A method for training a deep learning model of a patterning process. The method includes obtaining (i) training data including an input image of at least a part of a substrate having a plurality of features and including a truth image, (ii) a set of classes, each class corresponding to a feature of the plurality of features of the substrate within the input image, and (iii) a deep learning model configured to receive the training data and the set of classes, generating a predicted image, by modeling and/or simulation with the deep learning model using the input image, assigning a class of the set of classes to a feature within the predicted image based on matching of the feature with a corresponding feature within the truth image, and generating, by modeling and/or simulation, a trained deep learning model by iteratively assigning weights using a loss function.