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.
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.
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 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 | 0.0027 (best in column) | 0.0021 (best in column) | 0.0021 | 0.563 (best in column) | 0.514 (best in column) | 0.514 |
| Caduceus-Ps (zero-shot, GFMBench-API)Evaluation | 0.0022 | 0.0019 | 0.0019 | 0.524 | 0.486 | 0.49 |
| Evo2 (zero-shot, GFMBench-API)Evaluation | 0.002 | 0.002 | 0.0021 | 0.498 | 0.501 | 0.502 |
| DNABERT-2 (zero-shot, GFMBench-API)Evaluation | 0.0019 | 0.0021 (best in column) | 0.0022 (best in column) | 0.505 | 0.512 | 0.531 (best in column) |
| NTv3 (zero-shot, GFMBench-API)Evaluation | 0.0018 | 0.0018 | 0.0019 | 0.474 | 0.48 | 0.5 |
All 30 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence 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 checkedMethods, coverage and sourceCaduceus-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 checkedMethods, coverage and sourceCaduceus-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 checkedMethods, coverage and sourceCaduceus-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 checkedMethods, coverage and sourceCaduceus-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 checkedMethods, coverage and sourceCaduceus-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 checkedMethods, coverage and sourceCaduceus-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 checkedMethods, coverage and sourceDNA-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 checkedMethods, coverage and sourceDNA-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 checkedMethods, coverage and sourceDNA-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 checkedMethods, coverage and sourceDNA-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 checkedMethods, coverage and sourceDNA-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 checkedMethods, coverage and sourceDNA-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 checkedMethods, coverage and sourceDNABERT-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 checkedMethods, coverage and sourceDNABERT-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 checkedMethods, coverage and sourceDNABERT-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 checkedMethods, coverage and sourceDNABERT-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 checkedMethods, coverage and sourceDNABERT-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 checkedMethods, coverage and sourceDNABERT-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 checkedMethods, coverage and sourceEvo2 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 checkedMethods, coverage and sourceEvo2 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 checkedMethods, coverage and sourceEvo2 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 checkedMethods, coverage and sourceEvo2 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 checkedMethods, coverage and sourceEvo2 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 checkedMethods, coverage and sourceEvo2 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 checkedMethods, coverage and sourceNTv3 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.
- Caduceus-Ps on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- DNA-BERT on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- DNABERT-2 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- Evo2 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- NTv3 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
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
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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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
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
Related records
- part of: GFMBench-API
- uses data: LRB Variant Effect OMIM test set (GFMBench-API)
- assessment: Caduceus-Ps on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- assessment: DNA-BERT on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- assessment: DNABERT-2 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- assessment: Evo2 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)
- assessment: NTv3 on GFMBench-API LRB Variant Effect OMIM (zs-embedding)