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A data-driven model augmentation framework, referred to as Weakly-coupled Integrated Inference and Machine Learning (IIML), is presented to improve the predictive accuracy of physical models. In contrast to parameter calibration, this work seeks corrections to the structure of the model by a) inferring augmentation fields that are consistent with the underlying model, and b) transforming these fields into corrective model forms. The proposed approach couples the inference and learning steps in a weak sense via an alternating optimization approach. This coupling ensures that the augmentation fields remain learnable and maintain consistent functional relationships with local modeled quantities across the training dataset. An iterative solution procedure is presented in this paper, removing the need to embed the augmentation function during the inference process. This framework is used to infer an augmentation introduced within a Polymer electrolyte membrane fuel cell (PEMFC) model using a small amount of training data (from only 14 training cases.) These training cases belong to a dataset consisting of high-fidelity simulation data obtained from a high-fidelity model of a first generation Toyota Mirai. All cases in this dataset are characterized by different inflow and outflow conditions on the same geometry. When tested on 1224 different configurations, the inferred augmentation significantly improves the predictive accuracy for a wide range of physical conditions. Predictions and available data for the current density distribution are also compared to demonstrate the predictive capability of the model for quantities of interest which were not involved in the inference process. The results demonstrate that the weakly-coupled IIML framework offers sophisticated and robust model augmentation capabilities without requiring extensive changes to the numerical solver.