Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)
TF-cell-type binding on held-out chromosomes8and9 · Table 2.. 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.
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9Overview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. 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 in this paper
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.
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- TransBind: transcription-factor DNA binding-site prediction
- EPBDXDNABERT-2: TF-cell-type binding on held-out chromosomes8and9
- DanQ: TF-cell-type binding on held-out chromosomes8and9
- TBiNet: TF-cell-type binding on held-out chromosomes8and9
- DeepSEA: TF-cell-type binding on held-out chromosomes8and9
- finetuned DNABERT-2: TF-cell-type binding on held-out chromosomes8and9
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-6821afc366eb11d0c6Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
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
- Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper 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. Individual claims | 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 Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction TF-cell-type binding on held-out chromosomes8and9 · Table 2.. 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. Individual claims | 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 Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task reported-task-ac191e878dff5e Individual claims | 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 Version: version of record | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-dbec0ecce4f8d58b1e Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- 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: paper-protocol-6821afc366eb11d0c6
- areas
- molecular-interactions
- tasks
- transcription-factor DNA binding-site prediction
- entity level
- protocol
- protocol
- 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.
- 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: Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9; 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.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-transbind-2026; source locator: Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9; ambiguities: None recorded
Related records
- evaluates task: transcription-factor DNA binding-site prediction
- benchmark: TransBind: transcription-factor DNA binding-site prediction
- subject: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction): links:evaluates_task:reported-task-ac191e878dff5e
- benchmark: EPBDXDNABERT-2: TF-cell-type binding on held-out chromosomes8and9
- benchmark: DanQ: TF-cell-type binding on held-out chromosomes8and9
- benchmark: TBiNet: TF-cell-type binding on held-out chromosomes8and9
- benchmark: DeepSEA: TF-cell-type binding on held-out chromosomes8and9
- benchmark: finetuned DNABERT-2: TF-cell-type binding on held-out chromosomes8and9