GPN-MSA ablation 'w/o MSA' (Supplementary Table 4)
Ablation: trained only on the human sequence, without other species.
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Evaluations and results
4 evaluations · 8 results. Different protocols are not a single leaderboard.
Sorted by AUPRC (maximum over three random seeds; zero-shot) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | AUPRC (maximum over three random seeds; zero-shot) | AUPRC (mean over three random seeds; zero-shot) | AUROC (maximum over three random seeds; zero-shot) | AUROC (mean over three random seeds; zero-shot) | Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; maximum over three random seeds; zero-shot) | Odds ratio (rare (singletons) versus common (MAF > 5%) gnomAD variants in the tail of deleterious scores, threshold at 30 false discoveries, one-sided Fisher's exact test; all variant types, rare subsampled to the common count; mean over three random seeds; zero-shot) |
|---|---|---|---|---|---|---|---|
| GPN-MSA ablation 'w/o MSA' (Supplementary Table 4)Evaluation | COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4), COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper) | 0.012 (best in column) | 0.012 (best in column) | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA ablation 'w/o MSA' (Supplementary Table 4)Evaluation | OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4), OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper) | 0 | 0 | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA ablation 'w/o MSA' (Supplementary Table 4)Evaluation | ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4), ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper) | Not reported | Not reported | 0.585 | 0.584 | Not reported | Not reported |
| GPN-MSA ablation 'w/o MSA' (Supplementary Table 4)Evaluation | gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4), gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper) | Not reported | Not reported | Not reported | Not reported | 3.09 | 2.77 |
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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-ablation-without-msa
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- w/o MSA
- version
- Ablation model trained by the authors for bioRxiv v2 Supplementary Table 4; not a released checkpoint
- parameters
- Human sequence only; no MSA
- access reuse
- Ablation models are not listed among the published assets (gpn-msa.md); only songlab/gpn-msa-sapiens is released.
- foundation model eligible
- true
- source locator
- Supplementary Table 4 row 'w/o MSA'; Methods 'Ablation Study'