DNABERT2
Embeds mature mRNA with DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, for the mRNABench property prediction tasks.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
7 evaluations · 7 results. Different protocols are not a single leaderboard.
Sorted by AUPRC (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 7 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: DNABERT2 | Protocol: MIMIC mRNABench probes eCLIP: eCLIP prediction Dataset subset: mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split) | 0.371 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDNABERT2 on MIMIC mRNABench probes eCLIP: eCLIP prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 4 (DNABERT2 [ 33 ]), column 2 (eCLIP) |
| Pipeline: DNABERT2 | Protocol: MIMIC mRNABench probes GO: GO prediction Dataset subset: mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split) | 0.326 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDNABERT2 on MIMIC mRNABench probes GO: GO prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 4 (DNABERT2 [ 33 ]), column 3 (GO) |
| Pipeline: DNABERT2 | Protocol: MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction Dataset subset: mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split) | 0.534 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDNABERT2 on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 4 (DNABERT2 [ 33 ]), column 6 (MRL (LBKWK)) |
| Pipeline: DNABERT2 | Protocol: MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction Dataset subset: mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split) | 0.286 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDNABERT2 on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 4 (DNABERT2 [ 33 ]), column 7 (MRL (Sugimoto)) |
| Pipeline: DNABERT2 | Protocol: MIMIC mRNABench probes Protein Localization: Protein Localization prediction Dataset subset: mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split) | 0.325 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDNABERT2 on MIMIC mRNABench probes Protein Localization: Protein Localization prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 4 (DNABERT2 [ 33 ]), column 4 (Protein Localization) |
| Pipeline: DNABERT2 | Protocol: MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction Dataset subset: mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split) | 0.475 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDNABERT2 on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 4 (DNABERT2 [ 33 ]), column 8 (RNA Half Life) |
| Pipeline: DNABERT2 | Protocol: MIMIC mRNABench probes RNA Localization: RNA Localization prediction Dataset subset: mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split) | 0.675 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDNABERT2 on MIMIC mRNABench probes RNA Localization: RNA Localization prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 4 (DNABERT2 [ 33 ]), column 5 (RNA Localization) |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
Use this pipeline
How it works, versions and access
Underlying model: DNABERT-2. Results on this page belong to this pipeline and its evaluated settings.
Evidence
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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.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Embeds mature mRNA with DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, for the mRNABench property prediction tasks. Individual claims | 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 | conflicting claim ["automated-source-review","ai-assisted-source-review"] · 2026-10-10 Audit detailsDescription 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. Conflicting source claim: Field: Claim: metadata-correction-b13d281dd497e8554c37 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Embeds mature mRNA with DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, for the mRNABench property prediction tasks. Individual claims | 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 | conflicting claim ["automated-source-review","ai-assisted-source-review"] · 2026-10-10 Audit detailsDescription 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. Conflicting source claim: Field: Claim: metadata-correction-b13d281dd497e8554c37 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Description Embeds mature mRNA with DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, for the mRNABench property prediction tasks. Individual claims | 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) | conflicting claim ["automated-source-review","ai-assisted-source-review"] · 2026-10-10 Audit detailsDescription 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. Conflicting source claim: Field: Claim: metadata-correction-b13d281dd497e8554c37 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: uses model discovery-model-dnabert-2 Individual claims | MIMIC v1: Table S11 and Appendix D.3 Table S11, row DNABERT2 [ 33 ]; Appendix D.3 Version: arXiv version 1 | source checked ["automated-source-review"] · 2026-09-23 Audit detailsSource-backed evaluated identity only; no independent reproduction. Field: Claim: mimic-2026-mrnabench-method-dnabert2-discovery-model-dnabert-2-identity-claim 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: mimic-2026-mrnabench-method-dnabert2
- areas
- rna-transcriptomes
- source locator
- Table S11, row DNABERT2 [ 33 ]; Appendix D.3; Prior mRNABench evaluated pipeline, quoted in MIMIC Table S11; not a new execution
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
- provenance note
- Task scores quoted from prior work in MIMIC Table S11; not a new execution.
Related records
- uses model: DNABERT-2
- subject: DNABERT2: description
- system: DNABERT2 on MIMIC mRNABench probes eCLIP: eCLIP prediction
- system: DNABERT2 on MIMIC mRNABench probes GO: GO prediction
- system: DNABERT2 on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
- system: DNABERT2 on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
- system: DNABERT2 on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
- system: DNABERT2 on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
- system: DNABERT2 on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
- subject: DNABERT2: uses model discovery-model-dnabert-2