Datasets
No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.
inapplicable
Task
Enhancer / MPRA effects
Enhancer-effect evaluation asks whether sequence-based predictions track measured changes in regulatory activity.
Sources (2)
kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselinesNo reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Metrics
Use the metric attached to the concrete task: regulatory-element classification and quantitative effect prediction require different scoring.
Allowed inputs
Regulatory DNA or matched alleles and a specified experimental activity endpoint, with genome assembly and window placement recorded.
Sources (2)
kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselinesEvaluation procedure diagram
How it worksConceptual evaluation workflow
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
Sources (2)
kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselinesSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Results
All evaluations
0 evaluations · 0 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
No evaluations linked in this release.
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Choosing an evaluation
Separate detection of regulatory DNA from prediction of the effect of a sequence change. A reporter assay and endogenous chromatin-accessibility assay are different endpoints. DART-Eval provides concrete regulatory prediction tasks and comparisons across frozen, probed and fine-tuned models. Use its exact task and data release rather than treating every enhancer test as equivalent.
Sources (2)
kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselinesTask scope
This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.
Sources (2)
kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselinesRun 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 supported by sources
- A functional endpoint and matched learned baselines test usefulness beyond sequence-likelihood differences alone.
Sources (2)
kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines
Limitations and conditions
- Results from one reporter design or cellular context do not automatically transfer to endogenous regulation elsewhere.
Sources (2)
kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines
Profile review details
Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.
Stable record: catalog-task-enhancer-effectsSpecifications
Inputs, training, access and other details
Explanatory profile: source reviewed · 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 |
|---|---|
| Entity type | Task guide; concrete protocol identities remain separate.Sources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Allowed inputs | Regulatory DNA or matched alleles and a specified experimental activity endpoint, with genome assembly and window placement recorded.Sources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Metrics | Use the metric attached to the concrete task: regulatory-element classification and quantitative effect prediction require different scoring.Sources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
| Baselines | DART-Eval includes supervised models trained from scratch, including ChromBPNet-related baselines, alongside language-model evaluation modes.Sources (2)kundajelab/DART-Eval official source; DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · DART-Eval README Task 5; paper evaluation tasks and ab initio baselines |
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. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA | 2412.05430v1 | Read source |
Historical gaps recorded on 2026-09-17
- Regulatory sequence detection, TF motifs, cell-type activity and variant effects are distinct protocols. Enhancer broad-task record must link concrete tasks, not inherit every DART result. Existing DART observations require source-cell identity reuse.
Search and extraction details
broad task requires concrete protocol links
Searches
- DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA primary paper benchmark results
Evidence locations
- arXiv v1 main benchmark procedures and results tables
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.
34 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: NeurIPS 2024 Datasets and Benchmarks Track proceedings | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | kundajelab/DART-Eval official source DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: af2a86d666c35304257c2fa7e15180e1fbcabb01 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: NeurIPS 2024 Datasets and Benchmarks Track proceedings | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| kundajelab/DART-Eval official source DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: af2a86d666c35304257c2fa7e15180e1fbcabb01 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual evaluation workflow Individual claims | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: NeurIPS 2024 Datasets and Benchmarks Track proceedings | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual evaluation workflow Individual claims | kundajelab/DART-Eval official source DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: af2a86d666c35304257c2fa7e15180e1fbcabb01 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: NeurIPS 2024 Datasets and Benchmarks Track proceedings | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | kundajelab/DART-Eval official source DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: af2a86d666c35304257c2fa7e15180e1fbcabb01 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: NeurIPS 2024 Datasets and Benchmarks Track proceedings | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | kundajelab/DART-Eval official source DART-Eval README Task 5; paper evaluation tasks and ab initio baselines Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: af2a86d666c35304257c2fa7e15180e1fbcabb01 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. 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: discovered
7 source records and release history
- DNABERT-2 official resource · Original source · Not reported
- Nucleotide Transformer v2 official resource · Original source · Not reported
- Evo 2 official resource · Original source · Not reported
- AlphaGenome official resource · Original source · Not reported
- DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Original source · 2412.05430v1
- kundajelab/DART-Eval official source · Original source · af2a86d666c35304257c2fa7e15180e1fbcabb01
- DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Original source · NeurIPS 2024 Datasets and Benchmarks Track proceedings
Technical metadata and extraction receipts
Stable ID: catalog-task-enhancer-effects
- areas
- dna-genomes
- entity level
- task
- version
- Not reported
- task
- Enhancer / MPRA effects
- scope note
- Predict measured activity changes from regulatory sequence variants.
- benchmark research
- review date: 2026-09-17; status: broad_task_requires_concrete_protocol_links; primary sources: evidence-expansion-p2-evidence-discovery-final-dart-4194b137ba55; inspected locators: arXiv v1 main benchmark procedures and results tables; searched queries: DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA primary paper benchmark results; gaps: Regulatory sequence detection, TF motifs, cell-type activity and variant effects are distinct protocols. Enhancer broad-task record must link concrete tasks, not inherit every DART result. Existing DART observations require source-cell identity reuse.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- historical missing metadata
- protocol version: not_yet_extracted
- 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 record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: src-discovery-kundajelab-dart-eval; dart-eval-regulatory-2024; source locator: DART-Eval README Task 5; paper evaluation tasks and ab initio baselines; ambiguities: None recorded