Dataset

BRCA1 test set (GFMBench-API)

BRCA1 evaluation data as packaged in GFMBench-API.

Evaluation results

10 evaluations · 40 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 BRCA1, zs-embedding Dataset: BRCA1 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 Caduceus-Ps on GFMBench-API BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'Caduceus-Ps', column 'Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.555 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'Caduceus-Ps', column 'Cos AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.299 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'Caduceus-Ps', column 'L2 AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.563 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'Caduceus-Ps', column 'L2 AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.203 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'Caduceus-Ps', column 'SNV Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.469 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'Caduceus-Ps', column 'SNV Cos AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.218 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 BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'Caduceus-Ps', column 'Msk LLR PRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.483 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 BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'Caduceus-Ps', column 'Msk LLR ROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.216 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNA-BERT', column 'Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.514 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNA-BERT', column 'Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.216 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNA-BERT', column 'L2 AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.514 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNA-BERT', column 'L2 AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.227 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNA-BERT', column 'SNV Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.527 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNA-BERT', column 'SNV Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.179 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 BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'DNA-BERT', column 'Msk LLR PRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.434 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 BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'DNA-BERT', column 'Msk LLR ROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.214 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNABERT-2', column 'Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.487 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNABERT-2', column 'Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.199 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNABERT-2', column 'L2 AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.476 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNABERT-2', column 'L2 AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.206 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNABERT-2', column 'SNV Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-embedding Dataset: BRCA1 test set (GFMBench-API)	0.49 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 BRCA1 (zs-embedding) lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'BRCA1', row 'DNABERT-2', column 'SNV Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.239 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 BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'DNABERT-2', column 'Msk LLR PRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-mlm-llr Dataset: BRCA1 test set (GFMBench-API)	0.558 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 BRCA1 (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'BRCA1', row 'DNABERT-2', column 'Msk LLR ROC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API BRCA1, zs-ar-llr Dataset: BRCA1 test set (GFMBench-API)	0.533 AUPRC (zero-shot; autoregressive log-likelihood ratio over mean token probabilities) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on GFMBench-API BRCA1 (zs-ar-llr) lit-genomics-20261011-gfmbench-protocol-brca1-zs-ar-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 5, task 'BRCA1', row 'Evo2', column 'Mean LLR PRC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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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 BRCA1 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 BRCA1 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

1 source record and release history

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-brca1

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 BRCA1 (zs-embedding)
data: Caduceus-Ps on GFMBench-API BRCA1 (zs-mlm-llr)
data: DNA-BERT on GFMBench-API BRCA1 (zs-embedding)
data: DNA-BERT on GFMBench-API BRCA1 (zs-mlm-llr)
data: DNABERT-2 on GFMBench-API BRCA1 (zs-embedding)
data: DNABERT-2 on GFMBench-API BRCA1 (zs-mlm-llr)
data: Evo2 on GFMBench-API BRCA1 (zs-ar-llr)
data: Evo2 on GFMBench-API BRCA1 (zs-embedding)
data: NTv3 on GFMBench-API BRCA1 (zs-embedding)
data: NTv3 on GFMBench-API BRCA1 (zs-mlm-llr)
uses data: GFMBench-API BRCA1, zs-ar-llr
uses data: GFMBench-API BRCA1, zs-embedding
uses data: GFMBench-API BRCA1, zs-mlm-llr

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