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In this research work, we propose a soft sensor model based on deep learning which combines stacked autoencoders with neural network (SAE-NN). Firstly, based on experimental data, the secondary variables (easy-to-measure) which have a strong correlation with the biochemical oxygen demand (BOD5) are chosen as model inputs. Moreover, stochastic gradient descent (SGD) is used to train each layer of SAE to optimize weight parameters, while a strategy of genetic algorithms to identify the number of neurons in each hidden layer is developed. A soft sensor model is studied to predict the BOD5 in a wastewater treatment plant to evaluate the proposed approach. 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