Protocol

GFMBench-API Bend Variant Effects Disease, zs-embedding

GFMBench-API task Bend Variant Effects Disease: zero-shot; reference and alternate sequence embeddings compared by cosine similarity or L2 distance, scored by AUROC and AUPRC.

5 evaluations · 30 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

5 recorded evaluations, 30 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 · 30 results. Different protocols are not a single leaderboard.

Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding · Dataset: Bend Variant Effects Disease test set (GFMBench-API)

Sorted by AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) (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; cosine similarity of embeddings at the SNV position)	AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings)	AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings)	AUROC (zero-shot; cosine similarity of embeddings at the SNV position)	AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings)	AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings)
NTv3 (zero-shot, GFMBench-API)Evaluation	0.275 (best in column)	0.147	0.152	0.768 (best in column)	0.713	0.72
Caduceus-Ps (zero-shot, GFMBench-API)Evaluation	0.107	0.378	0.379	0.545	0.772	0.78
Evo2 (zero-shot, GFMBench-API)Evaluation	0.0944	0.474 (best in column)	0.596 (best in column)	0.615	0.872 (best in column)	0.912 (best in column)
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	0.0751	0.152	0.149	0.511	0.696	0.693
DNA-BERT (zero-shot, GFMBench-API)Evaluation	0.0731	0.073	0.0731	0.534	0.509	0.509

All 30 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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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 Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.378 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Caduceus-Ps', column 'Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.772 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Caduceus-Ps', column 'Cos AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.379 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Caduceus-Ps', column 'L2 AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.78 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Caduceus-Ps', column 'L2 AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.107 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Caduceus-Ps', column 'SNV Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.545 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Caduceus-Ps', column 'SNV Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.073 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNA-BERT', column 'Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.509 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNA-BERT', column 'Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0731 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNA-BERT', column 'L2 AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.509 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNA-BERT', column 'L2 AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0731 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNA-BERT', column 'SNV Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.534 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNA-BERT', column 'SNV Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.152 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.696 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.149 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'L2 AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.693 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'L2 AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0751 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'SNV Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.511 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'DNABERT-2', column 'SNV Cos AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.474 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Evo2', column 'Cos AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.872 AUROC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Evo2', column 'Cos AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.596 AUPRC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Evo2', column 'L2 AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.912 AUROC (zero-shot; L2 distance of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Evo2', column 'L2 AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.0944 AUPRC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Evo2', column 'SNV Cos AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.615 AUROC (zero-shot; cosine similarity of embeddings at the SNV position) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'Evo2', column 'SNV Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Disease, zs-embedding Dataset: Bend Variant Effects Disease test set (GFMBench-API)	0.147 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) 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 Bend Variant Effects Disease (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-disease-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Disease', row 'NTv3', column 'Cos AUPRC'

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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-bend-variant-effects-disease-zs-embedding

areas: dna-genomes
contexts: research
protocol: zero-shot; reference and alternate sequence embeddings compared by cosine similarity or L2 distance, 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: Bend Variant Effects Disease test set (GFMBench-API)
assessment: Caduceus-Ps on GFMBench-API Bend Variant Effects Disease (zs-embedding)
assessment: DNA-BERT on GFMBench-API Bend Variant Effects Disease (zs-embedding)
assessment: DNABERT-2 on GFMBench-API Bend Variant Effects Disease (zs-embedding)
assessment: Evo2 on GFMBench-API Bend Variant Effects Disease (zs-embedding)
assessment: NTv3 on GFMBench-API Bend Variant Effects Disease (zs-embedding)

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