Do you apply confidence threshold before calculating mAP for YOLOv2?
In the end the solution is not to apply the threshold prior to the mAP calculation. After researching further it turns out by definition that mAP is (roughly speaking) a measure of precision recall trade off calculated using all possible thresholds. By applying the threshold first you are not accounting for the higher recall the model would obtain by choosing a threshold less than or equal to the one applied.