The split of ENCODE CpG methylation 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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15 evaluations · 15 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 CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.81 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAWD-LSTM on BEND CPG: CpG methylation 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(CpG methylation) |
| Configuration: BASSET | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.93 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBASSET on BEND CPG: CpG methylation 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(CpG methylation) |
| Method: CNN | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.84 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN on BEND CPG: CpG methylation 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(CNN), column(CpG methylation) |
| Configuration: DNABERT-2 | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.9 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2 on BEND CPG: CpG methylation 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(CpG methylation) |
| Configuration: DNABERT | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.91 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT on BEND CPG: CpG methylation 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(CpG methylation) |
| Configuration: GENA-LM BERT | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.91 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 CPG: CpG methylation 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(CpG methylation) |
| Configuration: GENA-LM BigBird | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.91 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 CPG: CpG methylation 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(CpG methylation) |
| Configuration: GROVER | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.89 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGROVER on BEND CPG: CpG methylation 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(CpG methylation) |
| Configuration: HyenaDNA large | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.91 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHyenaDNA large on BEND CPG: CpG methylation 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(CpG methylation) |
| Configuration: HyenaDNA tiny | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.86 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHyenaDNA tiny on BEND CPG: CpG methylation 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(CpG methylation) |
| Configuration: NT-1000G | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.89 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-1000G on BEND CPG: CpG methylation 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(CpG methylation) |
| Method: NT-H | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.88 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-H on BEND CPG: CpG methylation 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(CpG methylation) |
| Method: NT-MS | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.92 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-MS on BEND CPG: CpG methylation 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(CpG methylation) |
| Configuration: NT-V2 | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.91 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT-V2 on BEND CPG: CpG methylation 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(CpG methylation) |
| Method: ResNet-LM | Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split) | 0.87 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceResNet-LM on BEND CPG: CpG methylation 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(CpG methylation) |
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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 ENCODE CpG methylation 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 ENCODE CpG methylation (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-encode-cpg-methylation