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Teaching centered on teacher–student interaction is fundamental to educational practice, with high-quality interaction shown to enhance student outcomes. To enable real-time, objective assessment of interaction quality, recent studies have proposed teacher–student inter-brain coupling as a potential neural indicator. While prior research has reported correlations, its meaning and causal role remain unclear. This study conducted an intervention in real-world junior secondary mathematics classrooms, enhancing teacher interaction with students of varying achievement levels to examine changes in inter-brain coupling and learning outcomes. Among low-achieving students, increased interaction led to higher inter-brain coupling, which was positively associated with academic improvement and perceived cognitive support. These findings suggest that inter-brain coupling reflects cognitive-level interaction and may serve as a real-time indicator of instructional quality.