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.
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71 evaluations · 71 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: 3UTRBERT | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 31.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and source3UTRBERT on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(3UTRBERT), column(VEP) |
| Configuration: AIDO.RNA | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 30.4% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAIDO.RNA on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(AIDO.RNA), column(VEP) |
| Configuration: DNABERT-S | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 30.6% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-S on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(DNABERT-S), column(VEP) |
| Configuration: DNABERT2 | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 26.4% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT2 on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(DNABERT2), column(VEP) |
| Configuration: ERNIE-RNA | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 28.9% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceERNIE-RNA on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(ERNIE-RNA), column(VEP) |
| Configuration: Evo1 | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 12% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEvo1 on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Evo1), column(VEP) |
| Configuration: Evo2 | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 32.1% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEvo2 on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Evo2), column(VEP) |
| Configuration: Helix-mRNA | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 7.6% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHelix-mRNA on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Helix-mRNA), column(VEP) |
| Configuration: HyenaDNA | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 23.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHyenaDNA on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(HyenaDNA), column(VEP) |
| Method: Naive Baseline | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 19.5% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNaive Baseline on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Naive Baseline), column(VEP) |
| Method: Naive Mamba | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 10.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNaive Mamba on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Naive Mamba), column(VEP) |
| Configuration: NT | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 31.8% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(NT), column(VEP) |
| Configuration: Orthrus | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 27% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOrthrus on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Orthrus), column(VEP) |
| Configuration: RiNALMo | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 31.6% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRiNALMo on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RiNALMo), column(VEP) |
| Configuration: RNA-FM | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 25.7% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRNA-FM on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(VEP) |
| Configuration: RNA-MSM | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 16.5% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRNA-MSM on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-MSM), column(VEP) |
| Configuration: RNABERT | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 19.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRNABERT on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(VEP) |
| Configuration: RNAErnie | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 17.3% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRNAErnie on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNAErnie), column(VEP) |
| Configuration: SpliceBERT | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 28.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSpliceBERT on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(SpliceBERT), column(VEP) |
| Method: Supervised CNN | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 33.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(Supervised CNN), column(VEP) |
| Configuration: UTR-LM | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 21.3% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTR-LM on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(UTR-LM), column(VEP) |
| Pipeline: aido-rna-1b600m-cds | Protocol: mRNABench variant probes VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 0.304 ± 0.029 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.029; aggregation: mean over ten random splits (table caption wording) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceaido-rna-1b600m-cds on mRNABench variant probes VEP: Variant effect prediction Frozen transcript representations with task-specific linear probes, or named supervised/naive controls. Homology splits where possible; random splits for MRL-MPRA, MRL-HL-Pair and VEP. Reported mean over ten splits; Appendix C enumerates nine seeds. Table captions say ten random splits, while Methods specify homology splits where possible. This source ambiguity and the nine explicitly listed seeds are retained; exact split manifests remain unextracted. Appendix C uses micro-averaged multilabel metrics. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 5 (XML T2), data row 2, XML tr 4, column 6 (VEP | AUPRC), model aido-rna-1b600m-cds |
| Pipeline: aido-rna-1b600m | Protocol: mRNABench variant probes VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 0.316 ± 0.032 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.032; aggregation: mean over ten random splits (table caption wording) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceaido-rna-1b600m on mRNABench variant probes VEP: Variant effect prediction Frozen transcript representations with task-specific linear probes, or named supervised/naive controls. Homology splits where possible; random splits for MRL-MPRA, MRL-HL-Pair and VEP. Reported mean over ten splits; Appendix C enumerates nine seeds. Table captions say ten random splits, while Methods specify homology splits where possible. This source ambiguity and the nine explicitly listed seeds are retained; exact split manifests remain unextracted. Appendix C uses micro-averaged multilabel metrics. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 5 (XML T2), data row 1, XML tr 3, column 6 (VEP | AUPRC), model aido-rna-1b600m |
| Pipeline: aido-rna-650m-cds | Protocol: mRNABench variant probes VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 0.312 ± 0.036 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.036; aggregation: mean over ten random splits (table caption wording) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceaido-rna-650m-cds on mRNABench variant probes VEP: Variant effect prediction Frozen transcript representations with task-specific linear probes, or named supervised/naive controls. Homology splits where possible; random splits for MRL-MPRA, MRL-HL-Pair and VEP. Reported mean over ten splits; Appendix C enumerates nine seeds. Table captions say ten random splits, while Methods specify homology splits where possible. This source ambiguity and the nine explicitly listed seeds are retained; exact split manifests remain unextracted. Appendix C uses micro-averaged multilabel metrics. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 5 (XML T2), data row 4, XML tr 6, column 6 (VEP | AUPRC), model aido-rna-650m-cds |
| Pipeline: aido-rna-650m | Protocol: mRNABench variant probes VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 0.309 ± 0.031 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.031; aggregation: mean over ten random splits (table caption wording) Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceaido-rna-650m on mRNABench variant probes VEP: Variant effect prediction Frozen transcript representations with task-specific linear probes, or named supervised/naive controls. Homology splits where possible; random splits for MRL-MPRA, MRL-HL-Pair and VEP. Reported mean over ten splits; Appendix C enumerates nine seeds. Table captions say ten random splits, while Methods specify homology splits where possible. This source ambiguity and the nine explicitly listed seeds are retained; exact split manifests remain unextracted. Appendix C uses micro-averaged multilabel metrics. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 5 (XML T2), data row 3, XML tr 5, column 6 (VEP | AUPRC), model aido-rna-650m |
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| 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. |
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Stable ID: mrnabench-dataset-mrnabench-vep