domains / families / science / bionemo-codonfm-embed

bionemo-codonfm-embed

separate

Validate coding-sequence CSVs, extract public CodonFM/Encodon embeddings, and choose checkpoints for downstream property modeling.

When to use

• Extract one frozen CLS vector per coding sequence with public Encodon v1. Support input validation, command preparation, extraction, and checkpoint selection for translation efficiency, expression, or mRNA stability modeling. Extraction do…

When not to use

• Public v1 has no Decodon model/inference implementation, Decodon notebooks,
• At context length `2048`, retain the first `2046` codons; any remaining
• `--dryrun` builds runtime configuration, may create directories, and needs
• Do not claim a benchmark-trained regressor generalizes to a new organism,
• Do not invoke this skill for a generic expression-prediction request that

Skill page

Source