ClinVar disease variants (BEND split)
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.
Subset and evaluation context
This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.
Evaluation results
Release 2026-09-17-134cd1815de8 · 14 evaluations · 14 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AWD-LSTM on BEND VARIANT-DISEASE: Noncoding variant effects on disease Method: AWD-LSTMTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.45 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(AWD-LSTM), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| DEEPSEA on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: DEEPSEATask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.56 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(Expert method), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| DNABERT-2 on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: DNABERT-2Task: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.51 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(DNABERT-2), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| DNABERT on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: DNABERTTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.56 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(DNABERT), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| GENA-LM BERT on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: GENA-LM BERTTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.55 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GENA-LM BERT), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| GENA-LM BigBird on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: GENA-LM BigBirdTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.52 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GENA-LM BigBird), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| GROVER on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: GROVERTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.51 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GROVER), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| HyenaDNA large on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: HyenaDNA largeTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.45 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| HyenaDNA tiny on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: HyenaDNA tinyTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.44 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA tiny), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| NT-1000G on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: NT-1000GTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.49 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-1000G), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| NT-H on BEND VARIANT-DISEASE: Noncoding variant effects on disease Method: NT-HTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.48 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-H), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| NT-MS on BEND VARIANT-DISEASE: Noncoding variant effects on disease Method: NT-MSTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.77 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-MS), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| NT-V2 on BEND VARIANT-DISEASE: Noncoding variant effects on disease Configuration: NT-V2Task: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.48 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-V2), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
| ResNet-LM on BEND VARIANT-DISEASE: Noncoding variant effects on disease Method: ResNet-LMTask: BEND VARIANT-DISEASE: Noncoding variant effects on diseaseDataset subset: ClinVar disease variants (BEND split) 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. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.55 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(ResNet-LM), column(Noncoding variant effects on disease) Source checking is not independent reproduction. |
Evidence table
Inspect claims, sources and review details
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.
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. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Technical metadata and extraction receipts
Stable ID: bend-dataset-clinvar-disease-variants
- areas
- dna-genomes
- missing metadata
- version: unreported; url: unextracted
Related records
- dataset: AWD-LSTM on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: DEEPSEA on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: DNABERT-2 on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: DNABERT on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: GENA-LM BERT on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: GENA-LM BigBird on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: GROVER on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: HyenaDNA large on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: HyenaDNA tiny on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: NT-1000G on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: NT-H on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: NT-MS on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: NT-V2 on BEND VARIANT-DISEASE: Noncoding variant effects on disease
- dataset: ResNet-LM on BEND VARIANT-DISEASE: Noncoding variant effects on disease