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I have built a FCN for image segmentation. The object to be segmented is only very few pixels relatively to the image size (1024x1024). This results in that the accuracy is very high, even if I only train with 10 images instead of 18000 (my full training set).

My approach to solve this is to use some kind of weighted accuracy, so that the accuracy actually say something about the performance of identifying the small object (now it gets high accuracy since so many pixels are not the object and by not classifying anything the accuracy still gets high).

How do I decide the weight, anybody with some experience?

Martin Isaksson
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As you wrote, use a custom weight function which penalizes misclassification of underrepresented pixels more. You can get the weight by calculating the quotient between the number of object pixels versus all of the pixels in the image, or you can try it by hand - just make sure you follow the metrics which tell you the accuracy of object pixels. Hope it helps.

johndodo
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You can use infogain loss layer for a "weighted" loss.
The infogain loss is a generalization of the cross entropy loss commonly used. It is defined using a weight matrix H (of size L-by-L, where L is the number of classes):

L(p) = -H log(p)

Where p is a vector of class probabilities.

You can find more details on this loss here.

Shai
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