mRNABench VEP: Variant effect prediction
Variant effect prediction. Scored with AUPRC (%) on mRNABench VEP. A linear probe over frozen embeddings, scored as the mean over ten random seeds.
Overview
Variant effect prediction. Scored with AUPRC (%) on mRNABench VEP. A linear probe over frozen embeddings, scored as the mean over ten random seeds.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
mRNABench VEP: Variant effect prediction
auprc (percent) · Higher values are better.
mRNABench VEP: Variant effect prediction · mRNABench VEP (mRNABench split)
Evidence origin: Author-reported evaluation.
mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, column(VEP)- Metrics alternate between AUPRC on a percentage scale and Pearson R, so figures in different columns are on different scales.
- Each row is the best checkpoint of a model family, chosen by the authors, not the family's average.
Comparison details and limitations
Every method mRNABench reports on Variant effect prediction, scored with AUPRC (%) on mRNABench VEP.
- Author-reported numbers, source checked but not independently reproduced.
Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 12 of 21 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- 3UTRBERT on mRNABench VEP: Variant effect prediction
- AIDO.RNA on mRNABench VEP: Variant effect prediction
- DNABERT-S on mRNABench VEP: Variant effect prediction
- DNABERT2 on mRNABench VEP: Variant effect prediction
- ERNIE-RNA on mRNABench VEP: Variant effect prediction
- Evo1 on mRNABench VEP: Variant effect prediction
- Evo2 on mRNABench VEP: Variant effect prediction
- Helix-mRNA on mRNABench VEP: Variant effect prediction
- HyenaDNA on mRNABench VEP: Variant effect prediction
- Naive Baseline on mRNABench VEP: Variant effect prediction
- Naive Mamba on mRNABench VEP: Variant effect prediction
- NT on mRNABench VEP: Variant effect prediction
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-mrnabench Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 2, column(VEP) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: mrnabench-association-vep Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · 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-task-vep
- areas
- rna-transcriptomes
- tasks
- Variant effect prediction
- metric
- AUPRC (%)
- metric direction
- higher
- dataset
- mRNABench VEP
- protocol
- A linear probe over frozen embeddings, scored as the mean over ten random seeds.
- source locator
- Table 2, column(VEP)
- comparison panels
- id: mrnabench-panel-vep; title: mRNABench VEP: Variant effect prediction; protocol id: mrnabench-task-vep; dataset id: mrnabench-dataset-mrnabench-vep; metric: auprc; unit: percent; direction: higher; result ids: mrnabench-result-naive-baseline-vep-auprc; mrnabench-result-naive-mamba-vep-auprc; mrnabench-result-supervised-cnn-vep-auprc; mrnabench-result-3utrbert-vep-auprc; mrnabench-result-aido-rna-vep-auprc; mrnabench-result-dnabert-s-vep-auprc; mrnabench-result-dnabert2-vep-auprc; mrnabench-result-ernie-rna-vep-auprc; mrnabench-result-evo1-vep-auprc; mrnabench-result-evo2-vep-auprc; mrnabench-result-helix-mrna-vep-auprc; mrnabench-result-hyenadna-vep-auprc; mrnabench-result-nt-vep-auprc; mrnabench-result-orthrus-vep-auprc; mrnabench-result-rna-fm-vep-auprc; mrnabench-result-rna-msm-vep-auprc; mrnabench-result-rnabert-vep-auprc; mrnabench-result-rnaernie-vep-auprc; mrnabench-result-rinalmo-vep-auprc; mrnabench-result-splicebert-vep-auprc; mrnabench-result-utr-lm-vep-auprc; source ids: expansion-p3-mrnabench-2025; source locator: Table 2, column(VEP); context: Every method mRNABench reports on Variant effect prediction, scored with AUPRC (%) on mRNABench VEP.; caveats: Author-reported numbers, source checked but not independently reproduced.; Metrics alternate between AUPRC on a percentage scale and Pearson R, so figures in different columns are on different scales.; Each row is the best checkpoint of a model family, chosen by the authors, not the family's average.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: mRNABench
- subject: mRNABench VEP: part of discovery-benchmark-mrnabench
- benchmark: 3UTRBERT on mRNABench VEP: Variant effect prediction
- benchmark: AIDO.RNA on mRNABench VEP: Variant effect prediction
- benchmark: DNABERT-S on mRNABench VEP: Variant effect prediction
- benchmark: DNABERT2 on mRNABench VEP: Variant effect prediction
- benchmark: ERNIE-RNA on mRNABench VEP: Variant effect prediction
- benchmark: Evo1 on mRNABench VEP: Variant effect prediction
- benchmark: Evo2 on mRNABench VEP: Variant effect prediction
- benchmark: Helix-mRNA on mRNABench VEP: Variant effect prediction
- benchmark: HyenaDNA on mRNABench VEP: Variant effect prediction
- benchmark: Naive Baseline on mRNABench VEP: Variant effect prediction
- benchmark: Naive Mamba on mRNABench VEP: Variant effect prediction
- benchmark: NT on mRNABench VEP: Variant effect prediction
- benchmark: Orthrus on mRNABench VEP: Variant effect prediction
- benchmark: RiNALMo on mRNABench VEP: Variant effect prediction
- benchmark: RNA-FM on mRNABench VEP: Variant effect prediction
- benchmark: RNA-MSM on mRNABench VEP: Variant effect prediction
- benchmark: RNABERT on mRNABench VEP: Variant effect prediction
- benchmark: RNAErnie on mRNABench VEP: Variant effect prediction
- benchmark: SpliceBERT on mRNABench VEP: Variant effect prediction
- benchmark: Supervised CNN on mRNABench VEP: Variant effect prediction
- benchmark: UTR-LM on mRNABench VEP: Variant effect prediction