Task

RNA secondary structure

RNA secondary-structure evaluation includes an explicit held-out-family generalization setting.

Sources

RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77

2 evaluations · 2 results

Overview

Datasets

Sources

RNA secondary structure prediction by conducting multi-class classifications · Materials and methods: Experimental settings; Table 1

Metrics

F1 and interaction network fidelity, with overall averages across family evaluations.

Sources

RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77

Allowed inputs

RNA sequence.

Sources

RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77

Evaluation procedure diagram

How it worksComputational evaluation flow

Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.

Sources

RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

2 evaluations · 2 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: TU-Fold (aug)	Task: RNA secondary structure Dataset: RNA8F	0.947 F1 unitless · unknown Uncertainty: ± 0.002 standard deviation Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source TU-Fold (aug): RNA secondary structure Three-fold training and evaluation; source reports mean and standard deviation. Aggregation: Not reported RNA secondary structure prediction by conducting multi-class classifications · Table 2, TU-Fold (aug) row, Overall F1 column
Configuration: UFold	Task: RNA secondary structure Dataset: RNA8F	0.938 F1 unitless · unknown Uncertainty: ± 0.004 standard deviation Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source UFold: RNA secondary structure Three-fold training and evaluation; source reports mean and standard deviation. Aggregation: Not reported RNA secondary structure prediction by conducting multi-class classifications · Table 2, UFold row, Overall F1 column

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation methodology

RNA8F combines RNAStrAlign, ArchiveII, bpRNA and CRW2, retaining sequences no longer than 500 nucleotides from eight RNA families. Table 1 gives family-by-length counts for training, validation and test subsets. Cross-family experiments train on the other families and test the held-out family. F1 and interaction network fidelity, with overall averages across family evaluations. CONTRAfold, RNAstructure, LinearFold and MXfold2; TU-Fold is also compared with its knowledge-merge variant. Family holdout is separated from ordinary sequence-level evaluation.

Sources

RNA secondary structure prediction by conducting multi-class classifications · Materials and methods: Experimental settings; Table 1; Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77

Recorded evaluations

Each evaluation records what was tested and under which conditions.

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 and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

RNA family and sequence-length imbalance affect pooled performance. Within-family and held-out-family tests are separate regimes; output constraints are part of the prediction procedure.
Sources
RNA secondary structure prediction by conducting multi-class classifications · Materials and methods: Experimental settings; Table 1

Profile review details

Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.

Stable record: reported-task-5ec7581b246ea6

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · 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
Datasets	RNA8F combines RNAStrAlign, ArchiveII, bpRNA and CRW2, retaining sequences no longer than 500 nucleotides from eight RNA families. Table 1 gives family-by-length counts for training, validation and test subsets. Sources RNA secondary structure prediction by conducting multi-class classifications · Materials and methods: Experimental settings; Table 1
Splits	Cross-family experiments train on the other families and test the held-out family. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Metrics	F1 and interaction network fidelity, with overall averages across family evaluations. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Baselines	CONTRAfold, RNAstructure, LinearFold and MXfold2; TU-Fold is also compared with its knowledge-merge variant. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Leakage controls	Family holdout is separated from ordinary sequence-level evaluation. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Uncertainty	The sequence-length-stratified tables report means and standard deviations over three folds. This does not establish a separate interval for every cross-family experiment. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Entity type	Paper-specific computational evaluation protocol. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Organisms	RNA8F combines RNAStrAlign, ArchiveII, bpRNA and CRW2 into eight RNA families. Table 1 stratifies by family and sequence length; the paper does not provide the organism distribution of the processed train/validation/test subsets. Family names are not organism labels. · Not reported in inspected sources Sources RNA secondary structure prediction by conducting multi-class classifications · Materials and methods: Experimental settings; Table 1
Assays	RNA secondary-structure annotations. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Allowed inputs	RNA sequence. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77
Adaptation	Supervised structure learning; cross-family runs train on other families and hold one family out. Sources RNA secondary structure prediction by conducting multi-class classifications · Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77

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. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.

Paper or primary resource	Version	Reference
RNA secondary structure prediction by conducting multi-class classifications	version of record	Read source DOI: 10.1016/j.csbj.2025.04.001

Historical gaps recorded on 2026-09-17

The catalogue now holds 2 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.

Complete raw comparison acquired,11 methods across overall and two length bands; means/SD preserved. F1/INF and precision/recall separate columns; no aggregate across different length cohorts. Structured extraction pending.

Search and extraction details

source found structured extraction pending

Searches

RNA secondary structure prediction by conducting multi-class classifications primary paper benchmark results

Evidence locations

Tables2–3; three-fold dataset evaluation and length strata

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.

17 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 summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Input: RNA sequence. Evaluation: Cross-family experiments train on the other families and test the held-out family. Readout: F1 and interaction network fidelity, with overall averages across family evaluations. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Computational evaluation flow Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Datasets RNA8F combines RNAStrAlign, ArchiveII, bpRNA and CRW2, retaining sequences no longer than 500 nucleotides from eight RNA families. Table 1 gives family-by-length counts for training, validation and test subsets. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Materials and methods: Experimental settings; Table 1 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits Cross-family experiments train on the other families and test the held-out family. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation Supervised structure learning; cross-family runs train on other families and hold one family out. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Metrics F1 and interaction network fidelity, with overall averages across family evaluations. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Baselines CONTRAfold, RNAstructure, LinearFold and MXfold2; TU-Fold is also compared with its knowledge-merge variant. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Leakage controls Family holdout is separated from ordinary sequence-level evaluation. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Uncertainty The sequence-length-stratified tables report means and standard deviations over three folds. This does not establish a separate interval for every cross-family experiment. Individual claims	RNA secondary structure prediction by conducting multi-class classifications Original source ↗ Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77 Version: version of record Retrieved: 2026-09-16T10:41:16.505799+00:00	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `5aa376d6466daee83fc307baa39fd48da0f185ff30a178624025032d4cbe597d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

View linked audit checks and correction history

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

2 source records and release history

RNA secondary structure prediction by conducting multi-class classifications · Original source · version of record
RNA secondary structure prediction by conducting multi-class classifications · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: reported-task-5ec7581b246ea6

areas: rna-transcriptomes
tasks: RNA secondary structure
entity level: task
version: Not reported
task: RNA secondary structure
scope note: Paper-specific evaluation task; protocol completeness requires further extraction.
benchmark research: review date: 2026-09-17; status: source_found_structured_extraction_pending; primary sources: evidence-expansion-p2-tu-fold-2025-5aa376d6466d; inspected locators: Tables2–3; three-fold dataset evaluation and length strata; searched queries: RNA secondary structure prediction by conducting multi-class classifications primary paper benchmark results; gaps: Complete raw comparison acquired,11 methods across overall and two length bands; means/SD preserved. F1/INF and precision/recall separate columns; no aggregate across different length cohorts. Structured extraction pending.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
historical missing metadata: protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
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 source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: tu-fold-2025; source locator: Methods: Evaluation method; Results: cross-RNA-family evaluation; cached text lines 23–25, 75–77; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.

Related records

dataset: RNA8F
benchmark: TU-Fold (aug): RNA secondary structure
benchmark: UFold: RNA secondary structure

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