MSE Loss is not capable of handling ignored targets

[SebieF]

The PyTorch nn.MSELoss is not able to handle ignored indices (like the nn.CrossEntropyLoss).

A solution provided by @mheinzinger would be as follows:

You could easily implement this by yourself by passing "reduce=None" when initializing your loss function. As a result it will return a loss for each residue in your input instead of a single scalar. Then you can manually multiply the masked elements by 0 and average. When averaging, divide only by the number of non-masked residues.

This must be kept in mind for implementing residue(s)_to_value protocols in the future.