Protocol

GFMBench-API Bend Variant Effects Expression, zs-embedding

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

5 evaluations · 30 results

Overview

An explanatory profile has not yet been reviewed for this record.

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.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

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

Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding · Dataset: Bend Variant Effects Expression 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)
DNA-BERT (zero-shot, GFMBench-API)Evaluation	0.0935 (best in column)	0.0812	0.0814	0.598 (best in column)	0.53	0.531
Evo2 (zero-shot, GFMBench-API)Evaluation	0.0887	0.0904 (best in column)	0.0897 (best in column)	0.557	0.582 (best in column)	0.573 (best in column)
Caduceus-Ps (zero-shot, GFMBench-API)Evaluation	0.0775	0.0676	0.0692	0.537	0.473	0.479
DNABERT-2 (zero-shot, GFMBench-API)Evaluation	0.0732	0.0848	0.0853	0.487	0.548	0.551
NTv3 (zero-shot, GFMBench-API)Evaluation	0.064	0.0789	0.0818	0.447	0.514	0.532

All 30 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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 Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0676 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Caduceus-Ps', column 'Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.473 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Caduceus-Ps', column 'Cos AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0692 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Caduceus-Ps', column 'L2 AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.479 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Caduceus-Ps', column 'L2 AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0775 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Caduceus-Ps', column 'SNV Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.537 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Caduceus-Ps', column 'SNV Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0812 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNA-BERT', column 'Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.53 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNA-BERT', column 'Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0814 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNA-BERT', column 'L2 AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.531 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNA-BERT', column 'L2 AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0935 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNA-BERT', column 'SNV Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.598 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNA-BERT', column 'SNV Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0848 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.548 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0853 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'L2 AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.551 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'L2 AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0732 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'SNV Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.487 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'DNABERT-2', column 'SNV Cos AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0904 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Evo2', column 'Cos AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.582 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Evo2', column 'Cos AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0897 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Evo2', column 'L2 AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.573 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Evo2', column 'L2 AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0887 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Evo2', column 'SNV Cos AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.557 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'Evo2', column 'SNV Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)	Protocol: GFMBench-API Bend Variant Effects Expression, zs-embedding Dataset: Bend Variant Effects Expression test set (GFMBench-API)	0.0789 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 Expression (zs-embedding) lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-zs-embedding Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'Bend Variant Effects Expression', row 'NTv3', column 'Cos AUPRC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

External evaluations: 5

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-valid seeded random ranking; no fitting on assay labels

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Established label-free reference with explicitly permitted sequence/MSA inputs

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-gfmbench-protocol-bend-variant-effects-expression-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 Expression test set (GFMBench-API)
assessment: Caduceus-Ps on GFMBench-API Bend Variant Effects Expression (zs-embedding)
assessment: DNA-BERT on GFMBench-API Bend Variant Effects Expression (zs-embedding)
assessment: DNABERT-2 on GFMBench-API Bend Variant Effects Expression (zs-embedding)
assessment: Evo2 on GFMBench-API Bend Variant Effects Expression (zs-embedding)
assessment: NTv3 on GFMBench-API Bend Variant Effects Expression (zs-embedding)

Suggest a correction