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Signals from peripheral physiology (e.g., ECG, EMG, and GSR) in conjunction with machine learning techniques can be used for the automatic detection of affective states. The affect detector can be user-independent, where it is expected to generalize to novel users, or user-dependent, where it is tailored to a specific user. Previous studies have reported some success in detecting affect from physiological signals, but much of the work has focused on induced affect or acted expressions instead of contextually constrained spontaneous expressions of affect. This study addresses these issues by developing and evaluating user-independent and user-dependent physiology-based detectors of nonbasic affective states (e.g., boredom, confusion, curiosity) that were trained and validated on naturalistic data collected during interactions between 27 students and AutoTutor, an intelligent tutoring system with conversational dialogues. There is also no consensus on which techniques (i.e., feature selection or classification methods) work best for this type of data. Therefore, this study also evaluates the efficacy of affect detection using a host of feature selection and classification techniques on three physiological signals (ECG, EMG, and GSR) and their combinations. Two feature selection methods and nine classifiers were applied to the problem of recognizing eight affective states (boredom, confusion, curiosity, delight, flow/-engagement, surprise, and neutral). The results indicated that the user-independent modeling approach was not feasible; however, a mean kappa score of 0.25 was obtained for user-dependent models that discriminated among the most frequent emotions. The results also indicated that k-nearest neighbor and Linear Bayes Normal Classifier (LBNC) classifiers yielded the best affect detection rates. Single channel ECG, EMG, and GSR and three-channel multimodal models were generally more diagnostic than two--channel models.