Evaluation

BPfold: Rfam12.3–14.10

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

Evaluation procedure

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

Configuration: BPfold
Protocol: Rfam12.3–14.10 (RNA secondary structure)
Dataset: Rfam12.3–14.10

origin: Author-reported evaluation
configuration: five-fold cross-validation; early stopping
protocol id: paper-protocol-4c3af10c18f615709d
dataset version: Not reported
split: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
subset: Not reported
population: count: 10791; unit: RNA sequences
aggregation: Not reported
inputs: Not reported
adaptation: five-fold cross-validation; early stopping
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
BPfold: Rfam12.3–14.10 Configuration: BPfoldProtocol: Rfam12.3–14.10 (RNA secondary structure)Dataset: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Author-reported evaluation · Evaluation metadata: needs review
0.741 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 2 (Tab2), row 3 BPfold, column 5: Rfam12.3–14.10 Recall Source checking is not independent reproduction.
0.660 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 2 (Tab2), row 3 BPfold, column 4: Rfam12.3–14.10 Precision Source checking is not independent reproduction.
0.694 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 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF Source checking is not independent reproduction.
0.689 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 2 (Tab2), row 3 BPfold, column 3: Rfam12.3–14.10 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 five-fold cross-validation; early stopping Context-only references	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	not individually reviewed No individual claim review recorded author reported 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 ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	missing or unspecified No individual claim review recorded author reported 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 ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	missing or unspecified No individual claim review recorded author reported 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 ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	missing or unspecified No individual claim review recorded author reported 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 ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	missing or unspecified No individual claim review recorded author reported 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 ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	missing or unspecified No individual claim review recorded author reported 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 10791 Context-only references	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	not individually reviewed No individual claim review recorded author reported 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 ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	not individually reviewed No individual claim review recorded author reported 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-4c3af10c18f615709d Context-only references	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	not individually reviewed No individual claim review recorded author reported 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 Family-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 ↗ Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	not individually reviewed No individual claim review recorded author reported 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-da5f778cb46bcc0a73

areas: rna-transcriptomes
tasks: RNA secondary structure
origin: author_reported
protocol: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
version: five-fold cross-validation; early stopping
comparison: protocol id: paper-protocol-4c3af10c18f615709d; dataset version: Not reported; split: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; subset: Not reported; population: count: 10791; unit: RNA sequences; aggregation: Not reported; inputs: Not reported; adaptation: five-fold cross-validation; early stopping; budget: Not reported; metric implementation: Not reported
source locator: Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n = 10,791 RNAs) and PDB ( n = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF
missing metadata: checkpoint revision: unextracted; budget: unreported; split manifest: unextracted

Related records

model: BPfold
benchmark: Rfam12.3–14.10 (RNA secondary structure)
dataset: Rfam12.3–14.10
evaluation: BPfold: Recall on Rfam12.3–14.10
evaluation: BPfold: Precision on Rfam12.3–14.10
evaluation: BPfold: INF on Rfam12.3–14.10
evaluation: BPfold: F1 on Rfam12.3–14.10

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