GPN-MSA, main results model (bioRxiv v2)
GPN-MSA, main results model (bioRxiv v2): GPN-MSA; log-likelihood ratio averaged over both strands; Log-likelihood ratio between alternate and reference allele, averaged over both strands.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records 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
- songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 · Original source · git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26)
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-gpnmsa-config-gpn-msa-main
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- GPN-MSA
- parameters
- Log-likelihood ratio between alternate and reference allele, averaged over both strands
- access reuse
- Published checkpoint songlab/gpn-msa-sapiens (gpn-msa.md); the preprint does not say which seed or checkpoint produced the DMS values
- foundation model eligible
- true
- source locator
- Methods 'VEP scores' (GPN-MSA); Results DMS paragraph
- missing metadata
- version: reason: unreported; note: Not stated whether the released checkpoint or one of the default-setting seeds was used
- provenance note
- GPN-MSA as used for the paper's main variant effect results; log-likelihood ratio averaged over both strands.
Related records
- configuration of: GPN-MSA
- system: GPN-MSA on ProteinGym DMS TADBP binary classification (GPN-MSA paper)