MSA frequency | method

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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)
MSA frequencyEvaluation	COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4), COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.27 (best in column)	0.27 (best in column)	Not reported	Not reported	Not reported	Not reported
MSA frequencyEvaluation	OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4), OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper)	0.031	0.031	Not reported	Not reported	Not reported	Not reported
MSA frequencyEvaluation	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	0.95	0.95	Not reported	Not reported
MSA frequencyEvaluation	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	15.1	15.1

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: MSA frequency	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.95 AUROC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'ClinVar' / 'max'
Method: MSA frequency	Protocol: ClinVar Pathogenic vs gnomAD common missense, AUROC (GPN-MSA Supplementary Table 4) Dataset: ClinVar Pathogenic vs gnomAD common missense variants (GPN-MSA paper)	0.95 AUROC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on ClinVar (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-clinvar-auroc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'ClinVar' / 'mean'
Method: MSA frequency	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.27 AUPRC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'COSMIC' / 'max'
Method: MSA frequency	Protocol: COSMIC frequent vs gnomAD common missense, AUPRC (GPN-MSA Supplementary Table 4) Dataset: COSMIC frequent vs gnomAD common missense variants (GPN-MSA paper)	0.27 AUPRC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on COSMIC (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-cosmic-auprc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'COSMIC' / 'mean'
Method: MSA frequency	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	15.1 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) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'gnomAD' / 'max'
Method: MSA frequency	Protocol: gnomAD rare vs common enrichment in the deleterious tail, odds ratio (GPN-MSA Supplementary Table 4) Dataset: gnomAD rare (singletons) vs common variants, ablation set (GPN-MSA paper)	15.1 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) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on gnomAD (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-gnomad-odds-ratio Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'gnomAD' / 'mean'
Method: MSA frequency	Protocol: OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4) Dataset: OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper)	0.031 AUPRC (maximum over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on OMIM (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-omim-auprc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'OMIM' / 'max'
Method: MSA frequency	Protocol: OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4) Dataset: OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper)	0.031 AUPRC (mean over three random seeds; zero-shot) unitless · higher Uncertainty: Not reported by the source: Only mean and max over seeds are printed Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSA frequency (no neural net) on OMIM (GPN-MSA Supplementary Table 4) gfm-guides-20261014-gpnmsa-protocol-ablation-omim-auprc Aggregation: Not reported GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Supplementary Table 4 (PDF page 23), row 'MSA frequency (no neural net)', column 'OMIM' / 'mean'

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GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Original source · bioRxiv v2, posted 2024-04-06

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Stable ID: gfm-guides-20261014-gpnmsa-method-msa-frequency

areas: dna-genomes
contexts: research
method types: specialist
reported name: MSA frequency (no neural net)
entity level: method
source locator: Supplementary Table 4 row 'MSA frequency (no neural net)'; Methods 'Ablation Study'
missing metadata: version: reason: inapplicable; note: Score defined in the paper's Methods

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