The split of ClinVar disease variants that BEND evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.
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14 evaluations · 14 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Method: AWD-LSTM | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.45 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAWD-LSTM on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(AWD-LSTM), column(Noncoding variant effects on disease) |
| Configuration: DEEPSEA | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.56 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDEEPSEA on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(Expert method), column(Noncoding variant effects on disease) |
| Configuration: DNABERT-2 | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.51 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(DNABERT-2), column(Noncoding variant effects on disease) |
| Configuration: DNABERT | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.56 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(DNABERT), column(Noncoding variant effects on disease) |
| Configuration: GENA-LM BERT | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.55 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGENA-LM BERT on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GENA-LM BERT), column(Noncoding variant effects on disease) |
| Configuration: GENA-LM BigBird | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.52 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGENA-LM BigBird on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GENA-LM BigBird), column(Noncoding variant effects on disease) |
| Configuration: GROVER | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.51 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGROVER on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GROVER), column(Noncoding variant effects on disease) |
| Configuration: HyenaDNA large | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.45 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHyenaDNA large on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Noncoding variant effects on disease) |
| Configuration: HyenaDNA tiny | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.44 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHyenaDNA tiny on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA tiny), column(Noncoding variant effects on disease) |
| Configuration: NT-1000G | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.49 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-1000G), column(Noncoding variant effects on disease) |
| Method: NT-H | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.48 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-H on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-H), column(Noncoding variant effects on disease) |
| Method: NT-MS | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.77 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-MS on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-MS), column(Noncoding variant effects on disease) |
| Configuration: NT-V2 | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.48 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-V2 on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-V2), column(Noncoding variant effects on disease) |
| Method: ResNet-LM | Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split) | 0.55 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceResNet-LM on BEND VARIANT-DISEASE: Noncoding variant effects on disease A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(ResNet-LM), column(Noncoding variant effects on disease) |
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description The split of ClinVar disease variants that BEND evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits. Context-only references | BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks No field-specific location recorded Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name ClinVar disease variants (BEND split) Context-only references | BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks No field-specific location recorded Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: bend-dataset-clinvar-disease-variants