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Task

BEND ENHANCER: Enhancer annotation

Enhancer annotation. Scored with AUPRC on Fulco 2019, Gasperini 2019 and Enformer enhancer set. 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.

16 evaluations · 16 results

Overview

Enhancer annotation. Scored with AUPRC on Fulco 2019, Gasperini 2019 and Enformer enhancer set. 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.

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

BEND ENHANCER: Enhancer annotation

auprc (fraction) · Higher values are better.

BEND ENHANCER: Enhancer annotation · Fulco 2019, Gasperini 2019 and Enformer enhancer set (BEND split)

Evidence origin: Author-reported evaluation.

BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 1, row(Enhancer annotation)
  • 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.
Comparison details and limitations

Every method BEND reports on Enhancer annotation, scored with AUPRC on Fulco 2019, Gasperini 2019 and Enformer enhancer set.

  • Author-reported numbers, source checked but not independently reproduced.

Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Showing 12 of 16 matching rows.

Tested configuration
00.250.50.751
Reported score
  1. ENFORMER0.07
  2. ResNet0.06
  3. NT-MS0.06
  4. NT-H0.05
  5. NT-V20.05
  6. NT-1000G0.04
  7. GENA-LM BigBird0.04
  8. CNN0.03
  9. AWD-LSTM0.03
  10. DNABERT0.03
  11. DNABERT-20.03
  12. GENA-LM BERT0.03

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

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Benchmarks

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Recorded evaluations

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Run instructions

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Strengths, limitations and unresolved questions

Evidence

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Evidence table

Inspect claims, sources and review details

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1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statementOriginal source and locationReview and provenance
Relationship: part of
discovery-benchmark-bend
Individual claims		BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks

Original source ↗

Table 1, row(Enhancer annotation)

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.183228+00:00

source checked

automated source review · 2026-09-18

Audit details

Primary-source transcription with no human sign-off and no independent reproduction.

Field: links:part_of:discovery-benchmark-bend

Claim: bend-association-enhancer

Source artifact SHA-256: f709b6bef3120eb979c0a0e02d2582475c49410f29850ed7601ba7a700ca379d

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: source checked

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: bend-task-enhancer

areas
dna-genomes
tasks
Enhancer annotation
metric
AUPRC
metric direction
higher
dataset
Fulco 2019, Gasperini 2019 and Enformer enhancer set
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(Enhancer annotation)
comparison panels
id: bend-panel-enhancer; title: BEND ENHANCER: Enhancer annotation; protocol id: bend-task-enhancer; dataset id: bend-dataset-fulco-2019-gasperini-2019-and-enformer-enhancer-set; metric: auprc; unit: fraction; direction: higher; result ids: bend-result-enformer-enhancer-auprc; bend-result-resnet-enhancer-auprc; bend-result-cnn-enhancer-auprc; bend-result-resnet-lm-enhancer-auprc; bend-result-awd-lstm-enhancer-auprc; bend-result-nt-h-enhancer-auprc; bend-result-nt-ms-enhancer-auprc; bend-result-nt-1000g-enhancer-auprc; bend-result-nt-v2-enhancer-auprc; bend-result-dnabert-enhancer-auprc; bend-result-dnabert-2-enhancer-auprc; bend-result-gena-lm-bert-enhancer-auprc; bend-result-gena-lm-bigbird-enhancer-auprc; bend-result-hyenadna-large-enhancer-auprc; bend-result-hyenadna-tiny-enhancer-auprc; bend-result-grover-enhancer-auprc; source ids: evidence-expansion-bend-final-f709b6be; source locator: Table 1, row(Enhancer annotation); context: Every method BEND reports on Enhancer annotation, scored with AUPRC on Fulco 2019, Gasperini 2019 and Enformer enhancer set.; 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
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