TDP-43 (TADBP) deep mutational scan from ProteinGym v0.1, binarised with a cutoff of 0.125 on the absolute value of relative toxicity.
2 evaluations · 2 results. Different protocols are not a single leaderboard.
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| 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) |
| Configuration: GPN-MSA, main results model (bioRxiv v2) | Protocol: ProteinGym DMS TADBP binary classification, AUROC (GPN-MSA paper) Dataset: ProteinGym v0.1 DMS TADBP_HUMAN Bolognesi 2019, binarised (GPN-MSA paper) | 0.83 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceGPN-MSA 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) |
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6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population Amino-acid substitutions in the TADBP assay; for genomic predictors the most deleterious score among the SNVs causing each substitution was used Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Table 3; Methods 'VEP data sources' (DMS) and 'Additional VEP metrics' (DMS) Version: bioRxiv v2, posted 2024-04-06 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Source location Supplementary Table 3; Methods 'VEP data sources' (DMS) and 'Additional VEP metrics' (DMS) Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Table 3; Methods 'VEP data sources' (DMS) and 'Additional VEP metrics' (DMS) Version: bioRxiv v2, posted 2024-04-06 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Split Whole assay; no training on labels (zero-shot scores) Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Table 3; Methods 'VEP data sources' (DMS) and 'Additional VEP metrics' (DMS) Version: bioRxiv v2, posted 2024-04-06 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Version ProteinGym v0.1, assay 'DMS TADBP HUMAN Bolognesi 2019' Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Table 3; Methods 'VEP data sources' (DMS) and 'Additional VEP metrics' (DMS) Version: bioRxiv v2, posted 2024-04-06 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Description TDP-43 (TADBP) deep mutational scan from ProteinGym v0.1, binarised with a cutoff of 0.125 on the absolute value of relative toxicity. Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Table 3; Methods 'VEP data sources' (DMS) and 'Additional VEP metrics' (DMS) Version: bioRxiv v2, posted 2024-04-06 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
| Name ProteinGym v0.1 DMS TADBP_HUMAN Bolognesi 2019, binarised (GPN-MSA paper) Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Supplementary Table 3; Methods 'VEP data sources' (DMS) and 'Additional VEP metrics' (DMS) Version: bioRxiv v2, posted 2024-04-06 | not individually reviewed No individual claim review recorded Audit detailsField: 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. |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: gfm-guides-20261014-gpnmsa-data-proteingym-dms-tadbp-bolognesi2019