Protocol

OMIM pathogenic vs gnomAD common regulatory variants, AUPRC (GPN-MSA Supplementary Table 4)

AUPRC of zero-shot variant scores for OMIM pathogenic regulatory variants versus matched gnomAD common variants.

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17 recorded evaluations, 34 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

17 evaluations · 34 results. Different protocols are not a single leaderboard.

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)

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	AUPRC (maximum over three random seeds; zero-shot)	AUPRC (mean over three random seeds; zero-shot)
GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)Evaluation	0.156 (best in column)	0.139 (best in column)
GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)Evaluation	0.152	0.133
GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)Evaluation	0.139	0.125
GPN-MSA ablation 'Default' (Supplementary Table 4)Evaluation	0.133	0.124
GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)Evaluation	0.128	0.119
GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)Evaluation	0.122	0.12
GPN-MSA ablation 'Window size = 32' (Supplementary Table 4)Evaluation	0.121	0.108
GPN-MSA ablation 'Window size = 64' (Supplementary Table 4)Evaluation	0.119	0.111
GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)Evaluation	0.112	0.111
GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)Evaluation	0.108	0.101
GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)Evaluation	0.106	0.095
GPN-MSA ablation 'Window size = 8' (Supplementary Table 4)Evaluation	0.086	0.08
GPN-MSA ablation '51 mammals' (Supplementary Table 4)Evaluation	0.076	0.073
GPN-MSA ablation 'Window size = 4' (Supplementary Table 4)Evaluation	0.053	0.052
Combined phyloP and phastConsEvaluation	0.039	0.039
MSA frequencyEvaluation	0.031	0.031
GPN-MSA ablation 'w/o MSA' (Supplementary Table 4)Evaluation	0	0

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GPN-MSA ablation '51 mammals' (Supplementary Table 4)	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)	0.076 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 51 mammals 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 '51 mammals', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation '51 mammals' (Supplementary Table 4)	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)	0.073 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 51 mammals 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 '51 mammals', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	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)	0.108 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 51 vertebrates 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 '51 vertebrates', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)	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)	0.101 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 51 vertebrates 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 '51 vertebrates', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	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)	0.133 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 Default 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 'Default', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Default' (Supplementary Table 4)	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)	0.124 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 Default 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 'Default', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	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)	0.156 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 Include closest primates 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 'Include closest primates', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)	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)	0.139 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 Include closest primates 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 'Include closest primates', column 'OMIM' / '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'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	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)	0.112 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 Don’t replace non-conserved 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 'Don’t replace non-conserved', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)	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)	0.111 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 Don’t replace non-conserved 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 'Don’t replace non-conserved', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	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)	0.152 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 Don’t upweight conserved 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 'Don’t upweight conserved', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)	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)	0.133 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 Don’t upweight conserved 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 'Don’t upweight conserved', column 'OMIM' / 'mean'
Method: Combined phyloP and phastCons	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)	0.039 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	Independent external evaluation · Source checked Methods, coverage and source Combined phyloP and phastCons 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 'Combined phyloP and phastCons', column 'OMIM' / 'max'
Method: Combined phyloP and phastCons	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)	0.039 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	Independent external evaluation · Source checked Methods, coverage and source Combined phyloP and phastCons 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 'Combined phyloP and phastCons', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	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)	0.122 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 Train on 100% of genome 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 'Train on 100% of genome', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)	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)	0.12 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 Train on 100% of genome 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 'Train on 100% of genome', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	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)	0.139 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 Train on 50% most conserved 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 'Train on 50% most conserved', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)	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)	0.125 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 Train on 50% most conserved 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 'Train on 50% most conserved', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	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)	0.106 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 Window size = 16 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 'Window size = 16', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)	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)	0.095 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 Window size = 16 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 'Window size = 16', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	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)	0.128 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 Window size = 256 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 'Window size = 256', column 'OMIM' / 'max'
Configuration: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)	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)	0.119 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 Window size = 256 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 'Window size = 256', column 'OMIM' / 'mean'
Configuration: GPN-MSA ablation 'Window size = 32' (Supplementary Table 4)	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)	0.121 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 Window size = 32 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 'Window size = 32', column 'OMIM' / 'max'

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Author-reported evaluations: 16
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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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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-gpnmsa-protocol-ablation-omim-auprc

areas: dna-genomes
contexts: research
protocol: Each model or score is applied zero-shot (no training on these labels). GPN-MSA scores are the log-likelihood ratio of alternate versus reference allele averaged over both strands. For each ablation setting three replicate models with different seeds were trained where applicable; the table prints the mean and the maximum over seeds.
version: bioRxiv v2 Supplementary Table 4
metric: auprc
metric direction: higher
unit: unitless
limitations: Benchmark built and run by the GPN-MSA authors (author-reported).; Controls are gnomAD common variants rather than ClinVar benign variants; the authors report that with ClinVar benign controls GPN-MSA is slightly behind CADD and ESM-1b (Supplementary Figure 4, figure only).; Variant counts are not printed.
source locator: Methods 'Main VEP metrics' (OMIM); Supplementary Table 4 column 'OMIM'

Related records

part of: GPN-MSA variant effect prediction evaluation (Benegas et al.)
uses data: OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper)
assessment: 51 mammals on OMIM (GPN-MSA Supplementary Table 4)
assessment: 51 vertebrates on OMIM (GPN-MSA Supplementary Table 4)
assessment: Default on OMIM (GPN-MSA Supplementary Table 4)
assessment: Include closest primates on OMIM (GPN-MSA Supplementary Table 4)
assessment: MSA frequency (no neural net) on OMIM (GPN-MSA Supplementary Table 4)
assessment: Don’t replace non-conserved on OMIM (GPN-MSA Supplementary Table 4)
assessment: Don’t upweight conserved on OMIM (GPN-MSA Supplementary Table 4)
assessment: Combined phyloP and phastCons on OMIM (GPN-MSA Supplementary Table 4)
assessment: Train on 100% of genome on OMIM (GPN-MSA Supplementary Table 4)
assessment: Train on 50% most conserved on OMIM (GPN-MSA Supplementary Table 4)
assessment: Window size = 16 on OMIM (GPN-MSA Supplementary Table 4)
assessment: Window size = 256 on OMIM (GPN-MSA Supplementary Table 4)
assessment: Window size = 32 on OMIM (GPN-MSA Supplementary Table 4)
assessment: Window size = 4 on OMIM (GPN-MSA Supplementary Table 4)
assessment: Window size = 64 on OMIM (GPN-MSA Supplementary Table 4)
assessment: Window size = 8 on OMIM (GPN-MSA Supplementary Table 4)
assessment: w/o MSA on OMIM (GPN-MSA Supplementary Table 4)

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