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Detecting healthcare-associated infections pose a major challenge in healthcare. Using natural language processing and machine learning applied on electronic patient records is one approach that has been shown to work. However the results indicate that there was room for improvement and therefore we have applied deep learning methods. Specifically we implemented a network of stacked sparse auto encoders and a network of stacked restricted Boltzmann machines. Our best results were obtained using the stacked restricted Boltzmann machines with a precision of 0.79 and a recall of 0.88.