Individual skill

codonfm-embed

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

skills/bionemo-codonfm-embed/SKILL.md

Read pinned source

Source commit fce3cca4170be75e82c64920654d56ee2811b005

What was checked

Matches the observed repository HEAD: Yes
Scanner rules are current: Yes
Repository scan complete: No
Skill scan complete: No
Observed behavior: Network or broad shell
Last checked: Nov 9, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings): 3,906
Repository last updated: Nov 6, 2026
License: Apache-2.0

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

agent-skills Repository topic
agentic-ai Repository topic
ai-agents Repository topic
claude-code Repository topic
codex Repository topic
coding-agents Repository topic
cuda Repository topic
developer-tools Repository topic
llm Repository topic
omniverse Repository topic
biology Declared skill tag
codonfm Declared skill tag
embeddings Declared skill tag
engineering Derived category

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files

BENCHMARK.mddoc · 7,284 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
SKILL.mdcore · 9,557 bytes
agents/openai.yamlasset · 212 bytes
evals/evals.jsonasset · 5,015 bytes
evals/files/codonfm_source.zipasset · 81,758 bytes
evals/files/encodon_checkpoint.jsonasset · 1,025 bytes
evals/files/sequences.csvasset · 102 bytes
evals/files/sequences_edge_cases.csvasset · 6,320 bytes
references/checkpoint-selection.mddoc · 3,154 bytes
scripts/validate_inputs.pyruns · 5,299 bytes
skill-card.mddoc · 4,816 bytes
skill.oms.sigasset · 6,529 bytes
tests/test_validate_inputs.pyruns · 5,623 bytes

Read excerpt


# Extract public Encodon embeddings

## Purpose

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 does not automatically train a downstream regressor.

## Prerequisites

- Validation needs Python 3 standard library only; no GPU, weights, or API key.
- Execution needs the public CodonFM checkout, its `requirements.txt` environment,
  a compatible NVIDIA GPU, and local checkpoint weights. A metadata JSON is not