Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
EPBDXDNABERT-2
EPBDXDNABERT-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 EPBDXDNABERT-2, column AUROC; XML row6 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: EPBDXDNABERT-2 | Protocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction) Dataset: genome-wide TF binding sites | 0.949 AUROC fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceEPBDXDNABERT-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 EPBDXDNABERT-2, column AUROC; XML row6 column2 |
| Configuration: EPBDXDNABERT-2 | Protocol: TF-cell-type binding on held-out chromosomes8and9 (transcription-factor DNA binding-site prediction) Dataset: genome-wide TF binding sites | 0.326 AUPR fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceEPBDXDNABERT-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 EPBDXDNABERT-2, column AUPR; XML row6 column3 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Use this model
How it works, versions and access
Underlying model: DNABERT-2. Results on this page belong to this configuration and its evaluated settings.
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 EPBDXDNABERT-2, column AUROC; XML row6 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-3627ef7080a5afc255Specifications
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 EPBDXDNABERT-2, column AUROC; XML row6 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 EPBDXDNABERT-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 EPBDXDNABERT-2, column AUROC; XML row6 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: uses model discovery-model-dnabert-2 Individual claims | MAGICS-LAB/DNABERT_2: README.md TransBind introduction EPBD×DNABERT-2 paragraph and Table 2 | Existing reviewed locator: Table 2., row EPBDXDNABERT-2, column AUROC; XML row6 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. Hybrid of DNABERT-2 embeddings and biophysical EPBD features. Currently typed configuration; use component relation, not family; consider separate pipeline reclassification review. Field: Claim: model-evaluation-identity-4e5f5fc5d4b8ae6a3453 Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Relationship: uses model discovery-model-dnabert-2 Individual claims | Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction TransBind introduction EPBD×DNABERT-2 paragraph and Table 2 | Existing reviewed locator: Table 2., row EPBDXDNABERT-2, column AUROC; XML row6 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. Hybrid of DNABERT-2 embeddings and biophysical EPBD features. Currently typed configuration; use component relation, not family; consider separate pipeline reclassification review. Field: Claim: model-evaluation-identity-4e5f5fc5d4b8ae6a3453 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-3627ef7080a5afc255
- 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 EPBDXDNABERT-2, column AUROC; XML row6 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.
Related records
- uses model: DNABERT-2
- subject: EPBDXDNABERT-2: uses model DNABERT-2
- model: EPBDXDNABERT-2: TF-cell-type binding on held-out chromosomes8and9