The Protein Signal Is Not the Whole Gain
TL;DR for operators Adding protein-sequence intelligence to a biological annotation system does not produce uniform gains. In SoftGene’s experiments, pretrained protein embeddings barely improve Gene Ontology biological-process annotations, but substantially improve cellular-component annotations. Removing learned soft prompts causes a much larger deterioration across both major benchmarks. For bioinformatics platform teams, the relevant decision is which components justify their additional complexity in a particular biological domain. The evidence supports evaluating sequence embeddings, soft prompting, and auxiliary context separately. Generated descriptions can assist research interpretation, but benchmark similarity and plausible attention rankings do not establish biological correctness. ...