rewirebio.iobenchmarks
Dataset

bpRNA-TS0

Dataset and cohort used in the cited comparison. Dataset population counts do not establish successful prediction coverage.

Evaluation results

10 evaluations · 40 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: BPfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.67 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

BPfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF
Configuration: EternaFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.539 F1
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 3: bpRNA-TS0 F1
Configuration: CONTRAfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.557 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

CONTRAfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF
Configuration: ContextFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.477 Precision
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

ContextFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 6 ContextFold, column 4: bpRNA-TS0 Precision
Configuration: BPfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.599 Precision
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

BPfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 3 BPfold, column 4: bpRNA-TS0 Precision
Configuration: RNAstructureProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.507 F1
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAstructure: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 12 RNAstructure, column 3: bpRNA-TS0 F1
Configuration: LinearFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.53 F1
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

LinearFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 9 LinearFold, column 3: bpRNA-TS0 F1
Configuration: SPOT-RNAProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.694 Recall
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SPOT-RNA: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 4 SPOT-RNA, column 5: bpRNA-TS0 Recall
Configuration: EternaFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.663 Recall
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 5: bpRNA-TS0 Recall
Configuration: SPOT-RNAProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.625 F1
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SPOT-RNA: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 4 SPOT-RNA, column 3: bpRNA-TS0 F1
Configuration: EternaFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.553 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF
Configuration: RNAstructureProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.52 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAstructure: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF
Configuration: SPOT-RNAProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.634 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SPOT-RNA: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF
Configuration: LinearFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.539 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

LinearFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF
Configuration: EternaFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.475 Precision
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 4: bpRNA-TS0 Precision
Configuration: LinearFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.539 Precision
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

LinearFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 9 LinearFold, column 4: bpRNA-TS0 Precision
Configuration: RNAfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.522 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF
Configuration: CONTRAfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.547 F1
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

CONTRAfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 3: bpRNA-TS0 F1
Configuration: SimFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.52 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SimFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF
Configuration: SimFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.626 Recall
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SimFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 5: bpRNA-TS0 Recall
Configuration: RNAfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.631 Recall
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 5: bpRNA-TS0 Recall
Configuration: MXfold2Protocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.587 Interaction network fidelity
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

MXfold2: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF
Configuration: BPfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.77 Recall
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

BPfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 3 BPfold, column 5: bpRNA-TS0 Recall
Configuration: CONTRAfoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.625 Recall
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

CONTRAfold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 5: bpRNA-TS0 Recall
Configuration: ContextFoldProtocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0
0.516 F1
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

ContextFold: bpRNA-TS0

Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.

Aggregation: Not reported

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 6 ContextFold, column 3: bpRNA-TS0 F1

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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.

6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Reported population: count
1305
Context-only references
Deep generalizable prediction of RNA secondary structure via base pair motif energy

Original source ↗

Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF

Version: version of record
Retrieved: 2026-09-16T10:41:16.502000+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.reported_population.count

Source artifact SHA-256: 976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Reported population: unit
RNA sequences
Context-only references
Deep generalizable prediction of RNA secondary structure via base pair motif energy

Original source ↗

Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF

Version: version of record
Retrieved: 2026-09-16T10:41:16.502000+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.reported_population.unit

Source artifact SHA-256: 976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Source location
Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF
Context-only references
Deep generalizable prediction of RNA secondary structure via base pair motif energy

Original source ↗

Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF

Version: version of record
Retrieved: 2026-09-16T10:41:16.502000+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Split
Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
Context-only references
Deep generalizable prediction of RNA secondary structure via base pair motif energy

Original source ↗

Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF

Version: version of record
Retrieved: 2026-09-16T10:41:16.502000+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: 976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Description
Dataset and cohort used in the cited comparison. Dataset population counts do not establish successful prediction coverage.
Context-only references
Deep generalizable prediction of RNA secondary structure via base pair motif energy

Original source ↗

Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF

Version: version of record
Retrieved: 2026-09-16T10:41:16.502000+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: 976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Name
bpRNA-TS0
Context-only references
Deep generalizable prediction of RNA secondary structure via base pair motif energy

Original source ↗

Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF

Version: version of record
Retrieved: 2026-09-16T10:41:16.502000+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: 976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: needs review

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Technical metadata and extraction receipts

Stable ID: paper-dataset-9a595197e5581413b6

areas
rna-transcriptomes
tasks
RNA secondary structure
split
Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
reported population
count: 1305; unit: RNA sequences
source locator
Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF
missing metadata
manifest: reason: unextracted; scored count: reason: unreported; subset: reason: unextracted
entity classification
review date: 2026-09-17; rationale: This record identifies a biological data collection or source-labelled evaluation cohort. Keep its dataset identity; split, assay, taxonomic level, candidate restrictions and comparison context remain attributes rather than automatically becoming new entity kinds.; source ids: bpfold-2025; source locator: Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF; ambiguities: None recorded
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