ESM-1b, precomputed log-likelihood ratios (GPN-MSA paper)
ESM-1b, precomputed log-likelihood ratios: ESM-1b precomputed log-likelihood ratios in protein coordinates, minimum over isoforms; Precomputed log-likelihood ratio between alternate and reference amino acid; for variants affecting multiple isoforms, the minimum score.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: ESM-1b, precomputed log-likelihood ratios (GPN-MSA paper) | Protocol: ProteinGym DMS TADBP binary classification, AUROC (GPN-MSA paper) Dataset: ProteinGym v0.1 DMS TADBP_HUMAN Bolognesi 2019, binarised (GPN-MSA paper) | 0.75 AUROC (binary labels from absolute relative toxicity > 0.125; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceESM-1b on ProteinGym DMS TADBP binary classification (GPN-MSA paper) gfm-guides-20261014-gpnmsa-protocol-dms-tadbp-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Results paragraph beginning 'We also evaluate on deep mutational scanning', sentence 'Nevertheless, GPN-MSA performs better than ESM-1b on some proteins (e.g., TADBP, for which GPN-MSA AUROC is 0.83, while ESM-1b AUROC is 0.75)' (PDF page 6) |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Use this configuration
How it works, versions and access
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Original source · bioRxiv v2, posted 2024-04-06
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-gpnmsa-config-esm-1b-precomputed-llr
- areas
- protein-function
- contexts
- research
- method types
- foundation_model
- reported name
- ESM-1b
- parameters
- Precomputed log-likelihood ratio between alternate and reference amino acid (reference [6] of the preprint, Brandes et al.); for variants affecting multiple isoforms, the minimum score
- access reuse
- Precomputed scores from the Brandes et al. release
- foundation model eligible
- true
- source locator
- Methods 'VEP scores' (ESM-1b)
- missing metadata
- version: reason: unreported; note: Score release and checkpoint not named in the GPN-MSA preprint
- provenance note
- ESM-1b precomputed log-likelihood ratios in protein coordinates (from Brandes et al.), minimum over isoforms, as used in the GPN-MSA paper.
Related records
- configuration of: ESM-1b
- system: ESM-1b on ProteinGym DMS TADBP binary classification (GPN-MSA paper)