The split of mRNABench eCLIP 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 ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 31.1% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and source3UTRBERT on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: AIDO.RNA | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 41.1% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAIDO.RNA on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: DNABERT-S | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 37.4% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-S on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: DNABERT2 | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 37.1% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT2 on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: ERNIE-RNA | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 37.3% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceERNIE-RNA on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: Evo1 | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 26.7% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEvo1 on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: Evo2 | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 47.3% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEvo2 on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: Helix-mRNA | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 29.1% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHelix-mRNA on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: HyenaDNA | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 37.4% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHyenaDNA on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Method: Naive Baseline | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 43.4% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNaive Baseline on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Method: Naive Mamba | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 26.5% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNaive Mamba on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: NT | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 40.5% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNT on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: Orthrus | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 43.6% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOrthrus on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: RiNALMo | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 39.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRiNALMo on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: RNA-FM | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 35% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRNA-FM on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: RNA-MSM | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 28.1% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRNA-MSM on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: RNABERT | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (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 ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: RNAErnie | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 29% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRNAErnie on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: SpliceBERT | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 37.7% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSpliceBERT on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Method: Supervised CNN | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 42% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Configuration: UTR-LM | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 33.7% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTR-LM on mRNABench ECLIP: eCLIP binding site 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(eCLIP) |
| Pipeline: aido-rna-1b600m-cds | Protocol: mRNABench variant probes eCLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 0.411 ± 0.003 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.003; 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 eCLIP: eCLIP binding site 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 4 (eCLIP | AUPRC), model aido-rna-1b600m-cds |
| Pipeline: aido-rna-1b600m | Protocol: mRNABench variant probes eCLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 0.420 ± 0.002 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.002; 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 eCLIP: eCLIP binding site 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 4 (eCLIP | AUPRC), model aido-rna-1b600m |
| Pipeline: aido-rna-650m-cds | Protocol: mRNABench variant probes eCLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 0.412 ± 0.002 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.002; 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 eCLIP: eCLIP binding site 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 4 (eCLIP | AUPRC), model aido-rna-650m-cds |
| Pipeline: aido-rna-650m | Protocol: mRNABench variant probes eCLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 0.408 ± 0.002 auprc fraction · higher Uncertainty: type: confidence_interval; confidence level: 0.95; reported half width: 0.002; 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 eCLIP: eCLIP binding site 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 4 (eCLIP | AUPRC), model aido-rna-650m |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description The split of mRNABench eCLIP 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 eCLIP (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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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: mrnabench-dataset-mrnabench-eclip