Result

F1 of BPfold on PDB RNA set

0.814 F1

Methods

Tested configuration: BPfold
Protocol: PDB (RNA secondary structure)
Dataset: PDB RNA set
Procedure: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
Evaluation: BPfold: RNA secondary structure
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not yet extracted
Evidence: Author-reported evaluation · source checkedDeep generalizable prediction of RNA secondary structure via base pair motif energy · Table 2, BPfold row, PDB F1 column

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: needs review. Source checked does not mean independently reproduced.

Reproduction

Split: Family-wise RNA secondary-structure evaluation; macro-average canonical base-pair metrics.
Adaptation: five-fold cross-validation; early stopping
Scoring implementation: Not reported

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Metric direction higher Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 2 (Tab2), row 3 BPfold, column 7: PDB F1 Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked ["automated-source-review"] · 2026-09-17 author reported Audit details Field: `attributes.metric_direction` Claim: paper-claim-bf082765830f25cd12 Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Printed value 0.814 Individual claims	Deep generalizable prediction of RNA secondary structure via base pair motif energy Original source ↗ Table 2, BPfold row, PDB F1 column Version: version of record Retrieved: 2026-09-16T10:41:16.502000+00:00	source checked ["ai-assisted-source-review"] · 2026-09-16T10:41:16.502000+00:00 author reported Audit details PDB is the second four-metric block; its F1 is numeric column six, not Rfam F1. This verifies the central score at its source location, not every metadata field or an experimental reproduction. Field: `attributes.printed_value` Claim: claim-lit-011 Source artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af` Extraction artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record 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: lit-011

areas: rna-transcriptomes
tasks: RNA secondary structure
printed value: 0.814
numeric value: 0.814
metric: f1-score
metric direction: higher
unit: unitless
source locator: Table 2, BPfold row, PDB F1 column
review: method: ai-assisted-source-review; reviewer: codex; reviewed at: 2026-09-16T10:41:16.502000+00:00; evidence: {"table_xml_id": "Tab2", "row_cells": ["BPfold", "0.694", "0.689", "0.660", "0.741", "0.817", "0.814", "0.840", "0.801"], "selected_cell_zero_based": 6, "selected_cell_xml": "<td colspan=\"1\" rowspan=\"1\">0.814</td>", "caption": "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"}; artifact sha256: 976218bd172998a1a6e7ed1609ecb8cb2ee380fb48a8dc7b25bc05ea8b0a49af; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12216785/fullTextXML; method note: independent; table-level review; reviewer note: role: omics research agent; independent source-table review; not human review; note: PDB is the second four-metric block; its F1 is numeric column six, not Rfam F1. This verifies the central score at its source location, not every metadata field or an experimental reproduction.
legacy id: lit-011
missing metadata: model version: reason: unextracted; split: reason: unextracted; uncertainty: reason: unextracted

Related records

evaluation: BPfold: RNA secondary structure
subject: Reported F1 for BPfold
subject: BPfold · F1 · PDB RNA set: attributes.metric_direction

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