Var Bench Expression evaluation data as packaged in GFMBench-API.
5 evaluations · 20 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.6 Accuracy (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'Caduceus-Ps', column 'Accuracy' |
| Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.592 AUPRC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'Caduceus-Ps', column 'AUPRC' |
| Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.636 AUROC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'Caduceus-Ps', column 'AUROC' |
| Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.201 MCC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'Caduceus-Ps', column 'MCC' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.651 Accuracy (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNA-BERT', column 'Accuracy' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.656 AUPRC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNA-BERT', column 'AUPRC' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.7 AUROC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNA-BERT', column 'AUROC' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.334 MCC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNA-BERT', column 'MCC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.683 Accuracy (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.712 AUPRC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.749 AUROC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.368 MCC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'DNABERT-2', column 'MCC' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.595 Accuracy (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Expression', row 'Evo2', column 'Accuracy' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.589 AUPRC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Expression', row 'Evo2', column 'AUPRC' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.628 AUROC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Expression', row 'Evo2', column 'AUROC' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.197 MCC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Expression', row 'Evo2', column 'MCC' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.674 Accuracy (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'NTv3', column 'Accuracy' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.706 AUPRC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'NTv3', column 'AUPRC' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.742 AUROC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'NTv3', column 'AUROC' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API) | 0.349 MCC (test set) 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 Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'NTv3', column 'MCC' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.
Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified
Exact outcomes, predictions, identifiers and evaluator are connected.
Missing or unresolved evidence
Verified: Not verified
Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.
Missing or unresolved evidence
Verified: Not verified
A pinned recipe describes the inputs, environment and resource requirements.
Missing or unresolved evidence
Verified: Not verified
Separate data and exposure records support an independent test.
Missing or unresolved evidence
Verified: Not verified
Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.
No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Source location Appendix task descriptions Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Split Test split as defined in GFMBench-API Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Var Bench Expression evaluation data as packaged in GFMBench-API. Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name Var Bench Expression test set (GFMBench-API) Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Appendix task descriptions Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: lit-genomics-20261011-gfmbench-data-var-bench-expression