Protein language models: residue embeddings, pooled vectors and mutation scores are different outputs
This story is from 2026-09-07. It is preserved in the archive; the latest stories are on the live feed.
Disclosure: I published the linked guide on rewire.it. One protein language-model checkpoint can produce a vector per residue, a pooled vector for the whole protein, or a mutation score from token probabilities. These are different artifacts: changing the pooling rule, layer, downstream head or eva…
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- 2026-09-07 15:34 · r/learnmachinelearning
Protein language models: residue embeddings, pooled vectors and mutation scores are different outputs