Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 4 results. Different protocols are not a single leaderboard.
Protocol: GFMBench-API Var Bench Expression, supervised · Dataset: Var Bench Expression test set (GFMBench-API)
Sorted by Accuracy (test set) (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 | Accuracy (test set) | AUPRC (test set) | AUROC (test set) | MCC (test set) |
|---|---|---|---|---|
| DNABERT-2 (full fine-tuning, GFMBench-API)Evaluation | 0.683 | 0.712 | 0.749 | 0.368 |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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GFMBench-API Var Bench Expression, supervised
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation full fine-tuning Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Not reported Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version Not reported Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs DNA sequence windows; task-specific context length Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: metric implementation GFMBench-API task metrics Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: population Not reported Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: protocol id lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: split Test split Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Origin independent_paper Context-only references | GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Table 1, task 'Var Bench Expression', model 'DNABERT-2' Version: bioRxiv preprint version 2, posted 2026-08-11 | not individually reviewed No individual claim review recorded independent paper 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-eval-dnabert-2-full-fine-tuning-var-bench-expression-supervised