Evaluation

RNAfold: bpRNA-TS0

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

Evaluation procedure

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

Configuration: RNAfold
Protocol: bpRNA-TS0 (RNA secondary structure)
Dataset: bpRNA-TS0

origin: Independent external evaluation
configuration: ViennaRNA version 2.6.4; default parameters
protocol id: paper-protocol-208a8085432aa64eb2
dataset version: Not reported
split: Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
subset: Not reported
population: count: 1305; unit: RNA sequences
aggregation: Not reported
inputs: Not reported
adaptation: ViennaRNA version 2.6.4; default parameters
budget: Not reported
metric implementation: Not reported

Metadata review: needs review. Unreported conditions prevent automatic comparisons.

Evaluation results

Release 2026-09-17-d277315f7d76 · 1 evaluation · 4 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
RNAfold: bpRNA-TS0 Configuration: RNAfoldProtocol: bpRNA-TS0 (RNA secondary structure)Dataset: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.522 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF Source checking is not independent reproduction.
0.631 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 5: bpRNA-TS0 Recall Source checking is not independent reproduction.
0.446 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 4: bpRNA-TS0 Precision Source checking is not independent reproduction.
0.508 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 3: bpRNA-TS0 F1 Source checking is not independent reproduction.

Evidence table

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.

20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation ViennaRNA version 2.6.4; default parameters 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 independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation No value recorded 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	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget No value recorded 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	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version No value recorded 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	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs No value recorded 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	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.metric_implementation No value recorded 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	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.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 independent paper Audit details Field: `attributes.comparison.population.count` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.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 independent paper Audit details Field: `attributes.comparison.population.unit` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.protocol_id paper-protocol-208a8085432aa64eb2 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 independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.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 independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: paper-evaluation-a633ebe90f1f0bf297

areas: rna-transcriptomes
tasks: RNA secondary structure
origin: independent_paper
protocol: Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
version: ViennaRNA version 2.6.4; default parameters
comparison: protocol id: paper-protocol-208a8085432aa64eb2; dataset version: Not reported; split: Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; subset: Not reported; population: count: 1305; unit: RNA sequences; aggregation: Not reported; inputs: Not reported; adaptation: ViennaRNA version 2.6.4; default parameters; budget: Not reported; metric implementation: Not reported
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: checkpoint revision: unextracted; budget: unreported; split manifest: unextracted

Related records

model: RNAfold
benchmark: bpRNA-TS0 (RNA secondary structure)
dataset: bpRNA-TS0
evaluation: RNAfold: INF on bpRNA-TS0
evaluation: RNAfold: Recall on bpRNA-TS0
evaluation: RNAfold: Precision on bpRNA-TS0
evaluation: RNAfold: F1 on bpRNA-TS0

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