DNABERT2: description
Description of DNABERT2
mRNABench evaluation of mature mRNA embeddings from DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, with task scores quoted from prior work in MIMIC Table S11.
Replace a placeholder or provenance description with a sourced functional description (issue #88a). Historical releases retain the original value.
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field description Context-only references | MIMIC v1: Table S11 and Appendix D.3 coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field description Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Claimed field description Context-only references | Abstract: DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv API entry for 2306.15006v2 (title and abstract) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Previous value Prior mRNABench evaluated pipeline, quoted in MIMIC Table S11; not a new execution. Context-only references | MIMIC v1: Table S11 and Appendix D.3 coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Previous value Prior mRNABench evaluated pipeline, quoted in MIMIC Table S11; not a new execution. Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Previous value Prior mRNABench evaluated pipeline, quoted in MIMIC Table S11; not a new execution. Context-only references | Abstract: DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv API entry for 2306.15006v2 (title and abstract) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Context-only references | MIMIC v1: Table S11 and Appendix D.3 coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Source location coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Context-only references | Abstract: DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv API entry for 2306.15006v2 (title and abstract) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed value mRNABench evaluation of mature mRNA embeddings from DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, with task scores quoted from prior work in MIMIC Table S11. Context-only references | MIMIC v1: Table S11 and Appendix D.3 coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
3 source records and release history
- MIMIC v1: Table S11 and Appendix D.3 · Original source · arXiv version 1
- mRNABench: A curated benchmark for mature mRNA property and function prediction · Original source · preprint archived 2025-07-08
- Abstract: DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome · Original source · arXiv API entry for 2306.15006v2 (title and abstract)
Technical metadata and extraction receipts
Stable ID: metadata-correction-b13d281dd497e8554c37
- areas
- rna-transcriptomes
- field
- description
- previous value
- Prior mRNABench evaluated pipeline, quoted in MIMIC Table S11; not a new execution.
- value
- mRNABench evaluation of mature mRNA embeddings from DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, with task scores quoted from prior work in MIMIC Table S11.
- source locator
- coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract
- review
- method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude research agent for issue #88a. Reviewer: separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-10; method note: Compared the description with the cited source text (abstract, README row, benchmark CSV header or full-text section) of re-downloaded artifacts, and previous_value with origin/main.; note: Description written from the cited source text; provenance text moved to attributes.source_locator. Independent review 2026-10-10: every stated fact is supported by the cited text.
Related records
- subject: DNABERT2