Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
finetuned DNABERT-2
finetuned DNABERT-2 as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2Overview
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
Evaluations and results
1 evaluation · 2 results. Different protocols are not a single leaderboard.
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: finetuned DNABERT-2 | Protocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction) Dataset: genome-wide TF binding sites | 0.918 AUROC fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcefinetuned DNABERT-2: TF-cell-type binding on held-out chromosomes8and9 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. Aggregation: Not reported Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2 |
| Configuration: finetuned DNABERT-2 | Protocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction) Dataset: genome-wide TF binding sites | 0.296 AUPR fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcefinetuned DNABERT-2: TF-cell-type binding on held-out chromosomes8and9 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. Aggregation: Not reported Integrating 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. Release 2026-09-29-06401fd5b220.
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How it works, versions and access
Related profile: DNABERT-2. This page retains the exact record and its evaluation context.
How it works
Evaluation in this paper
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
Sources
Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction · Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2Strengths, 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-model-5382c82497e0171114Specifications
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 |
|---|---|
| Model type | Not extracted or verified for this record. |
| Inputs | Not extracted or verified for this record. |
| Outputs | Not extracted or verified for this record. |
| Parameters | Not extracted or verified for this record. |
| Known versions | Not extracted or verified for this record. |
| Training data | Not extracted or verified for this record. |
| Context limits | Not extracted or verified for this record. |
| Access | Not extracted or verified for this record. |
| Code licence | Not extracted or verified for this record. |
| Weights licence | Not extracted or verified for this record. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2 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 finetuned DNABERT-2 as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2 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: family discovery-model-dnabert-2 Individual claims | MAGICS-LAB/DNABERT_2: README.md Cited primary paper comparison table and DNABERT-2 methods; official DNABERT-2 README; source-labelled configuration finetuned DNABERT-2 | Existing reviewed locator: Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f25bed9ee20db966dff39e5c1571249d04e36404 | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Reviewed primary source identifies DNABERT-2 as the evaluated backbone; no equivalence of adaptations or checkpoints inferred. Field: Claim: model-evaluation-identity-866e1730032a46fc006d Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Relationship: family discovery-model-dnabert-2 Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction Cited primary paper comparison table and DNABERT-2 methods; official DNABERT-2 README; source-labelled configuration finetuned DNABERT-2 | Existing reviewed locator: Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Reviewed primary source identifies DNABERT-2 as the evaluated backbone; no equivalence of adaptations or checkpoints inferred. Field: Claim: model-evaluation-identity-866e1730032a46fc006d 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-model-5382c82497e0171114
- areas
- molecular-interactions
- tasks
- transcription-factor DNA binding-site prediction
- entity level
- method
- configuration type
- reported_configuration
- version
- Paper-specific evaluated pipeline; exact checkpoint not inferred from label
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: part2-transbind-2026; source locator: Table 2., row finetuned DNABERT-2, column AUROC; XML row5 column2; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.