Configuration

DNA-BERT (zero-shot, GFMBench-API)

Configuration of DNABERT: About 110M 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)
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API ClinVar Indel Pathogenicity, zs-embedding, ClinVar Indel Pathogenicity test set (GFMBench-API)	0.853 (best in column)	0.854 (best in column)	0.501	0.501	Not reported	Not reported	Not reported	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API Songlab ClinVar, zs-embedding, Songlab ClinVar test set (GFMBench-API)	0.55	0.55	0.51	0.51	0.567 (best in column)	Not reported	0.539	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API VEP-eval, zs-embedding, VEP-eval test set (GFMBench-API)	0.31	0.31	0.511	0.511	0.366	Not reported	0.596	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API BRCA1, zs-embedding, BRCA1 test set (GFMBench-API)	0.216	0.216	0.514	0.514	0.227	Not reported	0.527	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Mendelian, zs-embedding, TraitGym Mendelian test set (GFMBench-API)	0.106	0.106	0.529	0.53	0.129	Not reported	0.597	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API TraitGym Complex, zs-embedding, TraitGym Complex test set (GFMBench-API)	0.104	0.104	0.509	0.509	0.111	Not reported	0.539	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Expression, zs-embedding, Bend Variant Effects Expression test set (GFMBench-API)	0.0812	0.0814	0.53 (best in column)	0.531 (best in column)	0.0935	Not reported	0.598 (best in column)	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API Bend Variant Effects Disease, zs-embedding, Bend Variant Effects Disease test set (GFMBench-API)	0.073	0.0731	0.509	0.509	0.0731	Not reported	0.534	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API LOL-EVE, zs-embedding, LOL-EVE test set (GFMBench-API)	0.0676	0.0681	0.448	0.449	Not reported	Not reported	Not reported	Not reported
DNA-BERT (zero-shot, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect OMIM, zs-embedding, LRB Variant Effect OMIM test set (GFMBench-API)	0.0021	0.0021	0.514	0.514	0.0027	Not reported	0.563	Not reported
DNA-BERT (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	0.0593	Not reported	0.432
DNA-BERT (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	0.0681	Not reported	0.479
DNA-BERT (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	0.179	Not reported	0.434
DNA-BERT (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	0.0021	Not reported	0.522 (best in column)
DNA-BERT (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	0.503 (best in column)	Not reported	0.452
DNA-BERT (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	0.0981	Not reported	0.499
DNA-BERT (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	0.0905	Not reported	0.469
DNA-BERT (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	0.262	Not reported	0.424

All 72 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.073 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 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 'DNA-BERT', column 'Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.509 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 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 'DNA-BERT', column 'Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0731 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 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 'DNA-BERT', column 'L2 AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.509 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 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 'DNA-BERT', column 'L2 AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0731 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 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 'DNA-BERT', column 'SNV Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.534 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 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 'DNA-BERT', column 'SNV Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-mlm-llr Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0593 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 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 'DNA-BERT', column 'Msk LLR PRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-mlm-llr Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.432 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 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 'DNA-BERT', column 'Msk LLR ROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0812 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 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 'DNA-BERT', column 'Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.53 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 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 'DNA-BERT', column 'Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0814 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 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 'DNA-BERT', column 'L2 AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.531 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 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 'DNA-BERT', column 'L2 AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0935 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 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 'DNA-BERT', column 'SNV Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.598 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 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 'DNA-BERT', column 'SNV Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-mlm-llr Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0681 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 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 'DNA-BERT', column 'Msk LLR PRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-mlm-llr Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.479 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 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 'DNA-BERT', 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: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API ClinVar Indel Pathogenicity, zs-embedding Dataset: ClinVar Indel Pathogenicity test set (GFMBench-API)	0.853 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 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 'DNA-BERT', column 'Cos AUPRC'

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

Use this configuration

How it works, versions and access

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-gfmbench-config-dna-bert-zero-shot

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: DNA-BERT
foundation model eligible: true
parameters: About 110M 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: DNA-BERT as evaluated in GFMBench-API, zero-shot.

Related records

Suggest a correction