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Although research on metacognition, often defined as “thinking about thinking,” has long provided valuable insights into cognitive engagement, its application to understanding how individuals interact with Generative Artificial Intelligence (GenAI) remains underexplored. In particular, little is known about how educators engage metacognitively with GenAI for professional learning or instructional purposes. Therefore, this study examined special education pre-service teachers’ (PSTs) metacognitive processes while using CoIEP, a GenAI system designed for individualized education programs (IEPs). Employing a mixed-methods design, we collected data from think-aloud protocols, follow-up interviews, and a metacognitive engagement survey to identify patterns and conditions influencing PSTs’ metacognitive engagement. Findings provide implications for designing GenAI systems that foster essential metacognitive engagement in the context of professional learning for PSTs.