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The Nitrogen Oxides (NOx) from engines aggravate natural environment and human health. Institutional regulations have attempted to protect the human body from them, while car manufacturers have tried to make NOx free vehicles. The formation of NOx emissions is highly dependent on the engine operating conditions and being able to predict NOx emissions would significantly help in enabling their reduction. This study investigates advanced method of predicting vehicle NOx emissions in pursuit of the sensorless engine. Sensors inside the engine are required to measure the operating condition. However, they can be removed or reduced if the sensing object such as the engine NOx emissions can be accurately predicted with a virtual model. This would result in cost reductions and overcome the sensor durability problem. To achieve such a goal, researchers have studied numerical analysis for the relationship between emissions and engine operating conditions. Also, a Deep Neural Network (DNN) is applied recently as a solution. However, the prediction accuracies were often not satisfactory where hyperparameter optimization was either overlooked or conducted manually. Therefore, this study proposes a virtual NOx sensor model based on the hyperparameter optimization. A Genetic Algorithm (GA) was adopted to establish a global optimum with DNN. Epoch size and learning rate are employed as the design variables, and R-squared based user defined function is adopted as the object function of GA. As a result, a more accurate and reliable virtual NOx sensor with the possibility of a sensorless engine could be developed and verified.