Datasets
K562 enhancer-promoter candidate pairs with positive and negative annotations from prior studies.
Task
Enhancer-target gene prediction
Enhancer-target classification tests whether sequence models distinguish experimentally annotated interaction candidates.
Sources
DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48Overview
Metrics
AUROC for enhancer-promoter interaction classification.
Allowed inputs
Long genomic sequence context for enhancer/target-gene pairs.
Sources
DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48Evaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: HyenaDNA | Task: Enhancer-target gene prediction Dataset: DNALongBench ETGP | 0.828 AUROC unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA: Enhancer-target gene prediction Long-range ETGP benchmark; source table reports AUROC. Aggregation: Not reported DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Table 3, HyenaDNA row, ETGP column |
| Configuration: Caduceus-Ph | Task: Enhancer-target gene prediction Dataset: DNALongBench ETGP | 0.826 AUROC unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph: Enhancer-target gene prediction Long-range ETGP benchmark; source table reports AUROC. Aggregation: Not reported DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Table 3, Caduceus-Ph row, ETGP column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
K562 enhancer-promoter candidate pairs with positive and negative annotations from prior studies. The enhancer-target task paragraph identifies the curated K562 pairs and evaluation metric but does not state its partition assignment; nearby split descriptions belong to other tasks. AUROC for enhancer-promoter interaction classification. A compact CNN and DNA foundation models are compared with the activity-by-contact expert model. The enhancer-target paragraph does not establish gene- or overlapping-interval-disjoint partitions; unrelated task split rules cannot be imported. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48Recorded evaluations
Each evaluation records what was tested and under which conditions.
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.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Limitations and conditions
- The activity-by-contact comparator receives functional assays and chromatin-contact data that sequence-only models do not. Splits described for other DNALongBench tasks are not imported into this record.
Sources
DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48
Profile review details
Task-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced.
Stable record: reported-task-2cbac97dd849f5Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | K562 enhancer-promoter candidate pairs with positive and negative annotations from prior studies.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Splits | The enhancer-target task paragraph identifies the curated K562 pairs and evaluation metric but does not state its partition assignment; nearby split descriptions belong to other tasks. · Not reported in inspected sourcesSourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Metrics | AUROC for enhancer-promoter interaction classification.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Baselines | A compact CNN and DNA foundation models are compared with the activity-by-contact expert model.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Leakage controls | The enhancer-target paragraph does not establish gene- or overlapping-interval-disjoint partitions; unrelated task split rules cannot be imported. · Not reported in inspected sourcesSourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Entity type | Paper-specific computational evaluation protocol.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Organisms | Human K562.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Assays | Enhancer–promoter link annotations.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Allowed inputs | Long genomic sequence context for enhancer/target-gene pairs.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
| Adaptation | Downstream DNA-model prediction compared with a CNN and the activity-by-contact expert model.SourcesDNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks | PMC11741265.1 | Read source |
Historical gaps recorded on 2026-09-17
The catalogue now holds 2 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.
- exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Search and extraction details
primary comparison tables located
Searches
- DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks 10.1101/2025.01.06.631595
Evidence locations
- Table 3:; XML table T3
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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets K562 enhancer-promoter candidate pairs with positive and negative annotations from prior studies. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits The enhancer-target task paragraph identifies the curated K562 pairs and evaluation metric but does not state its partition assignment; nearby split descriptions belong to other tasks. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | unreported automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Downstream DNA-model prediction compared with a CNN and the activity-by-contact expert model. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics AUROC for enhancer-promoter interaction classification. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines A compact CNN and DNA foundation models are compared with the activity-by-contact expert model. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The enhancer-target paragraph does not establish gene- or overlapping-interval-disjoint partitions; unrelated task split rules cannot be imported. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | unreported automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48 Version: PMC11741265.1 | unreported automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Original source · PMC11741265.1
- DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks · Original source · PMC11741265.1
Technical metadata and extraction receipts
Stable ID: reported-task-2cbac97dd849f5
- areas
- dna-genomes
- tasks
- Enhancer-target gene prediction
- entity level
- task
- version
- Not reported
- task
- Enhancer-target gene prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_tables_located; primary sources: evidence-expansion-dnalongbench-2025-fa440a17; inspected locators: Table 3:; XML table T3; searched queries: DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks 10.1101/2025.01.06.631595; gaps: complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.; exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: dnalongbench-2025; source locator: Proposed Dataset: enhancer-promoter interactions; Experiments; cached text lines 27–28, 48; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: DNALongBench ETGP
- benchmark: HyenaDNA: Enhancer-target gene prediction
- benchmark: Caduceus-Ph: Enhancer-target gene prediction