rewire.itbenchmarks
Dataset

ArchiveII

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

Research readiness

These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

Release 2026-09-29-06401fd5b220 · 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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • metric replay: verification is missing

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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • metric replay: verification is missing
  • annotations: verification is missing
  • dependence: verification is missing

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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • recipe pinned: verification is missing
  • resource estimate: verification is missing

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.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • independent validation: verification is missing
  • overlap checked: verification is missing

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.

Read reviewed discrepancy investigations

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: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.823 INF
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

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

BPfold: ArchiveII

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 6: ArchiveII INF
Configuration: ContextFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.824 Precision
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

ContextFold: ArchiveII

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 8: ArchiveII Precision
Configuration: RNAfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.577 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAfold: ArchiveII

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 7: ArchiveII F1
Configuration: SPOT-RNAProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.73 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SPOT-RNA: ArchiveII

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 7: ArchiveII F1
Configuration: BPfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.834 Recall
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

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

BPfold: ArchiveII

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 9: ArchiveII Recall
Configuration: RNAfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.551 Precision
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAfold: ArchiveII

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 8: ArchiveII Precision
Configuration: EternaFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.599 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: ArchiveII

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 7: ArchiveII F1
Configuration: RNAstructureProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.575 INF
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAstructure: ArchiveII

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 6: ArchiveII INF
Configuration: MXfold2Protocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.711 INF
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

MXfold2: ArchiveII

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 6: ArchiveII INF
Configuration: CONTRAfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.594 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

CONTRAfold: ArchiveII

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 7: ArchiveII F1
Configuration: MXfold2Protocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.697 Precision
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

MXfold2: ArchiveII

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 8: ArchiveII Precision
Configuration: SPOT-RNAProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.763 Precision
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SPOT-RNA: ArchiveII

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 8: ArchiveII Precision
Configuration: CONTRAfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.588 Recall
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

CONTRAfold: ArchiveII

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 9: ArchiveII Recall
Configuration: LinearFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.605 Recall
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

LinearFold: ArchiveII

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 9: ArchiveII Recall
Configuration: SimFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.568 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SimFold: ArchiveII

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 7: ArchiveII F1
Configuration: LinearFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.606 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

LinearFold: ArchiveII

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 7: ArchiveII F1
Configuration: CONTRAfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.612 Precision
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

CONTRAfold: ArchiveII

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 8: ArchiveII Precision
Configuration: SPOT-RNAProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.736 INF
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

SPOT-RNA: ArchiveII

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 6: ArchiveII INF
Configuration: EternaFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.573 Precision
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: ArchiveII

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 8: ArchiveII Precision
Configuration: RNAfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.613 Recall
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAfold: ArchiveII

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 9: ArchiveII Recall
Configuration: BPfoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.82 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

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

BPfold: ArchiveII

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 7: ArchiveII F1
Configuration: RNAstructureProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.573 F1
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

RNAstructure: ArchiveII

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 7: ArchiveII F1
Configuration: LinearFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.61 INF
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

LinearFold: ArchiveII

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 6: ArchiveII INF
Configuration: EternaFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.601 INF
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: ArchiveII

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 6: ArchiveII INF
Configuration: EternaFoldProtocol: ArchiveII (RNA secondary structure)
Dataset: ArchiveII
0.636 Recall
unitless · higher

Uncertainty: Not reported

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

EternaFold: ArchiveII

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 9: ArchiveII Recall

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

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.

7 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statementOriginal source and locationReview and provenance
attributes.reported_population.count
3966
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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII 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

attributes.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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII 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

attributes.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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII 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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII 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

attributes.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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII 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

attributes.subset
Not reported
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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII INF

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

missing or unspecified

No individual claim review recorded

Audit details

Field: attributes.subset

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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII 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
ArchiveII
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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII 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

View linked audit checks and correction history

Release 2026-09-29-06401fd5b220 · Record review: needs review

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: paper-dataset-be2c18a91718ba4592

areas
rna-transcriptomes
tasks
RNA secondary structure
split
Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
subset
Not reported
reported population
count: 3966; 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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII INF
missing metadata
manifest: unextracted; scored count: unreported
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 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII INF; ambiguities: None recorded
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