Individual skill

kermt-continue-pretrain

Continue KERMT pretraining on a custom SMILES corpus with a grover_base, cmim, or hybrid checkpoint. Use a local checkpoint or optionally download a pinned Hugging Face model bundle using HF_TOKEN if configured. Run containerized training and write model bundles, prepared data, logs, and checkpoints to user-selected host directories.

skills/bionemo-kermt-continue-pretrain/SKILL.md

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Last checked: Nov 2, 2026

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Repository stars (not skill ratings): 3,901
Repository last updated: Nov 6, 2026
License: Apache-2.0

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BENCHMARK.mddoc · 7,974 bytes
SKILL.mdcore · 16,335 bytes
SKILL.mdcore · 16,335 bytes
SKILL.mdcore · 16,335 bytes
SKILL.mdcore · 16,335 bytes
SKILL.mdcore · 16,335 bytes
SKILL.mdcore · 16,335 bytes
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SKILL.mdcore · 16,335 bytes
config/defaults_pretrain.jsonasset · 2,699 bytes
config/released_model.jsonasset · 398 bytes
evals/evals.jsonasset · 7,722 bytes
references/released-models.mddoc · 1,634 bytes
scripts/_utils.pyruns · 14,483 bytes
scripts/check_checkpoint.pyruns · 20,605 bytes
scripts/check_data.pyruns · 12,185 bytes
scripts/fetch_released_model.pyruns · 8,108 bytes
scripts/kermt_container.shruns · 19,370 bytes
scripts/prepare_data.pyruns · 37,383 bytes
scripts/run_pretrain_local.pyruns · 35,597 bytes
skill-card.mddoc · 4,727 bytes
skill.oms.sigasset · 6,981 bytes

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# kermt-continue-pretrain

Continue pretraining from a user-supplied KERMT checkpoint (grover_base /
cmim / hybrid). The skill is the workflow orchestrator: it validates inputs,
prepares the corpus, launches the runner, and returns a run directory.

## Skill and runtime paths

Set `SKILL_DIR` to the absolute path of this installed skill directory. Export
`KERMT_REPO` as the absolute path to the KERMT checkout used for model
execution. The bundled container helper mounts that checkout at
`/workspace` and this skill at `/skill` (read-only). Commands inside
the container use `/skill/scripts/`; defaults are bundled in `config/`.
See [Released models](references/released-models.md) for checkpoint bundle requirements.