By “bias” I didn’t mean biases in the learned model, I meant “the class of proteins whose structures can be predicted by ML algorithms at all is biased towards biomolecules”. What you’re suggesting is still within the local search paradigm, which might not be sufficient for the protein folding problem in general, any more than it is sufficient for 3-SAT in general. No sampling is dense enough if large swaths of the problem space is discontinuous.
By “bias” I didn’t mean biases in the learned model, I meant “the class of proteins whose structures can be predicted by ML algorithms at all is biased towards biomolecules”. What you’re suggesting is still within the local search paradigm, which might not be sufficient for the protein folding problem in general, any more than it is sufficient for 3-SAT in general. No sampling is dense enough if large swaths of the problem space is discontinuous.