Protocol

GFMBench-API VEP-eval, zs-mlm-llr

GFMBench-API task VEP-eval: zero-shot; masked log-likelihood ratio of alternate versus reference, scored by AUROC and AUPRC.

4 evaluations · 8 results

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4 recorded evaluations, 8 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

4 evaluations · 8 results. Different protocols are not a single leaderboard.

Protocol: GFMBench-API VEP-eval, zs-mlm-llr · Dataset: VEP-eval test set (GFMBench-API)

Sorted by AUPRC (zero-shot; masked log-likelihood ratio) (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	AUPRC (zero-shot; masked log-likelihood ratio)	AUROC (zero-shot; masked log-likelihood ratio)
NTv3 (zero-shot, GFMBench-API)Evaluation	0.573 (best in column)	0.712 (best in column)
Caduceus-Ps (zero-shot, GFMBench-API)Evaluation	0.478	0.662
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	0.312	0.522
DNA-BERT (zero-shot, GFMBench-API)Evaluation	0.262	0.424

All 8 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 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.478 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 Caduceus-Ps on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'Caduceus-Ps', column 'Msk LLR PRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.662 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 Caduceus-Ps on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'Caduceus-Ps', column 'Msk LLR ROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.262 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 VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNA-BERT', column 'Msk LLR PRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.424 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 VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNA-BERT', column 'Msk LLR ROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.312 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 DNABERT-2 on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNABERT-2', column 'Msk LLR PRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.522 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 DNABERT-2 on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'DNABERT-2', column 'Msk LLR ROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.573 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 NTv3 on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'NTv3', column 'Msk LLR PRC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API VEP-eval, zs-mlm-llr Dataset: VEP-eval test set (GFMBench-API)	0.712 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 NTv3 on GFMBench-API VEP-eval (zs-mlm-llr) lit-genomics-20261011-gfmbench-protocol-vep-eval-zs-mlm-llr Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 4, task 'VEP-eval', row 'NTv3', column 'Msk LLR ROC'

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External evaluations: 4

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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-vep-eval-zs-mlm-llr

areas: dna-genomes
contexts: research
protocol: zero-shot; masked log-likelihood ratio of alternate versus reference, scored by AUROC and AUPRC
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.
source locator: Appendix Tables 1-5; task descriptions

Related records

part of: GFMBench-API
uses data: VEP-eval test set (GFMBench-API)
assessment: Caduceus-Ps on GFMBench-API VEP-eval (zs-mlm-llr)
assessment: DNA-BERT on GFMBench-API VEP-eval (zs-mlm-llr)
assessment: DNABERT-2 on GFMBench-API VEP-eval (zs-mlm-llr)
assessment: NTv3 on GFMBench-API VEP-eval (zs-mlm-llr)

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