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In the YOLO9000 paper, they define the distance between a box and centroid as $d(box, centroid) = 1 - IOU(box, centroid)$. I think box here is a ground truth bounding box, but what is centroid?

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The centroid is referring to the central point of a k-means cluster.

Where does k-means come in? At the end of p.2 they say:

Instead of choosing priors by hand, we run k-means clustering on the training set bounding boxes to automatically find good priors.

Also see Figure 2.

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