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BEND

BEND evaluates DNA representations on biologically defined downstream tasks.

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At a glance

Explanatory profile: source reviewed · Automated source review, 2026-09-16. This does not change the review status of its results.

Data, procedure and scoring
PropertyDescription and evidence
Record typeTask suitefrederikkemarin/BEND official source · README: Tutorial / Data format, Computing embeddings, Evaluating models; FAQ / How are embeddings upsampled?
InputsGenomic intervals, genome sequence and task annotationsfrederikkemarin/BEND official source · README: Tutorial / Data format, Computing embeddings, Evaluating models; FAQ / How are embeddings upsampled?
Outputs and assessmentGene, regulatory or variant-related task predictionsfrederikkemarin/BEND official source · README: Tutorial / Data format, Computing embeddings, Evaluating models; FAQ / How are embeddings upsampled?
DatasetsNot extracted or verified for this record.
OrganismsNot extracted or verified for this record.
AssaysNot extracted or verified for this record.
SplitsNot extracted or verified for this record.
AdaptationNot extracted or verified for this record.
BaselinesNot extracted or verified for this record.

How it works

Procedure overview

Conceptual overview of the cited procedure; consult the pinned source for executable settings.

Procedure overviewGenomic intervals. Then: Compute DNA embeddings. Then: Apply task predictor. Then: Evaluate held-out labelsGenomic intervalsCompute DNA embeddingsApply task predictorEvaluate held-out labels
Read the diagram as text
  1. Genomic intervals
  2. Compute DNA embeddings
  3. Apply task predictor
  4. Evaluate held-out labels
frederikkemarin/BEND official source · README: Tutorial / Data format, Computing embeddings, Evaluating models; FAQ / How are embeddings upsampled?

Procedure

Generate embeddings for the released genomic intervals, then train the supplied supervised predictor or use the relevant unsupervised scoring procedure. Embeddings are expanded to nucleotide resolution according to each tokenizer.

frederikkemarin/BEND official source · README: Tutorial / Data format, Computing embeddings, Evaluating models; FAQ / How are embeddings upsampled?

Tested models and results

Release 2026-09-16-d74d282221a9 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

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Strengths and limitations

Strengths supported by sources

  • Includes one-hot and supervised baselines alongside pretrained representations.frederikkemarin/BEND official source · README: Tutorial / Data format, Computing embeddings, Evaluating models; FAQ / How are embeddings upsampled?

Limitations and conditions

  • Tokenizer upsampling and genomic coordinate handling affect what the predictor receives; task-specific splits and metrics remain necessary.frederikkemarin/BEND official source · README: Tutorial / Data format, Computing embeddings, Evaluating models; FAQ / How are embeddings upsampled?
Profile review details

Primary-source description checked by an automated research assistant. This is a profile review, not an independent execution or numerical reproduction.

Stable record: discovery-benchmark-bend

Sources and history

Release 2026-09-16-d74d282221a9 · Record review: discovered

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Technical metadata and extraction receipts

Stable ID: discovery-benchmark-bend

areas
genomics
entity level
suite
missing metadata
dataset release: unextracted; metric implementation: unextracted; split manifest: unextracted; version: unextracted
scope note
Specialist molecular or omics evaluation; protocol details require review before numerical comparison.
task
DNA representations on biological downstream tasks
version
Not reported
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