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This paper presents methods of modeling and predicting face recognition (FR) system performance based on analysis of similarity scores. We define the performance of an FR system as its recognition accuracy, and consider the intrinsic and extrinsic factors affecting its performance. The intrinsic factors of an FR system include the gallery images, the FR algorithm, and the tuning parameters. The extrinsic factors include mainly query image conditions. For performance modeling, we propose the concept of "perfect recognition,” based on which a performance metric is extracted from perfect recognition similarity scores (PRSS) to relate the performance of an FR system to its intrinsic factors. The PRSS performance metric allows tuning FR algorithm parameters offline for near optimal performance. In addition, the performance metric extracted from query images is used to adjust face alignment parameters online for improved performance. For online prediction of the performance of an FR system on query images, features are extracted from the actual recognition similarity scores and their corresponding PRSS. Using such features, we can predict online if an individual query image can be correctly matched by the FR system, based on which we can reduce the incorrect match rates. Experimental results demonstrate that the performance of an FR system can be significantly improved using the presented methods.