features, and it validates the procedure by comparing the estimation and the experimental measurement.