Curated OMIM pathogenic regulatory variants as positives and matched gnomAD common variants as controls (promoter with upstream-of-gene, enhancer with intergenic).
17 evaluations · 34 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| 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 checkedMethods, coverage and source51 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 checkedMethods, coverage and source51 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 checkedMethods, coverage and source51 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 checkedMethods, coverage and source51 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 checkedMethods, coverage and sourceDefault 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 checkedMethods, coverage and sourceDefault 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 checkedMethods, coverage and sourceInclude 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 checkedMethods, coverage and sourceInclude 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 checkedMethods, coverage and sourceMSA 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 checkedMethods, coverage and sourceMSA 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 checkedMethods, coverage and sourceDon’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 checkedMethods, coverage and sourceDon’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 checkedMethods, coverage and sourceDon’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 checkedMethods, coverage and sourceDon’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 checkedMethods, coverage and sourceCombined 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 checkedMethods, coverage and sourceCombined 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 checkedMethods, coverage and sourceTrain 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 checkedMethods, coverage and sourceTrain 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 checkedMethods, coverage and sourceTrain 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 checkedMethods, coverage and sourceTrain 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 checkedMethods, coverage and sourceWindow 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 checkedMethods, coverage and sourceWindow 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 checkedMethods, coverage and sourceWindow 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 checkedMethods, coverage and sourceWindow 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 checkedMethods, coverage and sourceWindow 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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6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population OMIM pathogenic regulatory variants versus gnomAD common (MAF > 5%) variants matched by category; 'all' is the union of the category matches Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Methods 'VEP data sources' (OMIM, gnomAD) and 'Main VEP metrics' (OMIM) 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 Methods 'VEP data sources' (OMIM, gnomAD) and 'Main VEP metrics' (OMIM) Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Methods 'VEP data sources' (OMIM, gnomAD) and 'Main VEP metrics' (OMIM) 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 labelled set; 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) Methods 'VEP data sources' (OMIM, gnomAD) and 'Main VEP metrics' (OMIM) 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 OMIM curated pathogenic regulatory variant set (download date not printed); gnomAD v3.1.2 Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Methods 'VEP data sources' (OMIM, gnomAD) and 'Main VEP metrics' (OMIM) 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 Curated OMIM pathogenic regulatory variants as positives and matched gnomAD common variants as controls (promoter with upstream-of-gene, enhancer with intergenic). Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Methods 'VEP data sources' (OMIM, gnomAD) and 'Main VEP metrics' (OMIM) 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 OMIM pathogenic vs gnomAD common regulatory variants (GPN-MSA paper) Context-only references | GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) Methods 'VEP data sources' (OMIM, gnomAD) and 'Main VEP metrics' (OMIM) 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-omim-vs-gnomad-common-regulatory