AUROC (binary labels from absolute relative toxicity > 0.125; zero-shot) of ESM-1b, precomputed log-likelihood ratios (GPN-MSA paper) on 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)
Methods
- Tested 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)
- Procedure
- ProteinGym DMS TADBP binary classification, AUROC (GPN-MSA paper)
- Evaluation
- ESM-1b on ProteinGym DMS TADBP binary classification (GPN-MSA paper)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedGPN-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)
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Whole assay
- Adaptation
- zero-shot
- Scoring implementation
- Not reported
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.75 Individual claims | 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) Version: bioRxiv v2, posted 2024-04-06 | source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-14 independent paper Audit detailsExtraction: Transcribed from the PDF text layer; extract/build_gpnmsa.py asserts the sentence verbatim and its page. Independent review 2026-10-14: matched. Field: Source artifact SHA-256: Hash scope: SHA-256 of the PDF bytes as downloaded 2026-10-14T12:02:16Z. bioRxiv rewrites the XMP dates and document IDs, the Info ModDate and the trailer /ID on download, so a re-download does not reproduce the hash; the review found a fresh copy of the same length differing only in those 51 bytes, with an identical pdftotext -layout text layer. Extraction artifact SHA-256: |
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-result-dms-tadbp-esm-1b-auroc
- printed value
- 0.75
- numeric value
- 0.75
- metric
- auroc
- metric direction
- higher
- unit
- unitless
- metric qualifier
- binary labels from absolute relative toxicity > 0.125; zero-shot
- source locator
- 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)
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; method note: Sentence re-read verbatim in the pdftotext layer of the pinned PDF; DMS TADBP binarisation checked in the Methods.; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent of the extractor; no human review claimed; date: 2026-10-14; artifact sha256: 10411077df1ae59614f9a9a9f85384103d54127ba67a9b3c469a4a2d6c33cee4; retrieval url: https://www.biorxiv.org/content/10.1101/2023.10.10.561776v2.full.pdf; note: Extraction: Transcribed from the PDF text layer; extract/build_gpnmsa.py asserts the sentence verbatim and its page. Independent review 2026-10-14: matched.