Dataset

VEP-eval test set (GFMBench-API)

VEP-eval evaluation data as packaged in GFMBench-API.

Evaluation results

8 evaluations · 32 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.556 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'Caduceus-Ps', column 'Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.702 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'Caduceus-Ps', column 'Cos AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.563 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'Caduceus-Ps', column 'L2 AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.707 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'Caduceus-Ps', column 'L2 AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.363 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'Caduceus-Ps', column 'SNV Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.511 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'Caduceus-Ps', column 'SNV Cos AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.478 AUPRC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'Caduceus-Ps', column 'Msk LLR PRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.662 AUROC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'Caduceus-Ps', column 'Msk LLR ROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.31 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNA-BERT', column 'Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.511 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNA-BERT', column 'Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.31 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNA-BERT', column 'L2 AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.511 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNA-BERT', column 'L2 AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.366 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNA-BERT', column 'SNV Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.596 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNA-BERT', column 'SNV Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.262 AUPRC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNA-BERT', column 'Msk LLR PRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.424 AUROC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNA-BERT on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNA-BERT', column 'Msk LLR ROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.291 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNABERT-2', column 'Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.473 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNABERT-2', column 'Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.291 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNABERT-2', column 'L2 AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.473 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNABERT-2', column 'L2 AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.293 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNABERT-2', column 'SNV Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.485 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'DNABERT-2', column 'SNV Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.312 AUPRC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNABERT-2', column 'Msk LLR PRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.522 AUROC (zero-shot; masked log-likelihood ratio) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNABERT-2', column 'Msk LLR ROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-embedding Dataset: VEP-eval test set (GFMBench-API)	0.472 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NTv3 on GFMBench-API VEP-eval (zs-embedding) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'VEP-eval', row 'NTv3', column 'Cos AUPRC'

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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4 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Source location Appendix task descriptions Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Test split as defined in GFMBench-API Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description VEP-eval evaluation data as packaged in GFMBench-API. Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name VEP-eval test set (GFMBench-API) Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Original source · bioRxiv preprint version 2, posted 2026-08-11

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-gfmbench-data-vep-eval

areas: dna-genomes
contexts: research
split: Test split as defined in GFMBench-API
source locator: Appendix task descriptions
missing metadata: version: reason: unreported

Related records

data: Caduceus-Ps on GFMBench-API VEP-eval (zs-embedding)
data: Caduceus-Ps on GFMBench-API VEP-eval (zs-mlm-llr)
data: DNA-BERT on GFMBench-API VEP-eval (zs-embedding)
data: DNA-BERT on GFMBench-API VEP-eval (zs-mlm-llr)
data: DNABERT-2 on GFMBench-API VEP-eval (zs-embedding)
data: DNABERT-2 on GFMBench-API VEP-eval (zs-mlm-llr)
data: NTv3 on GFMBench-API VEP-eval (zs-embedding)
data: NTv3 on GFMBench-API VEP-eval (zs-mlm-llr)
uses data: GFMBench-API VEP-eval, zs-embedding
uses data: GFMBench-API VEP-eval, zs-mlm-llr

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