RNA secondary-structure assessment emphasizes held-out structural families rather than only novel sequences from familiar families.
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 | bpRNA-1m-derived structural families and a separate bpRNA-new evaluation collection.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Splits | Family-wise training/validation/test partitioning with cross-validation inside the training process.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Metrics | Base-pair precision, recall and structure F1.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Baselines | Existing RNA structure predictors, including SPOT-RNA and SPOT-RNA2, are considered in the independent-set design.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Leakage controls | A separate bpRNA-new test set is constructed because some comparators were trained on bpRNA-1m.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Entity type | Paper-specific computational evaluation protocol.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Organisms | The evaluated RNA sets are selected by Rfam family, length and source rather than by organism. The dataset-construction sections identify bpRNA/Rfam and PDB origins but do not enumerate the organism composition of TestSet α, β and γ. · Not reported in inspected sourcesSourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods and Data Sets: Family-Wise Processed RNA Structure Ground-Truth Data Set, including all three test-set construction subsections |
| Assays | Reference secondary structures.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Allowed inputs | RNA sequences.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
| Adaptation | Supervised secondary-structure prediction with family-wise partitions and training cross-validation.SourcesDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 |
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
bpRNA-1m-derived structural families and a separate bpRNA-new evaluation collection. Family-wise training/validation/test partitioning with cross-validation inside the training process. Base-pair precision, recall and structure F1. Existing RNA structure predictors, including SPOT-RNA and SPOT-RNA2, are considered in the independent-set design. A separate bpRNA-new test set is constructed because some comparators were trained on bpRNA-1m.
Each evaluation records what was tested and under which conditions.
Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| DEBFold: RNA secondary structure Median F1 on the prepared TestSetβ. Author-reported evaluation · Evaluation metadata: needs review | ||
| 55.7 Median F1 Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Table 1, DEBFold row, TestSetβ F1 (%) column Source checking is not independent reproduction. |
| RNAfold: RNA secondary structure Median F1 on the prepared TestSetβ. Independent external evaluation · Evaluation metadata: needs review | ||
| 52.3 Median F1 Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedDEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning · Table 1, RNAfold row, TestSetβ F1 (%) column Source checking is not independent reproduction. |
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 |
|---|---|---|
| DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning | PMC11094721.1 | Read source DOI: 10.1021/acs.jcim.4c00458 |
source found structured extraction pending
Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.
Stable record: reported-task-016f70615f2cfcTrace 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.
18 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 | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: RNA sequences.","Evaluation: Family-wise training/validation/test partitioning with cross-validation inside the training process.","Readout: Base-pair precision, recall and structure F1."] Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets bpRNA-1m-derived structural families and a separate bpRNA-new evaluation collection. Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Family-wise training/validation/test partitioning with cross-validation inside the training process. Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised secondary-structure prediction with family-wise partitions and training cross-validation. Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Base-pair precision, recall and structure F1. Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Existing RNA structure predictors, including SPOT-RNA and SPOT-RNA2, are considered in the independent-set design. Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls A separate bpRNA-new test set is constructed because some comparators were trained on bpRNA-1m. Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning Methods: Family-Wise Processed RNA Structure Ground-Truth Data Set; Contamination-Free Family-Wise Independent Test Set; Structure Prediction Evaluation Metrics; cached text lines 26–31, 36–37 Version: PMC11094721.1 | unreported automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: reported-task-016f70615f2cfc