Configuration

DNA-BERT (full fine-tuning, GFMBench-API)

Configuration of DNABERT: About 110M parameters; Hugging Face checkpoint; full fine-tuning; full fine-tuning for 3 epochs.

10 evaluations · 40 results

Overview

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Evaluations and results

10 evaluations · 40 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (test set) (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	Accuracy (test set)	AUPRC (test set)	AUROC (test set)	MCC (test set)
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API GUE Promoter All, supervised, GUE Promoter All test set (GFMBench-API)	0.947 (best in column)	0.992 (best in column)	0.99 (best in column)	0.895 (best in column)
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API GUE Splice Site, supervised, GUE Splice Site test set (GFMBench-API)	0.92	0.965	0.982	0.865
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Non Coding Pathogenicity, supervised, Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.891	0.198	0.677	0.072
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API GUE Transcription Factor, supervised, GUE Transcription Factor test set (GFMBench-API)	0.807	0.893	0.896	0.618
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Expression, supervised, Var Bench Expression test set (GFMBench-API)	0.651	0.656	0.7	0.334
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect Causal eQTL, supervised, LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.601	0.657	0.633	0.232
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Coding Pathogenicity, supervised, Var Bench Coding Pathogenicity test set (GFMBench-API)	0.58	0.506	0.593	0.0858
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench meQTL, supervised, Var Bench meQTL test set (GFMBench-API)	0.558	0.539	0.633	0.0708
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Common Vs Rare, supervised, Var Bench Common Vs Rare test set (GFMBench-API)	0.5	0.5	0.5	0
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench sQTL, supervised, Var Bench sQTL test set (GFMBench-API)	0.495	0.526	0.52	0.0102

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.947 Accuracy (test set) 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 GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'DNA-BERT', column 'Accuracy'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.992 AUPRC (test set) 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 GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'DNA-BERT', column 'AUPRC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.99 AUROC (test set) 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 GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'DNA-BERT', column 'AUROC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.895 MCC (test set) 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 GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'DNA-BERT', column 'MCC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.92 Accuracy (test set) 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 GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'DNA-BERT', column 'Accuracy'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.965 AUPRC (test set) 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 GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'DNA-BERT', column 'AUPRC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.982 AUROC (test set) 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 GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'DNA-BERT', column 'AUROC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.865 MCC (test set) 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 GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'DNA-BERT', column 'MCC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.807 Accuracy (test set) 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 GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'DNA-BERT', column 'Accuracy'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.893 AUPRC (test set) 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 GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'DNA-BERT', column 'AUPRC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.896 AUROC (test set) 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 GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'DNA-BERT', column 'AUROC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.618 MCC (test set) 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 GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'DNA-BERT', column 'MCC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.601 Accuracy (test set) 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 LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'DNA-BERT', column 'Accuracy'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.657 AUPRC (test set) 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 LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'DNA-BERT', column 'AUPRC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.633 AUROC (test set) 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 LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'DNA-BERT', column 'AUROC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.232 MCC (test set) 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 LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'DNA-BERT', column 'MCC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.58 Accuracy (test set) 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 Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'Accuracy'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.506 AUPRC (test set) 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 Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'AUPRC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.593 AUROC (test set) 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 Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'AUROC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.0858 MCC (test set) 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 Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'MCC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.5 Accuracy (test set) 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 Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'DNA-BERT', column 'Accuracy'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.5 AUPRC (test set) 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 Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'DNA-BERT', column 'AUPRC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.5 AUROC (test set) 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 Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'DNA-BERT', column 'AUROC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0 MCC (test set) 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 Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'DNA-BERT', column 'MCC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API)	0.651 Accuracy (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNA-BERT', column 'Accuracy'

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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-config-dna-bert-full-fine-tuning

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: DNA-BERT
foundation model eligible: true
parameters: About 110M parameters; Hugging Face checkpoint; full fine-tuning; full fine-tuning for 3 epochs
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, full fine-tuning.

Related records

configuration of: DNABERT
system: DNA-BERT on GFMBench-API GUE Promoter All (supervised)
system: DNA-BERT on GFMBench-API GUE Splice Site (supervised)
system: DNA-BERT on GFMBench-API GUE Transcription Factor (supervised)
system: DNA-BERT on GFMBench-API LRB Variant Effect Causal eQTL (supervised)
system: DNA-BERT on GFMBench-API Var Bench Coding Pathogenicity (supervised)
system: DNA-BERT on GFMBench-API Var Bench Common Vs Rare (supervised)
system: DNA-BERT on GFMBench-API Var Bench Expression (supervised)
system: DNA-BERT on GFMBench-API Var Bench meQTL (supervised)
system: DNA-BERT on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)
system: DNA-BERT on GFMBench-API Var Bench sQTL (supervised)

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