Protocol

ArchiveII (RNA secondary structure)

ArchiveII · 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 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

10 evaluations · 40 metric rows

At a glance

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.

Data, procedure and scoring
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.

How it works

Evaluation in this paper

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

Sources

Evaluation design

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

Tasks

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

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Comparison and metric

ArchiveII · INF

INF (unitless) · Higher values are better for this metric.

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

Evaluation protocol · ArchiveII

BPfold · Configuration · Author-reported evaluation0.823
SPOT-RNA · Configuration · Independent external evaluation0.736
MXfold2 · Configuration · Independent external evaluation0.711
ContextFold · Configuration · Independent external evaluation0.820
CONTRAfold · Configuration · Independent external evaluation0.597
EternaFold · Configuration · Independent external evaluation0.601
LinearFold · Configuration · Independent external evaluation0.610
RNAfold · Configuration · Independent external evaluation0.579
SimFold · Configuration · Independent external evaluation0.570
RNAstructure · Configuration · Independent external evaluation0.575

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

Values, uncertainty and evidence

INF: original source values
Tested entity	Printed value	Uncertainty	Evidence
BPfold · Configuration	0.823 unitless	Not reported	Author-reported evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 3 BPfold, column 6: ArchiveII INF
SPOT-RNA · Configuration	0.736 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF
MXfold2 · Configuration	0.711 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF
ContextFold · Configuration	0.820 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF
CONTRAfold · Configuration	0.597 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF
EternaFold · Configuration	0.601 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF
LinearFold · Configuration	0.610 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF
RNAfold · Configuration	0.579 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF
SimFold · Configuration	0.570 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF
RNAstructure · Configuration	0.575 unitless	Not reported	Independent external evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII INF

Scope and limitations

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.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 10 evaluations · 40 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
BPfold: ArchiveII Configuration: BPfoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Author-reported evaluation · Evaluation metadata: needs review
0.823 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 3 BPfold, column 6: ArchiveII INF Source checking is not independent reproduction.
0.834 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 3 BPfold, column 9: ArchiveII Recall Source checking is not independent reproduction.
0.820 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 3 BPfold, column 7: ArchiveII F1 Source checking is not independent reproduction.
ContextFold: ArchiveII Configuration: ContextFoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.824 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 6 ContextFold, column 8: ArchiveII Precision Source checking is not independent reproduction.
RNAfold: ArchiveII Configuration: RNAfoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.577 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 7: ArchiveII F1 Source checking is not independent reproduction.
0.551 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 8: ArchiveII Precision Source checking is not independent reproduction.
0.613 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 10 RNAfold, column 9: ArchiveII Recall Source checking is not independent reproduction.
SPOT-RNA: ArchiveII Configuration: SPOT-RNAProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.730 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 4 SPOT-RNA, column 7: ArchiveII F1 Source checking is not independent reproduction.
0.763 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 4 SPOT-RNA, column 8: ArchiveII Precision Source checking is not independent reproduction.
0.736 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF Source checking is not independent reproduction.
EternaFold: ArchiveII Configuration: EternaFoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.599 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 7: ArchiveII F1 Source checking is not independent reproduction.
0.573 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 8: ArchiveII Precision Source checking is not independent reproduction.
0.601 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF Source checking is not independent reproduction.
0.636 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 8 EternaFold, column 9: ArchiveII Recall Source checking is not independent reproduction.
RNAstructure: ArchiveII Configuration: RNAstructureProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.575 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII INF Source checking is not independent reproduction.
0.573 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 12 RNAstructure, column 7: ArchiveII F1 Source checking is not independent reproduction.
MXfold2: ArchiveII Configuration: MXfold2Protocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.711 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF Source checking is not independent reproduction.
0.697 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 8: ArchiveII Precision Source checking is not independent reproduction.
CONTRAfold: ArchiveII Configuration: CONTRAfoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.594 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 7: ArchiveII F1 Source checking is not independent reproduction.
0.588 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 9: ArchiveII Recall Source checking is not independent reproduction.
0.612 Precision Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 7 CONTRAfold, column 8: ArchiveII Precision Source checking is not independent reproduction.
LinearFold: ArchiveII Configuration: LinearFoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.605 Recall Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 9 LinearFold, column 9: ArchiveII Recall Source checking is not independent reproduction.
0.606 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 9 LinearFold, column 7: ArchiveII F1 Source checking is not independent reproduction.
0.610 INF Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF Source checking is not independent reproduction.
SimFold: ArchiveII Configuration: SimFoldProtocol: ArchiveII (RNA secondary structure)Dataset: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Independent external evaluation · Evaluation metadata: needs review
0.568 F1 Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 11 SimFold, column 7: ArchiveII F1 Source checking is not 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

What is still missing

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 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

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

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-e8a1aa302bb8df1efd

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

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
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 Original source ↗ 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 Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Introduction ArchiveII · 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 Original source ↗ 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 Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: evaluates task catalog-task-rna-secondary-structure Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ 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 Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:catalog-task-rna-secondary-structure` Claim: paper-claim-bce80d3b38bac94c79 Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: evaluates task reported-task-dc82fcbfb44935 Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ 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 Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:reported-task-dc82fcbfb44935` Claim: paper-claim-d7e869186e1572821d Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

1 source records and release history

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: paper-protocol-e8a1aa302bb8df1efd

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-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
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 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; 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 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; ambiguities: None recorded

Related records

evaluates task: RNA secondary structure
evaluates task: RNA secondary structure
subject: ArchiveII (RNA secondary structure): links:evaluates_task:catalog-task-rna-secondary-structure
subject: ArchiveII (RNA secondary structure): links:evaluates_task:reported-task-dc82fcbfb44935
benchmark: ContextFold: ArchiveII
benchmark: CONTRAfold: ArchiveII
benchmark: RNAfold: ArchiveII
benchmark: SPOT-RNA: ArchiveII
benchmark: MXfold2: ArchiveII
benchmark: EternaFold: ArchiveII
benchmark: BPfold: ArchiveII
benchmark: LinearFold: ArchiveII
benchmark: RNAstructure: ArchiveII
benchmark: SimFold: ArchiveII

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