Comments (3)
Could the authors please comment on the above question? We are also curious why ProteinMPNN needs to peek at the sequence, was it just to compute sequence recovery rate at the end? Sequence prediction itself should not be influenced by the input sequence, right? Thanks!
from proteinmpnn.
Hello! The model.forward
function takes the input sequence because the model is autoregressive, i.e. it models p(AA_n|backbone, AA_1, AA_2,...,AA_{n_1})
. It uses the input sequence context when the model is trained, or being used to score a sequence. This is called teacher forcing. On the other hand, if you look at model.sample
function, in that case, the model can generate new sequences without relying on the input sequence.
from proteinmpnn.
Thank you so much!
from proteinmpnn.
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