esm2-protein-embeddings

name	esm2-protein-embeddings
description	Extract reproducible ESM-2 protein embeddings, residue representations, likelihoods, or zero-shot mutation scores. Use when a frozen protein language model is needed as a feature extractor or baseline.
license	MIT

ESM-2 Protein Embeddings

Gate

Ask once before installing a pinned ESM/Transformers revision, downloading model weights, or using GPU compute. Keep sequences local unless remote inference is explicitly approved. Follow $cx-compute-environment.

Workflow

1. Define the prediction unit, exact sequence/construct, downstream task, and inference-time information. Deduplicate and cluster sequences before splitting.
2. Pin model/checkpoint revision, tokenizer, representation layer, max length, truncation/chunk overlap, pooling, special-token handling, batch size, device, precision, and code revision.
3. Smoke-test one sequence alone and in a mixed batch; require invariant output within numerical tolerance. Extract into artifacts/<run-id>/esm2/ with sequence hashes, embeddings/scores, dimensions, masks, logs, and failures.
4. For supervised work, fit all transforms and heads on training data only. Compare nearest-homolog, composition, k-mer/profile, and simple linear baselines; report performance versus nearest-train identity.
5. Record with $science-provenance; review with $science-review.

Boundaries

• Pin the pretraining/model release and acknowledge database-cutoff leakage.
• Embedding similarity or mutation likelihood is not functional validation.