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.
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9At a glance
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.
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.
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
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.
TF-cell-type binding on held-out chromosomes8and9 · Table 2.
AUROC (fraction) · Higher values are better for this metric.
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.
- DeepSEA · Configuration · Independent external evaluation0.8934
- DanQ · Configuration · Independent external evaluation0.9254
- TBiNet · Configuration · Independent external evaluation0.9402
- finetuned DNABERT-2 · Configuration · Independent external evaluation0.9180
- EPBDXDNABERT-2 · Configuration · Result quoted from another source0.9490
- TransBind · Configuration · Author-reported evaluation0.9508
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2.: AUROC, TF-cell-type binding on held-out chromosomes8and9Values, uncertainty and evidence
Scope and limitations
- 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.
Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 6 evaluations · 12 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| TransBind: transcription-factor DNA binding-site prediction Configuration: TransBindProtocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)Dataset: genome-wide TF binding sites 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.9508 AUROC Unit: fraction · Direction: higher | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction; Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2, TransBind row, AUROC column Source checking is not independent reproduction. |
| 0.3741 AUPR Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row TransBind, column AUPR; XML row7 column3 Source checking is not independent reproduction. |
| DeepSEA: TF-cell-type binding on held-out chromosomes8and9 Configuration: DeepSEAProtocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)Dataset: genome-wide TF binding sites 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.2509 AUPR Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row DeepSEA, column AUPR; XML row2 column3 Source checking is not independent reproduction. |
| 0.8934 AUROC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row DeepSEA, column AUROC; XML row2 column2 Source checking is not independent reproduction. |
| TBiNet: TF-cell-type binding on held-out chromosomes8and9 Configuration: TBiNetProtocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)Dataset: genome-wide TF binding sites 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.9402 AUROC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row TBiNet, column AUROC; XML row4 column2 Source checking is not independent reproduction. |
| 0.3346 AUPR Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row TBiNet, column AUPR; XML row4 column3 Source checking is not independent reproduction. |
| DanQ: TF-cell-type binding on held-out chromosomes8and9 Configuration: DanQProtocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)Dataset: genome-wide TF binding sites 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.9254 AUROC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row DanQ, column AUROC; XML row3 column2 Source checking is not independent reproduction. |
| 0.3065 AUPR Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row DanQ, column AUPR; XML row3 column3 Source checking is not independent reproduction. |
| EPBDXDNABERT-2: TF-cell-type binding on held-out chromosomes8and9 Configuration: EPBDXDNABERT-2Protocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)Dataset: genome-wide TF binding sites 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.9490 AUROC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row EPBDXDNABERT-2, column AUROC; XML row6 column2 Source checking is not independent reproduction. |
| 0.3260 AUPR Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row EPBDXDNABERT-2, column AUPR; XML row6 column3 Source checking is not independent reproduction. |
| finetuned DNABERT-2: TF-cell-type binding on held-out chromosomes8and9 Configuration: finetuned DNABERT-2Protocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction)Dataset: genome-wide TF binding sites 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.9180 AUROC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2 Source checking is not independent reproduction. |
| 0.2960 AUPR Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedIntegrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row finetuned DNABERT-2, column AUPR; XML row5 column3 Source checking is not 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 |
What is still missing
- 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
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-6821afc366eb11d0c6Evidence table
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
Release 2026-09-17-d277315f7d76 · Record review: needs review
- 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