Task

RNA secondary structure

RNA secondary-structure prediction evaluates proposed nucleotide pairing rather than complete three-dimensional geometry.

Sources (2)

terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

40 evaluations · 160 results

Overview

Datasets

No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.

inapplicable

Metrics

Pairing or secondary-structure metrics from the selected protocol. This guide defines no common pseudoknot policy, matching tolerance or aggregation.

Allowed inputs

RNA sequence and any permitted auxiliary information; reference secondary-structure labels for scoring.

Sources (2)

terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

Evaluation procedure diagram

How it worksConceptual evaluation workflow

Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.

Sources (2)

terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

Find a protocol, dataset or metric

Evaluation scope and datasetMetric and reported setup

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.

Find a tested model or method

Showing 10 of 10 matching rows.

Zoom to observed range

Tested configuration

0.5110.5530.5950.6370.679

Reported score

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Choosing an evaluation

Use reference pairing labels and a declared scoring rule. BEACON includes a dedicated secondary-structure task, while RNA-FM supplies representations and pairing-related outputs used by downstream models. A representation, a pairing predictor and a complete benchmark are different records. Keep sequence-family overlap and reference-label construction visible.

Sources (2)

terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

Task scope

This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.

Sources (2)

terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Protocols

These source-backed links do not make different protocols or scores interchangeable.

Run this benchmark

Choose a concrete protocol before running an evaluation. Its inputs, split and scoring rules determine which results can be compared.

Run instructions

No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths supported by sources

Pairing labels give a distinct structural endpoint that can be evaluated separately from full 3D prediction.
Sources (2)
terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

Limitations and conditions

Secondary-structure accuracy does not establish tertiary-structure accuracy, and close sequence relatives can weaken a claimed generalisation test.
Sources (2)
terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

Profile review details

Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.

Stable record: catalog-task-rna-secondary-structure

Specifications

Inputs, training, access and other details

Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Entity type	Task guide; concrete protocol identities remain separate. Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Datasets	No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicable Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Organisms	No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicable Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Assays	No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicable Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Splits	No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicable Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Allowed inputs	RNA sequence and any permitted auxiliary information; reference secondary-structure labels for scoring. Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Adaptation	No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicable Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Metrics	Pairing or secondary-structure metrics from the selected protocol. This guide defines no common pseudoknot policy, matching tolerance or aggregation. Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs
Baselines	Compare the learned predictor with the conventional folding or learned baselines of the concrete task; do not infer a measured result from model availability. Sources (2) terry-r123/RNABenchmark official source; ml4bio/RNA-FM official source · BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs

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

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

BPfold Tables 1–2; Methods, Evaluation metrics

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.

34 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims	ml4bio/RNA-FM official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T10:30:26.372370+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: Hash scope not separately documented; inspect source record
Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims	terry-r123/RNABenchmark official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 Retrieved: 2026-09-16T10:30:21.025462+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `0403f84453aace301c7d02895d94a977ccbbec77c3a94a49a23d0d529dd48d31` Hash scope: Hash scope not separately documented; inspect source record
Diagram steps Select RNA references and split Declare permitted sequence context Predict pairing structure Apply the declared matching and scoring Individual claims	ml4bio/RNA-FM official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T10:30:26.372370+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: Hash scope not separately documented; inspect source record
Diagram steps Select RNA references and split Declare permitted sequence context Predict pairing structure Apply the declared matching and scoring Individual claims	terry-r123/RNABenchmark official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 Retrieved: 2026-09-16T10:30:21.025462+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `0403f84453aace301c7d02895d94a977ccbbec77c3a94a49a23d0d529dd48d31` Hash scope: Hash scope not separately documented; inspect source record
Diagram title Conceptual evaluation workflow Individual claims	ml4bio/RNA-FM official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T10:30:26.372370+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: Hash scope not separately documented; inspect source record
Diagram title Conceptual evaluation workflow Individual claims	terry-r123/RNABenchmark official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 Retrieved: 2026-09-16T10:30:21.025462+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `0403f84453aace301c7d02895d94a977ccbbec77c3a94a49a23d0d529dd48d31` Hash scope: Hash scope not separately documented; inspect source record
Entity type Task guide; concrete protocol identities remain separate. Individual claims	ml4bio/RNA-FM official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T10:30:26.372370+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: Hash scope not separately documented; inspect source record
Entity type Task guide; concrete protocol identities remain separate. Individual claims	terry-r123/RNABenchmark official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 Retrieved: 2026-09-16T10:30:21.025462+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `0403f84453aace301c7d02895d94a977ccbbec77c3a94a49a23d0d529dd48d31` Hash scope: Hash scope not separately documented; inspect source record
Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims	ml4bio/RNA-FM official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T10:30:26.372370+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: Hash scope not separately documented; inspect source record
Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims	terry-r123/RNABenchmark official source Original source ↗ BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 Retrieved: 2026-09-16T10:30:21.025462+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `0403f84453aace301c7d02895d94a977ccbbec77c3a94a49a23d0d529dd48d31` Hash scope: Hash scope not separately documented; inspect source record

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

6 source records and release history

RNA-FM official resource · Original source · Not reported
RhoFold+ official resource · Original source · Not reported
Deep generalizable prediction of RNA secondary structure via base pair motif energy · Original source · version of record
Deep generalizable prediction of RNA secondary structure via base pair motif energy · Original source · version of record
terry-r123/RNABenchmark official source · Original source · da7f9c7ac3f39605af27e1dfcdf879adba963d79
ml4bio/RNA-FM official source · Original source · 348951516e0963d22bbb33b3c9fc18c89081d38e

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Technical metadata and extraction receipts

Stable ID: catalog-task-rna-secondary-structure

areas: rna-transcriptomes
entity level: task
version: Not reported
task: RNA secondary structure
scope note: Compare predicted base pairs against held-out RNA structures.
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; id: bpfold-2025-tab1-archiveii-inf; title: ArchiveII · INF; protocol id: paper-protocol-e8a1aa302bb8df1efd; dataset id: paper-dataset-be2c18a91718ba4592; metric: INF; unit: unitless; direction: higher; result ids: paper-result-0201b139fce549eab3; paper-result-74f904c36aab24aa79; paper-result-4800ab44874448c8b4; paper-result-fcd63eea1286d760ab; paper-result-e6a6c3931d9266f05f; paper-result-9b4f92609217cc1fb6; paper-result-9110b71d1f8e197959; paper-result-ded0df417ed95f9f29; paper-result-e32db43eda24866957; paper-result-45847f62623b463cf2; 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; 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-archiveii-f1; title: ArchiveII · F1; protocol id: paper-protocol-e8a1aa302bb8df1efd; dataset id: paper-dataset-be2c18a91718ba4592; metric: F1; unit: unitless; direction: higher; result ids: paper-result-848e79a6dda494f6d2; paper-result-15bf14f0627ace6e51; paper-result-b261f94a241a11866c; paper-result-f6296b4b6029ae0c24; paper-result-4966fd60b18e79a44a; paper-result-3f5f78f9847ba7def0; paper-result-64436b2115ee5881b4; paper-result-145bc6b041b9d5dbe4; paper-result-61f86306875259316e; paper-result-8d618367d005102a41; 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 7: ArchiveII F1; Table 1 (Tab1), row 4 SPOT-RNA, column 7: ArchiveII F1; Table 1 (Tab1), row 5 MXfold2, column 7: ArchiveII F1; Table 1 (Tab1), row 6 ContextFold, column 7: ArchiveII F1; Table 1 (Tab1), row 7 CONTRAfold, column 7: ArchiveII F1; Table 1 (Tab1), row 8 EternaFold, column 7: ArchiveII F1; Table 1 (Tab1), row 9 LinearFold, column 7: ArchiveII F1; Table 1 (Tab1), row 10 RNAfold, column 7: ArchiveII F1; Table 1 (Tab1), row 11 SimFold, column 7: ArchiveII F1; Table 1 (Tab1), row 12 RNAstructure, column 7: ArchiveII 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-archiveii-precision; title: ArchiveII · Precision; protocol id: paper-protocol-e8a1aa302bb8df1efd; dataset id: paper-dataset-be2c18a91718ba4592; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-cab7a52a6159f4b3f5; paper-result-4e6b9de9fa6581febe; paper-result-4e335c3e3fc60bd7a3; paper-result-0d6f9ea5b80a61c517; paper-result-6fd617ba744c55f823; paper-result-80618ad04474cfdfa4; paper-result-d0f2c61c9603a219fd; paper-result-2bf7f6f35cb278b8b3; paper-result-b4a0a133d3c57bbd78; paper-result-af213ccd00f688f0e8; 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 8: ArchiveII Precision; Table 1 (Tab1), row 4 SPOT-RNA, column 8: ArchiveII Precision; Table 1 (Tab1), row 5 MXfold2, column 8: ArchiveII Precision; Table 1 (Tab1), row 6 ContextFold, column 8: ArchiveII Precision; Table 1 (Tab1), row 7 CONTRAfold, column 8: ArchiveII Precision; Table 1 (Tab1), row 8 EternaFold, column 8: ArchiveII Precision; Table 1 (Tab1), row 9 LinearFold, column 8: ArchiveII Precision; Table 1 (Tab1), row 10 RNAfold, column 8: ArchiveII Precision; Table 1 (Tab1), row 11 SimFold, column 8: ArchiveII Precision; Table 1 (Tab1), row 12 RNAstructure, column 8: ArchiveII 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-archiveii-recall; title: ArchiveII · Recall; protocol id: paper-protocol-e8a1aa302bb8df1efd; dataset id: paper-dataset-be2c18a91718ba4592; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-23d3090d9e3540349d; paper-result-b79992ef838378f5c1; paper-result-e038536d6f9b001984; paper-result-d82764605cdb73aad8; paper-result-57de4fbe015fbae501; paper-result-a8cf704b852f820e32; paper-result-5f273213a7f48d1b55; paper-result-8164922a733ea800eb; paper-result-ccd93245b92c3d3620; paper-result-cf786103471c989dd3; 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 9: ArchiveII Recall; Table 1 (Tab1), row 4 SPOT-RNA, column 9: ArchiveII Recall; Table 1 (Tab1), row 5 MXfold2, column 9: ArchiveII Recall; Table 1 (Tab1), row 6 ContextFold, column 9: ArchiveII Recall; Table 1 (Tab1), row 7 CONTRAfold, column 9: ArchiveII Recall; Table 1 (Tab1), row 8 EternaFold, column 9: ArchiveII Recall; Table 1 (Tab1), row 9 LinearFold, column 9: ArchiveII Recall; Table 1 (Tab1), row 10 RNAfold, column 9: ArchiveII Recall; Table 1 (Tab1), row 11 SimFold, column 9: ArchiveII Recall; Table 1 (Tab1), row 12 RNAstructure, column 9: ArchiveII 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; id: bpfold-2025-tab2-rfam12-3-14-10-inf; title: Rfam12.3–14.10 · INF; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: INF; unit: unitless; direction: higher; result ids: paper-result-bc33c532295af7b251; paper-result-d3521184aa90f4092f; paper-result-625df7ddcc5441ab69; paper-result-ae0e3455f6b89e6f70; paper-result-57fc7701f0c9da77d0; paper-result-26e74e5c77ce1570a9; paper-result-ad4f1a6205fecd1b6d; paper-result-d197148a19effcf018; paper-result-68b0000887cc4b5e80; paper-result-853e1b3f8354ef0290; source ids: bpfold-2025; 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; context: Family-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-tab2-rfam12-3-14-10-f1; title: Rfam12.3–14.10 · F1; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: F1; unit: unitless; direction: higher; result ids: paper-result-d8fb52a660fba363da; paper-result-3019f81982dc6332cf; paper-result-0ce94efc1ed30c3769; paper-result-a34fce1d750df98700; paper-result-ac79fb8c90b25f7318; paper-result-3db670da1582c96f89; paper-result-f60a9b4fba0bdd5bca; paper-result-5c3a3c43a76fcaeb84; paper-result-7f0004110bb610598b; paper-result-31c527dabf4e1f6958; source ids: bpfold-2025; 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 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 4 SPOT-RNA, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 5 MXfold2, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 6 ContextFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 7 CONTRAfold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 8 EternaFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 9 LinearFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 10 RNAfold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 11 SimFold, column 3: Rfam12.3–14.10 F1; Table 2 (Tab2), row 12 RNAstructure, column 3: Rfam12.3–14.10 F1; context: Family-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-tab2-rfam12-3-14-10-precision; title: Rfam12.3–14.10 · Precision; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-4c05190191ba52c1d1; paper-result-22774caf06553a0120; paper-result-03b61894f52b9f6a21; paper-result-39a55efc7440a14e65; paper-result-c859a2ad30d5982c35; paper-result-d49a44e7ee0390f25d; paper-result-6e6c7831c443afa6ed; paper-result-e59816ecb58e31617e; paper-result-b6a697b1154c255641; paper-result-f3fb35d7219cc3367e; source ids: bpfold-2025; 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 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 4 SPOT-RNA, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 5 MXfold2, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 6 ContextFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 7 CONTRAfold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 8 EternaFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 9 LinearFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 10 RNAfold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 11 SimFold, column 4: Rfam12.3–14.10 Precision; Table 2 (Tab2), row 12 RNAstructure, column 4: Rfam12.3–14.10 Precision; context: Family-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-tab2-rfam12-3-14-10-recall; title: Rfam12.3–14.10 · Recall; protocol id: paper-protocol-4c3af10c18f615709d; dataset id: paper-dataset-816ebb930725137655; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-399712a182e4786639; paper-result-c824c3c83e5e451637; paper-result-a1f081e3b661ff4c25; paper-result-99b4cc2229fcdd0626; paper-result-0c3b54bf620bf11af3; paper-result-b94255fbaa7ff64d55; paper-result-453956286dc654a2fc; paper-result-30d6b97036164e9290; paper-result-c7d3e722ba9b016c03; paper-result-975ccfae7d5107a44a; source ids: bpfold-2025; 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 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 4 SPOT-RNA, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 5 MXfold2, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 6 ContextFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 7 CONTRAfold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 8 EternaFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 9 LinearFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 10 RNAfold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 11 SimFold, column 5: Rfam12.3–14.10 Recall; Table 2 (Tab2), row 12 RNAstructure, column 5: Rfam12.3–14.10 Recall; context: Family-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-tab2-pdb-inf; title: PDB · INF; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: INF; unit: unitless; direction: higher; result ids: paper-result-97b54396c089187bac; paper-result-5465552e8e451ecd56; paper-result-e465e8b97a72acc635; paper-result-d1041275466a1cb1ae; paper-result-3d0a9108d41aebb9db; paper-result-3ddc4380f7d4e8cc34; paper-result-738dbc58785cabadb7; paper-result-c2cbc18894bd07f1a6; paper-result-155bc3cd1981f1e9fd; paper-result-cfbfd2a82ace58ed84; source ids: bpfold-2025; 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; context: Family-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-tab2-pdb-f1; title: PDB · F1; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: F1; unit: unitless; direction: higher; result ids: lit-011; paper-result-57c0ff7b77a652ab1c; paper-result-3d2877af386639e0ad; paper-result-4ae34e1cc310c60554; paper-result-b6a3c4b03b40732ef2; paper-result-96d2c93b67543eaa47; paper-result-9440f5e0b35b26980b; lit-012; paper-result-fda0f45ba9232f7233; paper-result-c35bfeb0f7fc67fda6; source ids: bpfold-2025; 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 7: PDB F1; Table 2 (Tab2), row 4 SPOT-RNA, column 7: PDB F1; Table 2 (Tab2), row 5 MXfold2, column 7: PDB F1; Table 2 (Tab2), row 6 ContextFold, column 7: PDB F1; Table 2 (Tab2), row 7 CONTRAfold, column 7: PDB F1; Table 2 (Tab2), row 8 EternaFold, column 7: PDB F1; Table 2 (Tab2), row 9 LinearFold, column 7: PDB F1; Table 2 (Tab2), row 10 RNAfold, column 7: PDB F1; Table 2 (Tab2), row 11 SimFold, column 7: PDB F1; Table 2 (Tab2), row 12 RNAstructure, column 7: PDB F1; context: Family-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-tab2-pdb-precision; title: PDB · Precision; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: Precision; unit: unitless; direction: higher; result ids: paper-result-8319fb26cf3f85d194; paper-result-eac4aa84532a86e39b; paper-result-b6a55e179b51c6398e; paper-result-5ae72ffe6dc5e67fcd; paper-result-d4877662e8f67af294; paper-result-49bafa3b1c623a5f8d; paper-result-c96dd6eb50a381f576; paper-result-2d080d038082cd24e2; paper-result-ddafb4472501414293; paper-result-c9d2c92f2b018f5062; source ids: bpfold-2025; 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 8: PDB Precision; Table 2 (Tab2), row 4 SPOT-RNA, column 8: PDB Precision; Table 2 (Tab2), row 5 MXfold2, column 8: PDB Precision; Table 2 (Tab2), row 6 ContextFold, column 8: PDB Precision; Table 2 (Tab2), row 7 CONTRAfold, column 8: PDB Precision; Table 2 (Tab2), row 8 EternaFold, column 8: PDB Precision; Table 2 (Tab2), row 9 LinearFold, column 8: PDB Precision; Table 2 (Tab2), row 10 RNAfold, column 8: PDB Precision; Table 2 (Tab2), row 11 SimFold, column 8: PDB Precision; Table 2 (Tab2), row 12 RNAstructure, column 8: PDB Precision; context: Family-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-tab2-pdb-recall; title: PDB · Recall; protocol id: paper-protocol-b8acf180ccd3e67923; dataset id: reported-dataset-8317793f18b026; metric: Recall; unit: unitless; direction: higher; result ids: paper-result-5afb76a439dd9677b9; paper-result-3ad0144bc78eae6759; paper-result-01efc77bc3fe0c8593; paper-result-5fe58d35cc68e79078; paper-result-11126a2ff54dbf3afb; paper-result-a45e9b5b53f964bd93; paper-result-8828c8e20f56d3d354; paper-result-6f6f94f1d2e661baac; paper-result-a7667b03bef3a87b94; paper-result-c0cf50ee8c90573ad2; source ids: bpfold-2025; 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 9: PDB Recall; Table 2 (Tab2), row 4 SPOT-RNA, column 9: PDB Recall; Table 2 (Tab2), row 5 MXfold2, column 9: PDB Recall; Table 2 (Tab2), row 6 ContextFold, column 9: PDB Recall; Table 2 (Tab2), row 7 CONTRAfold, column 9: PDB Recall; Table 2 (Tab2), row 8 EternaFold, column 9: PDB Recall; Table 2 (Tab2), row 9 LinearFold, column 9: PDB Recall; Table 2 (Tab2), row 10 RNAfold, column 9: PDB Recall; Table 2 (Tab2), row 11 SimFold, column 9: PDB Recall; Table 2 (Tab2), row 12 RNAstructure, column 9: PDB Recall; context: Family-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: evidence-expansion-bpfold-2025-976218bd; inspected locators: BPfold Tables 1–2; Methods, Evaluation metrics; searched queries: Deep generalizable prediction of RNA secondary structure via base pair motif energy 10.1038/s41467-025-60048-1; gaps: None recorded; 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.
historical missing metadata: protocol version: not_yet_extracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: This record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: src-discovery-terry-r123-rnabenchmark; src-discovery-ml4bio-rna-fm; source locator: BEACON README: Tasks and Datasets; RNA-FM README: secondary structure prediction and foundation-model outputs; ambiguities: None recorded

Related records

evaluates task: bpRNA-TS0 (RNA secondary structure)
evaluates task: Rfam12.3–14.10 (RNA secondary structure)
evaluates task: PDB (RNA secondary structure)
evaluates task: ArchiveII (RNA secondary structure)

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