Configuration

MXfold2

MXfold2 as evaluated in the cited study. version 0.1.2

Sources

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF

4 evaluations · 16 results

Overview

Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.

limited source coverage · Automated source review, 2026-09-17. All specifications and missing details

Evaluations and results

4 evaluations · 16 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MXfold2	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.733 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 9: PDB Recall
Configuration: MXfold2	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.632 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 4: Rfam12.3–14.10 Precision
Configuration: MXfold2	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.664 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 3: Rfam12.3–14.10 F1
Configuration: MXfold2	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.777 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 7: PDB F1
Configuration: MXfold2	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.711 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF
Configuration: MXfold2	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.697 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 8: ArchiveII Precision
Configuration: MXfold2	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.67 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF
Configuration: MXfold2	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.587 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF
Configuration: MXfold2	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.682 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 5: bpRNA-TS0 Recall
Configuration: MXfold2	Protocol: Rfam12.3–14.10 (RNA secondary structure) Dataset: Rfam12.3–14.10	0.72 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: Rfam12.3–14.10 Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 5: Rfam12.3–14.10 Recall
Configuration: MXfold2	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.575 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 3: bpRNA-TS0 F1
Configuration: MXfold2	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.709 F1 unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 7: ArchiveII F1
Configuration: MXfold2	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.842 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 8: PDB Precision
Configuration: MXfold2	Protocol: bpRNA-TS0 (RNA secondary structure) Dataset: bpRNA-TS0	0.521 Precision unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: bpRNA-TS0 Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 4: bpRNA-TS0 Precision
Configuration: MXfold2	Protocol: ArchiveII (RNA secondary structure) Dataset: ArchiveII	0.728 Recall unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: ArchiveII Sequence-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 9: ArchiveII Recall
Configuration: MXfold2	Protocol: PDB (RNA secondary structure) Dataset: PDB RNA set	0.782 INF unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MXfold2: PDB Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics. Aggregation: Not reported Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF

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

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How it works

Evaluation in this paper

version 0.1.2

Sources

Deep generalizable prediction of RNA secondary structure via base pair motif energy · Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF

Strengths, limitations and unresolved questions

Strengths and limitations

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Stable record: paper-model-eb6ed1e9fd7641220d

Specifications

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.

Inputs, outputs and configuration
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Evidence

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Evidence table

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2 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
Evaluation in this paper version 0.1.2 Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 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 MXfold2 as evaluated in the cited study. version 0.1.2 Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 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

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

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Technical metadata and extraction receipts

Stable ID: paper-model-eb6ed1e9fd7641220d

areas: rna-transcriptomes
tasks: RNA secondary structure
entity level: method
configuration type: reported_configuration
version: version 0.1.2
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: bpfold-2025; source locator: Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

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