Methods and systems for providing closed loop control of stimulation provided by an implantable stimulator device are disclosed herein. The disclosed methods and systems use a neural feature prediction model to predict a neural feature, which is used as a feedback control variable for adjusting stimulation. The predicted neural feature is determined based on one or more stimulation artifact features. The disclosed methods and systems can be used to provide closed loop feedback in situations, such as sub-perception therapy, when neural features cannot be readily directly measured.