BEND CHROMATIN: Chromatin accessibility
Chromatin accessibility. Scored with AUROC on ENCODE chromatin accessibility. 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.
Overview
Chromatin accessibility. Scored with AUROC on ENCODE chromatin accessibility. 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.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AWD-LSTM on BEND CHROMATIN: Chromatin accessibility
- BASSET on BEND CHROMATIN: Chromatin accessibility
- CNN on BEND CHROMATIN: Chromatin accessibility
- DNABERT-2 on BEND CHROMATIN: Chromatin accessibility
- DNABERT on BEND CHROMATIN: Chromatin accessibility
- GENA-LM BERT on BEND CHROMATIN: Chromatin accessibility
- GENA-LM BigBird on BEND CHROMATIN: Chromatin accessibility
- GROVER on BEND CHROMATIN: Chromatin accessibility
- HyenaDNA large on BEND CHROMATIN: Chromatin accessibility
- HyenaDNA tiny on BEND CHROMATIN: Chromatin accessibility
- NT-1000G on BEND CHROMATIN: Chromatin accessibility
- NT-H on BEND CHROMATIN: Chromatin accessibility
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
BEND CHROMATIN: Chromatin accessibility
auroc (fraction) · Higher values are better for this metric.
Every method BEND reports on Chromatin accessibility, scored with AUROC on ENCODE chromatin accessibility.
Evaluation protocol · ENCODE chromatin accessibility (BEND split)
- BASSET · Configuration · Author-reported evaluation0.85
- CNN · Method · Author-reported evaluation0.75
- ResNet-LM · Method · Author-reported evaluation0.82
- AWD-LSTM · Method · Author-reported evaluation0.69
- NT-H · Method · Author-reported evaluation0.74
- NT-MS · Method · Author-reported evaluation0.79
- NT-1000G · Configuration · Author-reported evaluation0.77
- NT-V2 · Configuration · Author-reported evaluation0.80
- DNABERT · Configuration · Author-reported evaluation0.85
- DNABERT-2 · Configuration · Author-reported evaluation0.81
- GENA-LM BERT · Configuration · Author-reported evaluation0.76
- GENA-LM BigBird · Configuration · Author-reported evaluation0.82
- HyenaDNA large · Configuration · Author-reported evaluation0.84
- HyenaDNA tiny · Configuration · Author-reported evaluation0.78
- GROVER · Configuration · Author-reported evaluation0.82
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 1, row(Chromatin accessibility)Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| BASSET · Configuration | 0.85 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(Expert method), column(Chromatin accessibility) |
| CNN · Method | 0.75 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(CNN), column(Chromatin accessibility) |
| ResNet-LM · Method | 0.82 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(ResNet-LM), column(Chromatin accessibility) |
| AWD-LSTM · Method | 0.69 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(AWD-LSTM), column(Chromatin accessibility) |
| NT-H · Method | 0.74 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-H), column(Chromatin accessibility) |
| NT-MS · Method | 0.79 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-MS), column(Chromatin accessibility) |
| NT-1000G · Configuration | 0.77 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-1000G), column(Chromatin accessibility) |
| NT-V2 · Configuration | 0.80 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(NT-V2), column(Chromatin accessibility) |
| DNABERT · Configuration | 0.85 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(DNABERT), column(Chromatin accessibility) |
| DNABERT-2 · Configuration | 0.81 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(DNABERT-2), column(Chromatin accessibility) |
| GENA-LM BERT · Configuration | 0.76 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GENA-LM BERT), column(Chromatin accessibility) |
| GENA-LM BigBird · Configuration | 0.82 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GENA-LM BigBird), column(Chromatin accessibility) |
| HyenaDNA large · Configuration | 0.84 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA large), column(Chromatin accessibility) |
| HyenaDNA tiny · Configuration | 0.78 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(HyenaDNA tiny), column(Chromatin accessibility) |
| GROVER · Configuration | 0.82 fraction | Not reported | Author-reported evaluation · source checkedBEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(GROVER), column(Chromatin accessibility) |
Scope and limitations
- Author-reported numbers, source checked but not independently reproduced.
- The expert entries are specialist published models, each compared on one task only.
- The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 15 evaluations · 15 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 CHROMATIN: Chromatin accessibility Method: AWD-LSTMTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.69 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(Chromatin accessibility) Source checking is not independent reproduction. |
| BASSET on BEND CHROMATIN: Chromatin accessibility Configuration: BASSETTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.85 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(Chromatin accessibility) Source checking is not independent reproduction. |
| CNN on BEND CHROMATIN: Chromatin accessibility Method: CNNTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.75 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(CNN), column(Chromatin accessibility) Source checking is not independent reproduction. |
| DNABERT-2 on BEND CHROMATIN: Chromatin accessibility Configuration: DNABERT-2Task: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.81 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(Chromatin accessibility) Source checking is not independent reproduction. |
| DNABERT on BEND CHROMATIN: Chromatin accessibility Configuration: DNABERTTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.85 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(Chromatin accessibility) Source checking is not independent reproduction. |
| GENA-LM BERT on BEND CHROMATIN: Chromatin accessibility Configuration: GENA-LM BERTTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.76 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(Chromatin accessibility) Source checking is not independent reproduction. |
| GENA-LM BigBird on BEND CHROMATIN: Chromatin accessibility Configuration: GENA-LM BigBirdTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.82 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(Chromatin accessibility) Source checking is not independent reproduction. |
| GROVER on BEND CHROMATIN: Chromatin accessibility Configuration: GROVERTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.82 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(Chromatin accessibility) Source checking is not independent reproduction. |
| HyenaDNA large on BEND CHROMATIN: Chromatin accessibility Configuration: HyenaDNA largeTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.84 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(Chromatin accessibility) Source checking is not independent reproduction. |
| HyenaDNA tiny on BEND CHROMATIN: Chromatin accessibility Configuration: HyenaDNA tinyTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.78 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(Chromatin accessibility) Source checking is not independent reproduction. |
| NT-1000G on BEND CHROMATIN: Chromatin accessibility Configuration: NT-1000GTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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-1000G), column(Chromatin accessibility) Source checking is not independent reproduction. |
| NT-H on BEND CHROMATIN: Chromatin accessibility Method: NT-HTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.74 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(Chromatin accessibility) Source checking is not independent reproduction. |
| NT-MS on BEND CHROMATIN: Chromatin accessibility Method: NT-MSTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.79 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(Chromatin accessibility) Source checking is not independent reproduction. |
| NT-V2 on BEND CHROMATIN: Chromatin accessibility Configuration: NT-V2Task: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.80 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(Chromatin accessibility) Source checking is not independent reproduction. |
| ResNet-LM on BEND CHROMATIN: Chromatin accessibility Method: ResNet-LMTask: BEND CHROMATIN: Chromatin accessibilityDataset subset: ENCODE chromatin accessibility (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 | ||
| 0.82 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(Chromatin accessibility) 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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-bend Individual claims | BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks Table 1, row(Chromatin accessibility) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: bend-association-chromatin 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-task-chromatin
- areas
- dna-genomes
- tasks
- Chromatin accessibility
- metric
- AUROC
- metric direction
- higher
- dataset
- ENCODE chromatin accessibility
- protocol
- 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.
- source locator
- Table 1, row(Chromatin accessibility)
- comparison panels
- id: bend-panel-chromatin; title: BEND CHROMATIN: Chromatin accessibility; protocol id: bend-task-chromatin; dataset id: bend-dataset-encode-chromatin-accessibility; metric: auroc; unit: fraction; direction: higher; result ids: bend-result-basset-chromatin-auroc; bend-result-cnn-chromatin-auroc; bend-result-resnet-lm-chromatin-auroc; bend-result-awd-lstm-chromatin-auroc; bend-result-nt-h-chromatin-auroc; bend-result-nt-ms-chromatin-auroc; bend-result-nt-1000g-chromatin-auroc; bend-result-nt-v2-chromatin-auroc; bend-result-dnabert-chromatin-auroc; bend-result-dnabert-2-chromatin-auroc; bend-result-gena-lm-bert-chromatin-auroc; bend-result-gena-lm-bigbird-chromatin-auroc; bend-result-hyenadna-large-chromatin-auroc; bend-result-hyenadna-tiny-chromatin-auroc; bend-result-grover-chromatin-auroc; source ids: evidence-expansion-bend-final-f709b6be; source locator: Table 1, row(Chromatin accessibility); context: Every method BEND reports on Chromatin accessibility, scored with AUROC on ENCODE chromatin accessibility.; caveats: Author-reported numbers, source checked but not independently reproduced.; The expert entries are specialist published models, each compared on one task only.; The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: BEND
- subject: BEND CHROMATIN: part of discovery-benchmark-bend
- benchmark: AWD-LSTM on BEND CHROMATIN: Chromatin accessibility
- benchmark: BASSET on BEND CHROMATIN: Chromatin accessibility
- benchmark: CNN on BEND CHROMATIN: Chromatin accessibility
- benchmark: DNABERT-2 on BEND CHROMATIN: Chromatin accessibility
- benchmark: DNABERT on BEND CHROMATIN: Chromatin accessibility
- benchmark: GENA-LM BERT on BEND CHROMATIN: Chromatin accessibility
- benchmark: GENA-LM BigBird on BEND CHROMATIN: Chromatin accessibility
- benchmark: GROVER on BEND CHROMATIN: Chromatin accessibility
- benchmark: HyenaDNA large on BEND CHROMATIN: Chromatin accessibility
- benchmark: HyenaDNA tiny on BEND CHROMATIN: Chromatin accessibility
- benchmark: NT-1000G on BEND CHROMATIN: Chromatin accessibility
- benchmark: NT-H on BEND CHROMATIN: Chromatin accessibility
- benchmark: NT-MS on BEND CHROMATIN: Chromatin accessibility
- benchmark: NT-V2 on BEND CHROMATIN: Chromatin accessibility
- benchmark: ResNet-LM on BEND CHROMATIN: Chromatin accessibility