Datasets
EPBDXDNA/ENCODE ChIP-seq-derived human genomic bins with multilabel binding annotations.
Task
transcription-factor DNA binding-site prediction
Transcription-factor binding classification evaluates many TF–cell-type labels on chromosome-held-out genomic sequences.
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passagesOverview
Metrics
Per-label AUROC and AUPR are macro-averaged across TF–cell-type experiments.
Allowed inputs
Genomic sequence bins with multilabel targets.
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passagesEvaluation 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
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passageslimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
TF-cell-type binding on held-out chromosomes8and9 · Table 2.
AUROC (fraction) · Higher values are better.
TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction) · genome-wide TF binding sites
Evidence origin: Independent external evaluation, Result quoted from another source, Author-reported evaluation.
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9- Chromosome separation does not itself eliminate pretraining overlap.
- Within-paper aggregate only; do not compare against different label sets.
- EPBDXDNABERT-2 values are quoted from its original publication because retraining code/data were unavailable; its predictions were not available for paired testing.
Comparison details and limitations
Per-label AUROC/AUPR macro-averaged over 690 labels. Same Table 2 test cohort; methods differ in additional protein/dynamics inputs. DeepSEA-derived 690 TF-cell-type labels; chr 7 validation; remaining autosomes+X training; chr 8/9 test.
- No interval assigned unless printed in source cell.
Automated source review: 2026-09-17. 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 6 of 6 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
EPBDXDNA/ENCODE ChIP-seq-derived human genomic bins with multilabel binding annotations. Chromosomes 8/9 are held out for testing, chromosome 7 for validation and remaining specified chromosomes for training. Per-label AUROC and AUPR are macro-averaged across TF–cell-type experiments. TBiNet and EPBDXDNABERT-2 are explicit comparators; the latter’s underlying predictions were unavailable for paired statistical analysis. Chromosome-separated partitions reduce direct genomic overlap; validation data drive hyperparameter selection. Paired t-tests against TBiNet use TF–cell-type combinations as the comparison units; unavailable comparator predictions prevent the same paired analysis for every baseline.
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passagesEvaluation design
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Choose a concrete protocol before running an evaluation. Its inputs, split and scoring rules determine which results can be compared.
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
- Equal label weighting differs from pooling all bins and labels. Exact comparator identities, confidence intervals and long-range/homology overlap remain unextracted.
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages
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-ac191e878dff5eSpecifications
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 | EPBDXDNA/ENCODE ChIP-seq-derived human genomic bins with multilabel binding annotations.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Splits | Chromosomes 8/9 are held out for testing, chromosome 7 for validation and remaining specified chromosomes for training.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Metrics | Per-label AUROC and AUPR are macro-averaged across TF–cell-type experiments.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Baselines | TBiNet and EPBDXDNABERT-2 are explicit comparators; the latter’s underlying predictions were unavailable for paired statistical analysis.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Leakage controls | Chromosome-separated partitions reduce direct genomic overlap; validation data drive hyperparameter selection.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Uncertainty | Paired t-tests against TBiNet use TF–cell-type combinations as the comparison units; unavailable comparator predictions prevent the same paired analysis for every baseline.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Entity type | Paper-specific computational evaluation protocol.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Organisms | Human.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Assays | ENCODE ChIP-seq transcription-factor binding annotations.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Allowed inputs | Genomic sequence bins with multilabel targets.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
| Adaptation | Supervised binding prediction with chromosome-separated training/validation/test data.SourcesIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages |
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 |
|---|---|---|
| Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction | version of record | Read source DOI: 10.1093/nargab/lqag047 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 12 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.
- Independent batch review before import; preserve existing observation identities.
Search and extraction details
complete comparison tables extracted pending publication review
Searches
- Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction primary paper benchmark results
Evidence locations
- Table2; chromosome partition Table1; Training and evaluation
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 | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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
| Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 EPBDXDNA/ENCODE ChIP-seq-derived human genomic bins with multilabel binding annotations. Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 Chromosomes 8/9 are held out for testing, chromosome 7 for validation and remaining specified chromosomes for training. Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 |
| Adaptation Supervised binding prediction with chromosome-separated training/validation/test data. Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 Per-label AUROC and AUPR are macro-averaged across TF–cell-type experiments. Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 TBiNet and EPBDXDNABERT-2 are explicit comparators; the latter’s underlying predictions were unavailable for paired statistical analysis. Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 Chromosome-separated partitions reduce direct genomic overlap; validation data drive hyperparameter selection. Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 |
| Uncertainty Paired t-tests against TBiNet use TF–cell-type combinations as the comparison units; unavailable comparator predictions prevent the same paired analysis for every baseline. Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages Version: version of record | 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 |
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
- Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Original source · version of record
- Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-ac191e878dff5e
- areas
- molecular-interactions
- tasks
- transcription-factor DNA binding-site prediction
- entity level
- task
- version
- Not reported
- task
- transcription-factor DNA binding-site prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- comparison panels
- id: part2-transbind-2026-tbl2-06294a7ed9; title: TF-cell-type binding on held-out chromosomes8and9 · Table 2.; protocol id: paper-protocol-6821afc366eb11d0c6; dataset id: reported-dataset-034c60a2dabc73; metric: AUROC; unit: fraction; direction: higher; result ids: paper-result-8e4b88567c025003ed; paper-result-5c446c8d7902f5ff2b; paper-result-1d4fe2cf1475e26a45; paper-result-ced903b7d93ba17186; paper-result-684ff8c686809c84b0; lit-b4-023; source ids: part2-transbind-2026; source locator: Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9; context: Per-label AUROC/AUPR macro-averaged over 690 labels. Same Table 2 test cohort; methods differ in additional protein/dynamics inputs. DeepSEA-derived 690 TF-cell-type labels; chr 7 validation; remaining autosomes+X training; chr 8/9 test.; caveats: Chromosome separation does not itself eliminate pretraining overlap.; Within-paper aggregate only; do not compare against different label sets.; EPBDXDNABERT-2 values are quoted from its original publication because retraining code/data were unavailable; its predictions were not available for paired testing.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-transbind-2026-tbl2-fe3d7b6ab2; title: TF-cell-type binding on held-out chromosomes8and9 · Table 2.; protocol id: paper-protocol-6821afc366eb11d0c6; dataset id: reported-dataset-034c60a2dabc73; metric: AUPR; unit: fraction; direction: higher; result ids: paper-result-0f2759fe5b6ccce7e1; paper-result-d386eaf35eb25ef60a; paper-result-a2922906b449e8d5c5; paper-result-ec2a592fbd35502a5b; paper-result-afd5bc7f082f6ab7e4; paper-result-1237415199f36ae278; source ids: part2-transbind-2026; source locator: Table 2.: AUPR, TF-cell-type binding on held-out chromosomes8and9; context: Per-label AUROC/AUPR macro-averaged over 690 labels. Same Table 2 test cohort; methods differ in additional protein/dynamics inputs. DeepSEA-derived 690 TF-cell-type labels; chr 7 validation; remaining autosomes+X training; chr 8/9 test.; caveats: Chromosome separation does not itself eliminate pretraining overlap.; Within-paper aggregate only; do not compare against different label sets.; EPBDXDNABERT-2 values are quoted from its original publication because retraining code/data were unavailable; its predictions were not available for paired testing.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-transbind-2026; inspected locators: Table2; chromosome partition Table1; Training and evaluation; searched queries: Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction primary paper benchmark results; gaps: Independent batch review before import; preserve existing observation identities.; 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_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: transbind-2026; source locator: Methods: DNA data; Training and evaluation; cached text lines 13–18, 49–51; comparative evaluation and ablation passages; uncertainty/repeat-run/statistical-comparison passages; 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.