Function prediction

[galkesten]

What is the expected way to perform function prediction?

I read the FunctionTokenizer class and noticed that if we provide even one FunctionAnnotation, all other residues without a specified function are labeled with the <none> token. I also observed that the <mask> token is equal to the <pad> token, and when there are no function annotations, all residues are tokenized as <pad>, which is also treated as <mask>.

What does this mean? Are we supposed to make function predictions without providing known keyword annotations?

[JWGuo330]

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