kermt-embed SKILL.md skillA
kermt-embed from nvidia-bionemo/bionemo-agent-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nvidia-bionemo/bionemo-agent-toolkit/kermt-embed@git:20260720.4c21e4fPins git:20260720.4c21e4f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nvidia-bionemo/bionemo-agent-toolkit
- Path
open-models-skills/kermt/kermt-embed/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260720.4c21e4f, committed Jul 20, 2026
- Size
- 6,762 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (grover_base / cmim / hybrid / finetuned). Writes one .npy per readout type (atom_from_atom, bond_from_atom, atom_from_bond, bond_from_bond) plus canonical_smiles.npy and validity.npy. Calls task/extract_embeddings.py (which featurizes SMILES on the fly — no pre-computed features needed).
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# kermt-embed Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint. The skill is the workflow orchestrator: validate ckpt, validate CSV, clean SMILES, launch the runner blocking, return the per-readout `.npy` files. ## Hardware requirements - **GPUs**: 1 (single-GPU). - **VRAM**: ≥ 4 GB for the default `batch_size 64`. - **Disk**: depends on output size — roughly a few MB per 1k molecules at `hidden 800` per readout, so ~10–20 MB per 1k molecules across the 4 readouts. Plus a small `canonical_smiles.npy` + `validity.npy` per run. - **Driver / CUDA**: any host supporting CUDA 12.6. ## Inputs Required: - `--csv <path>` — SMILES CSV. First column is `smiles`; other columns are ignored (no targets needed). Checkpoint (optional — defaults to the released model if omitted): - `--ckpt <path>` — any encoder-bearing checkpoint. Grover_base, cmim, hybrid, and finetuned ckpts are all accepted. The validator only refuses ckpts with no encoder. **If omitted**, the skill offers to download the released pretrained hybrid model **nvidia/NV-KERMT-70M-v2** and embed with it — see "Resolve & validate the checkpoint" (workflow step 3). …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/kermt-embed@sha256:9e4ff3ae2e741558The line at the top of this page pins the label git:20260720.4c21e4f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_2jck5ba6ozdb5e3w)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Jul 20, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (6762 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
nvidia-bionemo/bionemo-agent-toolkit · 503 stars · license a license file GitHub does not identify · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_2jck5ba6ozdb5e3w GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/kermt-embed GET https://markdownregistry.com/api/v1/blob/9e4ff3ae2e74155866e7a5bd664f5a4f260b3f27a55d645fb0d1b4b5a165465d
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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