Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
bpRNA-TS0 (RNA secondary structure)
bpRNA-TS0 · INF. Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
Sources
Deep generalizable prediction of RNA secondary structure via base pair motif energy · 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 INFOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
bpRNA-TS0 · INF
INF (unitless) · Higher values are better.
bpRNA-TS0 (RNA secondary structure) · bpRNA-TS0
Evidence origin: Author-reported evaluation, Independent external evaluation.
Deep generalizable prediction of RNA secondary structure via base pair motif energy · 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- Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.
Comparison details and limitations
Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 10 of 10 matching rows.
Tested configuration
0.5110.5530.5950.6370.679
Reported scoreMethods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation in this paper
Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
Sources
Deep generalizable prediction of RNA secondary structure via base pair motif energy · 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 INFEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
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Recorded evaluations
Each evaluation records what was tested and under which conditions.
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Protocol-valid structural control
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Thermodynamic folding with protocol-compatible input constraints
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-208a8085432aa64eb2Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Deep generalizable prediction of RNA secondary structure via base pair motif energy | version of record | Read source DOI: 10.1038/s41467-025-60048-1 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 40 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Search and extraction details
complete tables extracted
Searches
- Deep generalizable prediction of RNA secondary structure via base pair motif energy 10.1038/s41467-025-60048-1
Evidence locations
- 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
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.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Individual claims | Deep generalizable prediction of RNA secondary structure via base pair motif energy 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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Introduction bpRNA-TS0 · INF. Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Individual claims | Deep generalizable prediction of RNA secondary structure via base pair motif energy 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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: evaluates task catalog-task-rna-secondary-structure Individual claims | Deep generalizable prediction of RNA secondary structure via base pair motif energy 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 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-e8258aa43fc8a44431 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: evaluates task reported-task-dc82fcbfb44935 Individual claims | Deep generalizable prediction of RNA secondary structure via base pair motif energy 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 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-a931b2ca994c264ed6 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- Deep generalizable prediction of RNA secondary structure via base pair motif energy · Original source · version of record
Technical metadata and extraction receipts
Stable ID: paper-protocol-208a8085432aa64eb2
- areas
- rna-transcriptomes
- tasks
- RNA secondary structure
- entity level
- protocol
- protocol
- Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
- comparison panels
- id: bpfold-2025-tab1-bprna-ts0-inf; title: bpRNA-TS0 · INF; protocol id: paper-protocol-208a8085432aa64eb2; dataset id: paper-dataset-9a595197e5581413b6; metric: INF; unit: unitless; direction: higher; result ids: paper-result-0458271bb982e75179; paper-result-5a1624fdb7640263f2; paper-result-7b916d75babf7a4d06; paper-result-e8e6954c70547446a1; paper-result-0da7bdbbf7b43c8456; paper-result-5249c6fca0adf30079; paper-result-5ebc9d5244115922e3; paper-result-66830706f75e525dbf; paper-result-711a4c604b04a9b0f2; paper-result-53887e7500c1cf009e; 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; context: Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: bpfold-2025-tab1-bprna-ts0-f1; title: bpRNA-TS0 · F1; protocol id: paper-protocol-208a8085432aa64eb2; dataset id: paper-dataset-9a595197e5581413b6; metric: F1; unit: unitless; direction: higher; result ids: paper-result-f0f7111a6ec6426675; paper-result-4cd8df587d039cd7e1; paper-result-a5fe28b91e06263870; paper-result-8a436775a6db0626a1; paper-result-681cbde13cc79ef7ca; paper-result-0a1d1b57a38ce34e75; paper-result-35d6ca02cce090966b; paper-result-dcf0e23f78d1cb6fc0; paper-result-c536ed0e0b21471c4e; paper-result-1ccf4abe34808409ff; 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 3: bpRNA-TS0 F1; Table 1 (Tab1), row 4 SPOT-RNA, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 5 MXfold2, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 6 ContextFold, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 7 CONTRAfold, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 8 EternaFold, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 9 LinearFold, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 10 RNAfold, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 11 SimFold, column 3: bpRNA-TS0 F1; Table 1 (Tab1), row 12 RNAstructure, column 3: bpRNA-TS0 F1; context: Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: bpfold-2025-tab1-bprna-ts0-precision; title: bpRNA-TS0 · Precision; protocol id: paper-protocol-208a8085432aa64eb2; dataset id: paper-dataset-9a595197e5581413b6; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-11c1675cb5828808ab; paper-result-cb40146a919da9086a; paper-result-b78905513200ad10fe; paper-result-1069d4f8df9404d6e5; paper-result-deff3015ebe9868640; paper-result-5efbf1aebc52ee2283; paper-result-62e9fb6e2b7036a5d5; paper-result-ce1b188daa1f9f9fa6; paper-result-d7b4db6a7311486ac5; paper-result-bae3bdb96c31f1a771; 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 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 4 SPOT-RNA, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 5 MXfold2, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 6 ContextFold, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 7 CONTRAfold, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 8 EternaFold, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 9 LinearFold, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 10 RNAfold, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 11 SimFold, column 4: bpRNA-TS0 Precision; Table 1 (Tab1), row 12 RNAstructure, column 4: bpRNA-TS0 Precision; context: Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: bpfold-2025-tab1-bprna-ts0-recall; title: bpRNA-TS0 · Recall; protocol id: paper-protocol-208a8085432aa64eb2; dataset id: paper-dataset-9a595197e5581413b6; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-84076a2caea4d91a05; paper-result-362a0ed0c13044cdfc; paper-result-9fcdf129530b83f00e; paper-result-b31f8dc93eb733d9c3; paper-result-889ce61bcef60c0f8c; paper-result-3b51165690d6d453ee; paper-result-c785e6f619ae381da7; paper-result-7b019b2b8bb9da3d29; paper-result-725d822668ea6d7acd; paper-result-d7a88bfa84a1748144; 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 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 4 SPOT-RNA, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 5 MXfold2, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 6 ContextFold, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 7 CONTRAfold, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 8 EternaFold, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 9 LinearFold, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 10 RNAfold, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 11 SimFold, column 5: bpRNA-TS0 Recall; Table 1 (Tab1), row 12 RNAstructure, column 5: bpRNA-TS0 Recall; context: Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.; caveats: Within each dataset and metric only. Distinct training data, thermodynamic priors and learned methods are retained; dataset size is not a base-pair denominator. These are BPfold-author evaluations of external methods, not Rewire reproductions. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_tables_extracted; primary sources: bpfold-2025; inspected locators: 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; searched queries: Deep generalizable prediction of RNA secondary structure via base pair motif energy 10.1038/s41467-025-60048-1; gaps: exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; 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
Related records
- evaluates task: RNA secondary structure
- evaluates task: RNA secondary structure
- subject: bpRNA-TS0 (RNA secondary structure): links:evaluates_task:reported-task-dc82fcbfb44935
- subject: bpRNA-TS0 (RNA secondary structure): links:evaluates_task:catalog-task-rna-secondary-structure
- benchmark: RNAstructure: bpRNA-TS0
- benchmark: SimFold: bpRNA-TS0
- benchmark: EternaFold: bpRNA-TS0
- benchmark: SPOT-RNA: bpRNA-TS0
- benchmark: RNAfold: bpRNA-TS0
- benchmark: MXfold2: bpRNA-TS0
- benchmark: CONTRAfold: bpRNA-TS0
- benchmark: ContextFold: bpRNA-TS0
- benchmark: LinearFold: bpRNA-TS0
- benchmark: BPfold: bpRNA-TS0