Var Bench Coding Pathogenicity 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 Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.575 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'Accuracy' |
| Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.507 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'AUPRC' |
| Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.606 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'AUROC' |
| Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.0594 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'MCC' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.58 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'Accuracy' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.506 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'AUPRC' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.593 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'AUROC' |
| Configuration: DNA-BERT (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.0858 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNA-BERT', column 'MCC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.627 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNABERT-2', column 'Accuracy' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.599 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNABERT-2', column 'AUPRC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.697 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNABERT-2', column 'AUROC' |
| Configuration: DNABERT-2 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.215 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'DNABERT-2', column 'MCC' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.58 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'Accuracy' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.568 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'AUPRC' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.658 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'AUROC' |
| Configuration: Evo2 (linear probing, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.0941 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 2, task 'Var Bench Coding Pathogenicity', row 'Evo2', column 'MCC' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.622 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'NTv3', column 'Accuracy' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.579 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'NTv3', column 'AUPRC' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.683 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'NTv3', column 'AUROC' |
| Configuration: NTv3 (full fine-tuning, GFMBench-API) | Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API) | 0.204 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 Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'NTv3', column 'MCC' |
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| 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 Coding Pathogenicity 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 Coding Pathogenicity 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-coding-pathogenicity