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Evidence of the strong relationship between learning and emotion has fueled recent work in modeling affective states in intelligent tutoring systems. Many of these models are based on general models of affect without a specific focus on learner emotions. This paper presents work that investigates the benefits of using theoretical models of learner emotions to guide the development of Bayesian networks for prediction of student affect. Predictive models are empirically learned from data acquired from 260 students interacting with the game-based learning environment, CRYSTAL ISLAND. Results indicate the benefits of using theoretical models of learner emotions to inform predictive models. The most successful model, a dynamic Bayesian network, also highlights the importance of temporal information in predicting learner emotions. This work demonstrates the benefits of basing predictive models of learner emotions on theoretical foundations and has implications for how these models may be used to validate theoretical models of emotion.