Configuration

DNABERT-2 (zero-shot, GFMBench-API)

Configuration of DNABERT-2: About 117M parameters; Hugging Face checkpoint; zero-shot.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

18 evaluations · 72 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings)	AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings)	AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings)	AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings)	AUPRC (zero-shot; cosine similarity of embeddings at the SNV position)	AUPRC (zero-shot; masked log-likelihood ratio)	AUROC (zero-shot; cosine similarity of embeddings at the SNV position)	AUROC (zero-shot; masked log-likelihood ratio)
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API ClinVar Indel Pathogenicity, zs-embedding, ClinVar Indel Pathogenicity test set (GFMBench-API)	0.86 (best in column)	0.862 (best in column)	0.508	0.508	Not reported	Not reported	Not reported	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Songlab ClinVar, zs-embedding, Songlab ClinVar test set (GFMBench-API)	0.547	0.547	0.496	0.495	0.552 (best in column)	Not reported	0.501	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API VEP-eval, zs-embedding, VEP-eval test set (GFMBench-API)	0.291	0.291	0.473	0.473	0.293	Not reported	0.485	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API BRCA1, zs-embedding, BRCA1 test set (GFMBench-API)	0.214	0.199	0.487	0.476	0.206	Not reported	0.49	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Disease, zs-embedding, Bend Variant Effects Disease test set (GFMBench-API)	0.152	0.149	0.696 (best in column)	0.693 (best in column)	0.0751	Not reported	0.511 (best in column)	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Mendelian, zs-embedding, TraitGym Mendelian test set (GFMBench-API)	0.147	0.153	0.594	0.605	0.089	Not reported	0.463	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Complex, zs-embedding, TraitGym Complex test set (GFMBench-API)	0.109	0.112	0.53	0.536	0.0986	Not reported	0.498	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API LOL-EVE, zs-embedding, LOL-EVE test set (GFMBench-API)	0.105	0.0947	0.601	0.579	Not reported	Not reported	Not reported	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Expression, zs-embedding, Bend Variant Effects Expression test set (GFMBench-API)	0.0848	0.0853	0.548	0.551	0.0732	Not reported	0.487	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect OMIM, zs-embedding, LRB Variant Effect OMIM test set (GFMBench-API)	0.0021	0.0022	0.512	0.531	0.0019	Not reported	0.505	Not reported
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Disease, zs-mlm-llr, Bend Variant Effects Disease test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0706	Not reported	0.504
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Expression, zs-mlm-llr, Bend Variant Effects Expression test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0732	Not reported	0.5
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API BRCA1, zs-mlm-llr, BRCA1 test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.239	Not reported	0.558 (best in column)
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect OMIM, zs-mlm-llr, LRB Variant Effect OMIM test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0019	Not reported	0.477
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API Songlab ClinVar, zs-mlm-llr, Songlab ClinVar test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.553 (best in column)	Not reported	0.519
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Complex, zs-mlm-llr, TraitGym Complex test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0977	Not reported	0.493
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Mendelian, zs-mlm-llr, TraitGym Mendelian test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.0949	Not reported	0.482
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	GFMBench-API VEP-eval, zs-mlm-llr, VEP-eval test set (GFMBench-API)	Not reported	Not reported	Not reported	Not reported	Not reported	0.312	Not reported	0.522

All 72 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.152 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.696 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.149 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'L2 AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.693 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'L2 AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0751 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'SNV Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease 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 DNABERT-2 on GFMBench-API Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'SNV Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-mlm-llr Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0706 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 Bend Variant Effects Disease (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'Msk LLR PRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-mlm-llr Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.504 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 Bend Variant Effects Disease (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'Msk LLR ROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0848 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 Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.548 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 Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0853 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 Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'L2 AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.551 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 Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'L2 AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0732 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 Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'SNV Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.487 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 Bend Variant Effects Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'SNV Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-mlm-llr Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0732 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 Bend Variant Effects Expression (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'Msk LLR PRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-mlm-llr Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.5 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 Bend Variant Effects Expression (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'Bend Variant Effects Expression', row 'DNABERT-2', 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: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API ClinVar Indel Pathogenicity, zs-embedding Dataset: ClinVar Indel Pathogenicity test set (GFMBench-API)	0.86 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 ClinVar Indel Pathogenicity (zs-embedding) lit-genomics-20261011-gfmbench-protocol-clinvar-indel-pathogenicity-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'ClinVar Indel Pathogenicity', row 'DNABERT-2', column 'Cos AUPRC'

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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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Stable ID: lit-genomics-20261011-gfmbench-config-dnabert-2-zero-shot

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: DNABERT-2
foundation model eligible: true
parameters: About 117M parameters; Hugging Face checkpoint; zero-shot
access reuse: Public checkpoint (Hugging Face; Evo2 via NVIDIA BioNeMo)
source locator: Benchmark Results sections A and B
missing metadata: version: reason: unreported; note: Checkpoint revision not printed; parameter count only
provenance note: DNABERT-2 as evaluated in GFMBench-API, zero-shot.

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