Evaluation

ContextFold: PDB

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: ContextFold
Protocol: PDB (RNA secondary structure)
Dataset: PDB RNA set

origin: Independent external evaluation
configuration: version 1.0, default parameters
protocol id: paper-protocol-b8acf180ccd3e67923
dataset version: Not reported
split: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
subset: Not reported
population: count: 116; unit: RNA sequences
aggregation: Not reported
inputs: Not reported
adaptation: version 1.0, 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
ContextFold: PDB Configuration: ContextFoldProtocol: PDB (RNA secondary structure)Dataset: PDB RNA set Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.737 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 6 ContextFold, column 7: PDB F1 Source checking is not independent reproduction.
0.795 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 6 ContextFold, column 8: PDB Precision Source checking is not independent reproduction.
0.702 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 6 ContextFold, column 9: PDB Recall Source checking is not independent reproduction.
0.743 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 6 ContextFold, column 6: PDB INF 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 version 1.0, default parameters 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 ↗ 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 ↗ 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 ↗ 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 ↗ 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 ↗ 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 116 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 ↗ 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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-b8acf180ccd3e67923 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB 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-baa48d66ec1674ccc7

areas: rna-transcriptomes
tasks: RNA secondary structure
origin: independent_paper
protocol: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
version: version 1.0, default parameters
comparison: protocol id: paper-protocol-b8acf180ccd3e67923; dataset version: Not reported; split: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; subset: Not reported; population: count: 116; unit: RNA sequences; aggregation: Not reported; inputs: Not reported; adaptation: version 1.0, default parameters; 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 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB INF
missing metadata: checkpoint revision: unextracted; budget: unreported; split manifest: unextracted

Related records

model: ContextFold
benchmark: PDB (RNA secondary structure)
dataset: PDB RNA set
evaluation: ContextFold: F1 on PDB
evaluation: ContextFold: Precision on PDB
evaluation: ContextFold: Recall on PDB
evaluation: ContextFold: INF on PDB

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