DNABERT-2 (full fine-tuning, GFMBench-API)
Configuration of DNABERT-2: About 117M parameters; Hugging Face checkpoint; full fine-tuning; full fine-tuning for 3 epochs.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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.
All 40 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API) | 0.931 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API) | 0.986 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API) | 0.985 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API) | 0.862 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'MCC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API) | 0.923 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API) | 0.957 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API) | 0.977 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API) | 0.868 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'MCC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API) | 0.821 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API) | 0.902 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API) | 0.904 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API) | 0.643 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'MCC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API) | 0.629 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API) | 0.685 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API) | 0.678 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API) | 0.285 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'MCC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.627 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.599 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.697 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.215 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'MCC' |
| Configuration: DNABERT-2 (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 checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API) | 0.502 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API) | 0.503 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (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 checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'MCC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.683 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 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 'DNABERT-2', column 'Accuracy' |
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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
Technical metadata and extraction receipts
Stable ID: lit-genomics-20261011-gfmbench-config-dnabert-2-full-fine-tuning
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- DNABERT-2
- foundation model eligible
- true
- parameters
- About 117M 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
- DNABERT-2 as evaluated in GFMBench-API, full fine-tuning.
Related records
- configuration of: DNABERT-2
- system: DNABERT-2 on GFMBench-API GUE Promoter All (supervised)
- system: DNABERT-2 on GFMBench-API GUE Splice Site (supervised)
- system: DNABERT-2 on GFMBench-API GUE Transcription Factor (supervised)
- system: DNABERT-2 on GFMBench-API LRB Variant Effect Causal eQTL (supervised)
- system: DNABERT-2 on GFMBench-API Var Bench Coding Pathogenicity (supervised)
- system: DNABERT-2 on GFMBench-API Var Bench Common Vs Rare (supervised)
- system: DNABERT-2 on GFMBench-API Var Bench Expression (supervised)
- system: DNABERT-2 on GFMBench-API Var Bench meQTL (supervised)
- system: DNABERT-2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)
- system: DNABERT-2 on GFMBench-API Var Bench sQTL (supervised)