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Facial expression recognition software is becoming more commonly used by affective scientists to measure facial expressions. Although the use of this software has exciting implications, there are persistent and concerning issues regarding the validity and reliability of these programs. In this paper, we highlight three of these issues: biases of the programs against certain skin colors and genders; the common inability of these programs to capture facial expressions made in non-idealized conditions (e.g., “in the wild”); and programs being forced to adopt the underlying assumptions of the specific theory of emotion on which each software is based. We then discuss three directions for the future of affective science in the area of automated facial coding. First, researchers need to be cognizant of exactly how and on which data sets the machine learning algorithms underlying these programs are being trained. In addition …