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I want to confirm that the issues I'm experiencing are a fundamental issue with the loss and not my implementation (which is a slight modification of this).
It seems to me that because the final loss is a sum of different paths, changing the (0, 0,) entry in the cost matrix will cause a much larger change in the loss than changing a later entry, as changing (0, 0,) influences every other entry in the cost matrix. Some simple test cases seem to confirm this. Can someone else confirm?