Protocol

GFMBench-API Var Bench Non Coding Pathogenicity, supervised

GFMBench-API task Var Bench Non Coding Pathogenicity: supervised classification; Accuracy, MCC, AUROC and AUPRC on the test set.

5 evaluations · 20 results

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5 recorded evaluations, 20 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

5 evaluations · 20 results. Different protocols are not a single leaderboard.

Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised · Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)

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	Accuracy (test set)	AUPRC (test set)	AUROC (test set)	MCC (test set)
NTv3 (full fine-tuning, GFMBench-API)Evaluation	0.981 (best in column)	0.931 (best in column)	0.952 (best in column)	0.894 (best in column)
Evo2 (linear probing, GFMBench-API)Evaluation	0.898	0.415	0.659	0.204
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	0.893	0.241	0.683	0
DNABERT-2 (full fine-tuning, GFMBench-API)Evaluation	0.893	0.107	0.505	0
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	0.891	0.198	0.677	0.072

All 20 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.893 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 Caduceus-Ps on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.241 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 Caduceus-Ps on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.683 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 Caduceus-Ps on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity 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 Caduceus-Ps on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'Caduceus-Ps', column 'MCC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.891 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 Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNA-BERT', column 'Accuracy'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.198 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 Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNA-BERT', column 'AUPRC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.677 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 Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNA-BERT', column 'AUROC'
Configuration: DNA-BERT (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.072 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 Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNA-BERT', column 'MCC'
Configuration: DNABERT-2 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.893 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 DNABERT-2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNABERT-2', column 'Accuracy'
Configuration: DNABERT-2 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.107 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 DNABERT-2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNABERT-2', column 'AUPRC'
Configuration: DNABERT-2 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.505 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 DNABERT-2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNABERT-2', column 'AUROC'
Configuration: DNABERT-2 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity 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 DNABERT-2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'DNABERT-2', column 'MCC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.898 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 Evo2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Non Coding Pathogenicity', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.415 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 Evo2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Non Coding Pathogenicity', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.659 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 Evo2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Non Coding Pathogenicity', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.204 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 Evo2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Non Coding Pathogenicity', row 'Evo2', column 'MCC'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.981 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 NTv3 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'NTv3', column 'Accuracy'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.931 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 NTv3 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'NTv3', column 'AUPRC'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.952 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 NTv3 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'NTv3', column 'AUROC'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Non Coding Pathogenicity, supervised Dataset: Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.894 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 NTv3 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-non-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Non Coding Pathogenicity', row 'NTv3', column 'MCC'

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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-protocol-var-bench-non-coding-pathogenicity-supervised

areas: dna-genomes
contexts: research
protocol: supervised classification; Accuracy, MCC, AUROC and AUPRC on the test set
version: GFMBench-API preprint v2
metric: auroc
metric direction: higher
unit: unitless
limitations: Single run per cell; no uncertainty printed.; The task re-implements an earlier benchmark and may not match the original split or scoring.; Supervised protocols hold both the Table 1 full fine-tuning rows and the Table 2 Evo2 linear-probing rows; comparison.adaptation separates them.
source locator: Appendix Tables 1-5; task descriptions

Related records

part of: GFMBench-API
uses data: Var Bench Non Coding Pathogenicity test set (GFMBench-API)
assessment: Caduceus-Ps on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)
assessment: DNA-BERT on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)
assessment: DNABERT-2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)
assessment: Evo2 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)
assessment: NTv3 on GFMBench-API Var Bench Non Coding Pathogenicity (supervised)

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