rewirebio.iobenchmarks
Protocol

GFMBench-API LRB Variant Effect OMIM, zs-embedding

GFMBench-API task LRB Variant Effect OMIM: 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 LRB Variant Effect OMIM, zs-embedding · Dataset: LRB Variant Effect OMIM 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 configurationAUPRC (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)Evaluation0.0027 (best in column)0.0021 (best in column)0.00210.563 (best in column)0.514 (best in column)0.514
Caduceus-Ps (zero-shot, GFMBench-API)Evaluation0.00220.00190.00190.5240.4860.49
Evo2 (zero-shot, GFMBench-API)Evaluation0.0020.0020.00210.4980.5010.502
DNABERT-2 (zero-shot, GFMBench-API)Evaluation0.00190.0021 (best in column)0.0022 (best in column)0.5050.5120.531 (best in column)
NTv3 (zero-shot, GFMBench-API)Evaluation0.00180.00180.00190.4740.480.5
All 30 result rows with coverage, uncertainty and sources
Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0019 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Caduceus-Ps', column 'Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.486 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Caduceus-Ps', column 'Cos AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0019 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Caduceus-Ps', column 'L2 AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.49 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Caduceus-Ps', column 'L2 AUROC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0022 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Caduceus-Ps', column 'SNV Cos AUPRC'
Configuration: Caduceus-Ps (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.524 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Caduceus-Ps', column 'SNV Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0021 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNA-BERT', column 'Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.514 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNA-BERT', column 'Cos AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0021 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNA-BERT', column 'L2 AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.514 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNA-BERT', column 'L2 AUROC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0027 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNA-BERT', column 'SNV Cos AUPRC'
Configuration: DNA-BERT (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.563 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNA-BERT', column 'SNV Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0021 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNABERT-2', column 'Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.512 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNABERT-2', column 'Cos AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0022 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNABERT-2', column 'L2 AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM 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

DNABERT-2 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNABERT-2', column 'L2 AUROC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0019 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNABERT-2', column 'SNV Cos AUPRC'
Configuration: DNABERT-2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.505 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'DNABERT-2', column 'SNV Cos AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.002 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Evo2', column 'Cos AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.501 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Evo2', column 'Cos AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0021 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Evo2', column 'L2 AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.502 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Evo2', column 'L2 AUROC'
Configuration: Evo2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.002 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Evo2', column 'SNV Cos AUPRC'
Configuration: Evo2 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.498 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', row 'Evo2', column 'SNV Cos AUROC'
Configuration: NTv3 (zero-shot, GFMBench-API)Protocol: GFMBench-API LRB Variant Effect OMIM, zs-embedding
Dataset: LRB Variant Effect OMIM test set (GFMBench-API)
0.0018 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 LRB Variant Effect OMIM (zs-embedding)

lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-zs-embedding

Aggregation: Not reported

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'LRB Variant Effect OMIM', 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.

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Evidence table

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-omim-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
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