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I'm not sure why this is happening. I remember I had the exact same problem with the training code of fcn-matconvet (https://github.com/vlfeat/matconvnet-fcn). I could resolve the problem by using a smaller learning rate for just first few epochs. Maybe you can also try this.
Can I ask what version of Matconvnet do you use? Also what is your gpu?
When I run the training demo LRR4xTrainVGG16Pascal, it goes fine at the beginning. However, after several iterations, I got the following output:
What's wrong with it? I didn't change anything expect for the directories of the dataset.
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