Source

Benchmarking DNA large language models on quadruplexes

2025 · version of record · Peer-reviewed

DOI: 10.1016/j.csbj.2025.03.007 Original source

What this source contributed

Records in this release that cite this source. A record can cite several sources.

2 configurations
1 task
1 dataset
2 evaluations
2 results
3 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Model or configuration	Metric	Value	Dataset	Evaluation
Caduceus	Accuracy	95.0 percent	KEx	Caduceus: G-quadruplex classification
DNABERT-2	Accuracy	97.0 percent	KEx	DNABERT-2: G-quadruplex classification

Claims

Statements this source supports, each with where in the source it was checked.

DNABERT-2: family DNABERT-2: Family DNABERT-2 (Cited primary paper comparison table and DNABERT-2 methods; official DNABERT-2 README; source-labelled configuration DNABERT-2 | Existing reviewed locator: Discussion and conclusions (paragraph 6); Results/LLM performance at the genome-wide level (paragraph 4))
Reported Accuracy for Caduceus: Printed value 95.0 (Table 5, Caduceus (8 M) row, Accuracy column)
Reported Accuracy for DNABERT-2: Printed value 97.0 (Table 5, DNABERT-2 (117 M) row, Accuracy column)

Models, benchmarks and other records

Configurations (2)

Tasks (1)

G-quadruplex classification

Datasets (1)

Evaluations (2)

Evidence

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Evidence table

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18 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
Artifact retrieved at 2026-09-16T10:33:35.379Z Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_retrieved_at` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact SHA-256 c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11953744/fullTextXML Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Doi 10.1016/j.csbj.2025.03.007 Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Missing metadata: licence: reason unextracted Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.missing_metadata.licence.reason` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Publication status peer_reviewed Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-09-15T23:25:00Z Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Scope decision included Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.scope_decision` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Url https://pmc.ncbi.nlm.nih.gov/articles/PMC11953744/ Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version version of record Source metadata	Benchmarking DNA large language models on quadruplexes Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: discovered

Primary paper retained with its original identifier. Metadata inherited from the literature collection; individual result checks are separate.

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Technical metadata and extraction receipts

Stable ID: quadruplex-llm-benchmark-2025

areas: dna-genomes
url: https://pmc.ncbi.nlm.nih.gov/articles/PMC11953744/
version: version of record
retrieved at: 2026-09-15T23:25:00Z
doi: 10.1016/j.csbj.2025.03.007
publication status: peer_reviewed
year: 2025
artifact sha256: c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11953744/fullTextXML
artifact retrieved at: 2026-09-16T10:33:35.379Z
scope decision: included
missing metadata: licence: reason: unextracted

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