Protocol

GFMBench-API GUE Splice Site, supervised

GFMBench-API task GUE Splice Site: supervised classification; Accuracy, MCC, AUROC and AUPRC on the test set.

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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 GUE Splice Site, supervised · Dataset: GUE Splice Site 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	0.932 (best in column)	0.968 (best in column)	0.981	0.884 (best in column)
DNABERT-2 (full fine-tuning, GFMBench-API)Evaluation	0.923	0.957	0.977	0.868
DNA-BERT (full fine-tuning, GFMBench-API)Evaluation	0.92	0.965	0.982 (best in column)	0.865
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	0.896	0.917	0.955	0.821
Evo2 (linear probing, GFMBench-API)Evaluation	0.565	0.46	0.657	0.0384

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 GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.896 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 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 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.917 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 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 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.955 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 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 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.821 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 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 'Caduceus-Ps', 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: 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 checked Methods, coverage and source DNABERT-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 checked Methods, coverage and source DNABERT-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 checked Methods, coverage and source DNABERT-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 checked Methods, coverage and source DNABERT-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: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.565 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 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 2, task 'GUE Splice Site', row 'Evo2', column 'Accuracy'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.46 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 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 2, task 'GUE Splice Site', row 'Evo2', column 'AUPRC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.657 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 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 2, task 'GUE Splice Site', row 'Evo2', column 'AUROC'
Configuration: Evo2 (linear probing, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.0384 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 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 2, task 'GUE Splice Site', row 'Evo2', column 'MCC'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.932 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 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 'NTv3', column 'Accuracy'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.968 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 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 'NTv3', column 'AUPRC'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.981 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 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 'NTv3', column 'AUROC'
Configuration: NTv3 (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.884 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 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 '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-gue-splice-site-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: GUE Splice Site test set (GFMBench-API)
assessment: Caduceus-Ps on GFMBench-API GUE Splice Site (supervised)
assessment: DNA-BERT on GFMBench-API GUE Splice Site (supervised)
assessment: DNABERT-2 on GFMBench-API GUE Splice Site (supervised)
assessment: Evo2 on GFMBench-API GUE Splice Site (supervised)
assessment: NTv3 on GFMBench-API GUE Splice Site (supervised)

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