mRNABench VEP (mRNABench split)
The split of mRNABench VEP that mRNABench evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.
Subset and evaluation context
This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.
Evaluation results
Release 2026-09-17-134cd1815de8 · 21 evaluations · 21 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| 3UTRBERT on mRNABench VEP: Variant effect prediction Configuration: 3UTRBERTTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 31.2% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(3UTRBERT), column(VEP) Source checking is not independent reproduction. |
| AIDO.RNA on mRNABench VEP: Variant effect prediction Configuration: AIDO.RNATask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 30.4% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(AIDO.RNA), column(VEP) Source checking is not independent reproduction. |
| DNABERT-S on mRNABench VEP: Variant effect prediction Configuration: DNABERT-STask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 30.6% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(DNABERT-S), column(VEP) Source checking is not independent reproduction. |
| DNABERT2 on mRNABench VEP: Variant effect prediction Configuration: DNABERT2Task: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 26.4% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(DNABERT2), column(VEP) Source checking is not independent reproduction. |
| ERNIE-RNA on mRNABench VEP: Variant effect prediction Configuration: ERNIE-RNATask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 28.9% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(ERNIE-RNA), column(VEP) Source checking is not independent reproduction. |
| Evo1 on mRNABench VEP: Variant effect prediction Configuration: Evo1Task: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 12.0% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Evo1), column(VEP) Source checking is not independent reproduction. |
| Evo2 on mRNABench VEP: Variant effect prediction Configuration: Evo2Task: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 32.1% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Evo2), column(VEP) Source checking is not independent reproduction. |
| Helix-mRNA on mRNABench VEP: Variant effect prediction Configuration: Helix-mRNATask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 7.6% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Helix-mRNA), column(VEP) Source checking is not independent reproduction. |
| HyenaDNA on mRNABench VEP: Variant effect prediction Configuration: HyenaDNATask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 23.2% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(HyenaDNA), column(VEP) Source checking is not independent reproduction. |
| Naive Baseline on mRNABench VEP: Variant effect prediction Method: Naive BaselineTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 19.5% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Naive Baseline), column(VEP) Source checking is not independent reproduction. |
| Naive Mamba on mRNABench VEP: Variant effect prediction Method: Naive MambaTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 10.2% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Naive Mamba), column(VEP) Source checking is not independent reproduction. |
| NT on mRNABench VEP: Variant effect prediction Configuration: NTTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 31.8% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(NT), column(VEP) Source checking is not independent reproduction. |
| Orthrus on mRNABench VEP: Variant effect prediction Configuration: OrthrusTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 27.0% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Orthrus), column(VEP) Source checking is not independent reproduction. |
| RiNALMo on mRNABench VEP: Variant effect prediction Configuration: RiNALMoTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 31.6% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RiNALMo), column(VEP) Source checking is not independent reproduction. |
| RNA-FM on mRNABench VEP: Variant effect prediction Configuration: RNA-FMTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 25.7% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(VEP) Source checking is not independent reproduction. |
| RNA-MSM on mRNABench VEP: Variant effect prediction Configuration: RNA-MSMTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 16.5% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-MSM), column(VEP) Source checking is not independent reproduction. |
| RNABERT on mRNABench VEP: Variant effect prediction Configuration: RNABERTTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 19.2% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(VEP) Source checking is not independent reproduction. |
| RNAErnie on mRNABench VEP: Variant effect prediction Configuration: RNAErnieTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 17.3% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNAErnie), column(VEP) Source checking is not independent reproduction. |
| SpliceBERT on mRNABench VEP: Variant effect prediction Configuration: SpliceBERTTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 28.2% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(SpliceBERT), column(VEP) Source checking is not independent reproduction. |
| Supervised CNN on mRNABench VEP: Variant effect prediction Method: Supervised CNNTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 33.2% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Supervised CNN), column(VEP) Source checking is not independent reproduction. |
| UTR-LM on mRNABench VEP: Variant effect prediction Configuration: UTR-LMTask: mRNABench VEP: Variant effect predictionDataset subset: mRNABench VEP (mRNABench split) A linear probe over frozen embeddings, scored as the mean over ten random seeds. Author-reported evaluation · Evaluation metadata: source checked | ||
| 21.3% auprc Unit: percent · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(UTR-LM), column(VEP) Source checking is not 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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description The split of mRNABench VEP that mRNABench evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits. Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction No field-specific location recorded 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. |
| name mRNABench VEP (mRNABench split) Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction No field-specific location recorded 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. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- mRNABench: A curated benchmark for mature mRNA property and function prediction · Original source · preprint archived 2025-07-08
Technical metadata and extraction receipts
Stable ID: mrnabench-dataset-mrnabench-vep
- areas
- rna-transcriptomes
- missing metadata
- version: unreported; url: unextracted
Related records
- dataset: 3UTRBERT on mRNABench VEP: Variant effect prediction
- dataset: AIDO.RNA on mRNABench VEP: Variant effect prediction
- dataset: DNABERT-S on mRNABench VEP: Variant effect prediction
- dataset: DNABERT2 on mRNABench VEP: Variant effect prediction
- dataset: ERNIE-RNA on mRNABench VEP: Variant effect prediction
- dataset: Evo1 on mRNABench VEP: Variant effect prediction
- dataset: Evo2 on mRNABench VEP: Variant effect prediction
- dataset: Helix-mRNA on mRNABench VEP: Variant effect prediction
- dataset: HyenaDNA on mRNABench VEP: Variant effect prediction
- dataset: Naive Baseline on mRNABench VEP: Variant effect prediction
- dataset: Naive Mamba on mRNABench VEP: Variant effect prediction
- dataset: NT on mRNABench VEP: Variant effect prediction
- dataset: Orthrus on mRNABench VEP: Variant effect prediction
- dataset: RiNALMo on mRNABench VEP: Variant effect prediction
- dataset: RNA-FM on mRNABench VEP: Variant effect prediction
- dataset: RNA-MSM on mRNABench VEP: Variant effect prediction
- dataset: RNABERT on mRNABench VEP: Variant effect prediction
- dataset: RNAErnie on mRNABench VEP: Variant effect prediction
- dataset: SpliceBERT on mRNABench VEP: Variant effect prediction
- dataset: Supervised CNN on mRNABench VEP: Variant effect prediction
- dataset: UTR-LM on mRNABench VEP: Variant effect prediction