Configuration

DNABERT-2

This genomic model is adapted to predict G-quadruplex-associated sequence regions.

Sources

Benchmarking DNA large language models on quadruplexes · Discussion and conclusions (paragraph 6); Results/LLM performance at the genome-wide level (paragraph 4)

1 evaluation · 1 result

How it worksEvaluated procedure (conceptual)

Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.

Sources

Benchmarking DNA large language models on quadruplexes · Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2)

Overview

Model type

DNA sequence transformer; this record is the paper-specific evaluated configuration.

Sources

MAGICS-LAB/DNABERT_2 README.md · README.md model description

Biological inputs

DNA sequences for G-quadruplex classification and genomic scanning

Sources

Benchmarking DNA large language models on quadruplexes · Results/LLM comparison on quadruplex datasets (paragraph 1); Materials and methods/Data preparation (paragraph 1)

Outputs

G4-associated sequence predictions

Sources

Benchmarking DNA large language models on quadruplexes · Introduction (paragraph 3); CRediT authorship contribution statement (paragraph 1)

Access

Official upstream implementation and usage documentation: https://github.com/MAGICS-LAB/DNABERT_2/blob/f25bed9ee20db966dff39e5c1571249d04e36404/README.md. This pinned documentation revision is not automatically the evaluated weight revision.

Sources

MAGICS-LAB/DNABERT_2 README.md · README.md; installation, model download and usage instructions

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

Evaluations and results

1 evaluation · 1 result. 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: DNABERT-2	Task: G-quadruplex classification Dataset: KEx	97 Accuracy % · unknown Uncertainty: ± 0.5 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2: G-quadruplex classification Pretrained model evaluated on KEx as reported in Table 5. Aggregation: Not reported Benchmarking DNA large language models on quadruplexes · Table 5, DNABERT-2 (117 M) row, Accuracy column

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

Use this model

How it works, versions and access

Related profile: DNABERT-2. This page retains the exact record and its evaluation context.

How it works

How the evaluated method works

The study fine-tunes genomic sequence models for G4 classification and applies them to whole-genome annotation, retaining each model’s native tokenisation.

Sources

Benchmarking DNA large language models on quadruplexes · Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2)

Underlying method and version boundaries

DNABERT-2 replaces overlapping k-mer tokens with byte-pair encoding and uses ALiBi positional biases. The official 117M model produces 768-dimensional token representations; downstream classifiers and pooling choices are separate configuration details.

Sources

MAGICS-LAB/DNABERT_2 README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revision

What was evaluated

The linked evaluation record identifies DNABERT-2: G-quadruplex classification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

Benchmarking DNA large language models on quadruplexes · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-005

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Compares transformer, long-convolution and state-space architectures on a specialised non-B-DNA task.
Sources
Benchmarking DNA large language models on quadruplexes · Introduction (paragraph 1); Abstract (paragraph 1)

Limitations and conditions

Predicted G4 sequence potential is not a direct measurement of structure formation in a particular cellular context.
Sources
Benchmarking DNA large language models on quadruplexes · Introduction (paragraph 6); Discussion and conclusions (paragraph 1)

Profile review details

Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.

Stable record: reported-model-ade36035f58f27

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.

Inputs, outputs and configuration
Property	Description and evidence
Model type	DNA sequence transformer; this record is the paper-specific evaluated configuration. Sources MAGICS-LAB/DNABERT_2 README.md · README.md model description
Architecture / procedure	The study fine-tunes genomic sequence models for G4 classification and applies them to whole-genome annotation, retaining each model’s native tokenisation. Sources Benchmarking DNA large language models on quadruplexes · Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2)
Biological inputs	DNA sequences for G-quadruplex classification and genomic scanning Sources Benchmarking DNA large language models on quadruplexes · Results/LLM comparison on quadruplex datasets (paragraph 1); Materials and methods/Data preparation (paragraph 1)
Outputs	G4-associated sequence predictions Sources Benchmarking DNA large language models on quadruplexes · Introduction (paragraph 3); CRediT authorship contribution statement (paragraph 1)
Parameters	117 million parameters, as identified for this row Sources Benchmarking DNA large language models on quadruplexes · Materials and methods/Low Rank Adaptation (LoRA) (paragraph 1); Discussion and conclusions (paragraph 3)
Known versions / configuration	117M Sources Benchmarking DNA large language models on quadruplexes · Table tbl0030 (paragraph 1); Table tbl0025 (paragraph 1)
Training data / fitting	Task-specific fine-tuning for approximately four to ten epochs, depending on model performance, with gradient accumulation. Sources Benchmarking DNA large language models on quadruplexes · Results/LLM comparison on quadruplex datasets (paragraph 5); Materials and methods/Fine-tuning (paragraph 1)
Context limits	A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sources Sources (2) Benchmarking DNA large language models on quadruplexes; MAGICS-LAB/DNABERT_2 README.md · Materials and methods/Data preparation; Materials and methods/Tokenization for G4s; Materials and methods/Metrics of evaluation; Materials and methods/Fine-tuning; Materials and methods/Low Rank Adaptation (LoRA); inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision
Access	Official upstream implementation and usage documentation: https://github.com/MAGICS-LAB/DNABERT_2/blob/f25bed9ee20db966dff39e5c1571249d04e36404/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources MAGICS-LAB/DNABERT_2 README.md · README.md; installation, model download and usage instructions
Code licence	Apache 2.0 (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence). Sources MAGICS-LAB/DNABERT_2 LICENSE · LICENSE; complete licence text
Weights licence	The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sources Sources MAGICS-LAB/DNABERT_2 README.md · README.md; checkpoint/access documentation and licence scope

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.

24 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 input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps DNA sequences for G-quadruplex classification and genomic scanning DNABERT-2 G4-associated sequence predictions Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type DNA sequence transformer; this record is the paper-specific evaluated configuration. Individual claims	MAGICS-LAB/DNABERT_2 README.md Original source ↗ README.md model description Version: f25bed9ee20db966dff39e5c1571249d04e36404 Retrieved: 2026-09-16T20:00:02.624261+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `734a8cec5f667d74d421bf3b273ad7e256216109636da45aa7ceba21cd34de16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure The study fine-tunes genomic sequence models for G4 classification and applies them to whole-genome annotation, retaining each model’s native tokenisation. Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims	MAGICS-LAB/DNABERT_2 README.md Original source ↗ README.md; checkpoint/access documentation and licence scope Version: f25bed9ee20db966dff39e5c1571249d04e36404 Retrieved: 2026-09-16T20:00:02.624261+00:00	unreported automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `734a8cec5f667d74d421bf3b273ad7e256216109636da45aa7ceba21cd34de16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs DNA sequences for G-quadruplex classification and genomic scanning Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Results/LLM comparison on quadruplex datasets (paragraph 1); Materials and methods/Data preparation (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs G4-associated sequence predictions Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Introduction (paragraph 3); CRediT authorship contribution statement (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters 117 million parameters, as identified for this row Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Materials and methods/Low Rank Adaptation (LoRA) (paragraph 1); Discussion and conclusions (paragraph 3) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Known versions / configuration 117M Individual claims	Benchmarking DNA large language models on quadruplexes Original source ↗ Table tbl0030 (paragraph 1); Table tbl0025 (paragraph 1) Version: version of record Retrieved: 2026-09-16T10:33:35.379Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `c3d7c6d068d3c11a9c8255a932197ece3804d94e8b2d4f858bea373a1b6eb32f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

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

3 source records and release history

Benchmarking DNA large language models on quadruplexes · Original source · version of record
MAGICS-LAB/DNABERT_2 README.md · Original source · f25bed9ee20db966dff39e5c1571249d04e36404
MAGICS-LAB/DNABERT_2 LICENSE · Original source · f25bed9ee20db966dff39e5c1571249d04e36404

Download this release

Technical metadata and extraction receipts

Stable ID: reported-model-ade36035f58f27

areas: dna-genomes
entity level: method
version: 117M
reported name: DNABERT-2
historical missing metadata: checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: 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: 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: quadruplex-llm-benchmark-2025; evidence-reported-base-dnabert2-readme-md; source locator: Materials and methods/Data preparation (paragraph 2); Results/Interpretation of LLMs (paragraph 2) | README.md model description | Discussion and conclusions (paragraph 6); Results/LLM performance at the genome-wide level (paragraph 4); 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.

Related records

family: DNABERT-2
model: DNABERT-2: G-quadruplex classification
subject: DNABERT-2: family DNABERT-2

Suggest a correction