mRNABench variant probes eCLIP: eCLIP binding site prediction
eCLIP binding site prediction. Scored with AUPRC on mRNABench eCLIP (mRNABench split). 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.
Overview
eCLIP binding site prediction. Scored with AUPRC on mRNABench eCLIP (mRNABench split). 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.
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 variant probes eCLIP: eCLIP binding site prediction
auprc (fraction) · Higher values are better.
Every method mRNABench variant probes reports on eCLIP binding site prediction, scored with AUPRC on mRNABench eCLIP (mRNABench split).
mRNABench variant probes eCLIP: eCLIP binding site prediction · mRNABench eCLIP (mRNABench split)
Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.
mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 5 (XML T2), eCLIP column; Methods S17/S18; Appendix C (APP3)These are configuration-level details of the experiment set summarized by the paper’s Table 2; they are not new independent experiments.
All comparison limitations (5)
- These are configuration-level details of the experiment set summarized by the paper’s Table 2; they are not new independent experiments.
- Tables report means over ten splits and 95% confidence intervals. Appendix C lists only nine seeds; the missing seed is not inferred.
- Two localization columns are excluded because Table 2 and Table 5 disagree about their metric.
- Supervised CNN and naive feature controls are retained; not every method is a pretrained model.
- 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.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
Showing 12 of 50 matching rows.
- evo2–7b0.477 ± 0.005
- evo2–7b-base0.473 ± 0.004
- orthrus-mlm0.465 ± 0.003
- evo2–1b-base0.461 ± 0.004
- orthrus-large-60.436 ± 0.004
- naive-60.434 ± 0.004
- naive-40.430 ± 0.004
- supervised-cnn0.421 ± 0.005
- aido-rna-1b600m0.420 ± 0.002
- orthrus-base-40.413 ± 0.003
- aido-rna-650m-cds0.412 ± 0.002
- aido-rna-1b600m-cds0.411 ± 0.003
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.
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.
- aido-rna-1b600m-cds on mRNABench variant probes eCLIP: eCLIP binding site prediction
- aido-rna-1b600m on mRNABench variant probes eCLIP: eCLIP binding site prediction
- aido-rna-650m-cds on mRNABench variant probes eCLIP: eCLIP binding site prediction
- aido-rna-650m on mRNABench variant probes eCLIP: eCLIP binding site prediction
- dnabert-s on mRNABench variant probes eCLIP: eCLIP binding site prediction
- dnabert2 on mRNABench variant probes eCLIP: eCLIP binding site prediction
- ernierna on mRNABench variant probes eCLIP: eCLIP binding site prediction
- ernierna-ss on mRNABench variant probes eCLIP: eCLIP binding site prediction
- evo-1–131k-base on mRNABench variant probes eCLIP: eCLIP binding site prediction
- evo-1.5–8k-base on mRNABench variant probes eCLIP: eCLIP binding site prediction
- evo-1–8k-base on mRNABench variant probes eCLIP: eCLIP binding site prediction
- evo2–1b-base on mRNABench variant probes eCLIP: eCLIP binding site prediction
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 50
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set mean where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Simple features with train-only ridge regression
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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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 5 (XML T2), eCLIP column; Methods S17/S18; Appendix C (APP3) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-23 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: mrnabench-variants-2025-association-eclip Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
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Release 2026-09-23-2b89723c6dd9 · 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-variants-2025-task-eclip
- areas
- rna-transcriptomics
- tasks
- eCLIP binding site prediction
- metric
- AUPRC
- metric direction
- higher
- dataset
- mRNABench eCLIP (mRNABench split)
- protocol
- 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.
- source locator
- Table 5 (XML T2), eCLIP column; Methods S17/S18; Appendix C (APP3)
- comparison panels
- id: mrnabench-variants-2025-panel-eclip; title: mRNABench variant probes eCLIP: eCLIP binding site prediction; protocol id: mrnabench-variants-2025-task-eclip; dataset id: mrnabench-dataset-mrnabench-eclip; metric: auprc; unit: fraction; direction: higher; result ids: mrnabench-variants-2025-result-aido-rna-1b600m-eclip-auprc; mrnabench-variants-2025-result-aido-rna-1b600m-cds-eclip-auprc; mrnabench-variants-2025-result-aido-rna-650m-eclip-auprc; mrnabench-variants-2025-result-aido-rna-650m-cds-eclip-auprc; mrnabench-variants-2025-result-dnabert-s-eclip-auprc; mrnabench-variants-2025-result-dnabert2-eclip-auprc; mrnabench-variants-2025-result-ernierna-eclip-auprc; mrnabench-variants-2025-result-ernierna-ss-eclip-auprc; mrnabench-variants-2025-result-evo-1-131k-base-eclip-auprc; mrnabench-variants-2025-result-evo-1-8k-base-eclip-auprc; mrnabench-variants-2025-result-evo-1-5-8k-base-eclip-auprc; mrnabench-variants-2025-result-evo2-1b-base-eclip-auprc; mrnabench-variants-2025-result-evo2-7b-eclip-auprc; mrnabench-variants-2025-result-evo2-7b-base-eclip-auprc; mrnabench-variants-2025-result-helix-mrna-eclip-auprc; mrnabench-variants-2025-result-hyenadna-large-1m-eclip-auprc; mrnabench-variants-2025-result-hyenadna-medium-160k-eclip-auprc; mrnabench-variants-2025-result-hyenadna-medium-450k-eclip-auprc; mrnabench-variants-2025-result-hyenadna-small-32k-eclip-auprc; mrnabench-variants-2025-result-hyenadna-tiny-16k-d128-eclip-auprc; mrnabench-variants-2025-result-mrna-fm-eclip-auprc; mrnabench-variants-2025-result-naive-4-eclip-auprc; mrnabench-variants-2025-result-naive-6-eclip-auprc; mrnabench-variants-2025-result-naive-mamba-eclip-auprc; mrnabench-variants-2025-result-nt-2-5b-1000g-eclip-auprc; mrnabench-variants-2025-result-nt-2-5b-multi-species-eclip-auprc; mrnabench-variants-2025-result-nt-500m-1000g-eclip-auprc; mrnabench-variants-2025-result-nt-500m-human-ref-eclip-auprc; mrnabench-variants-2025-result-nt-v2-100m-multi-species-eclip-auprc; mrnabench-variants-2025-result-nt-v2-250m-multi-species-eclip-auprc; mrnabench-variants-2025-result-nt-v2-500m-multi-species-eclip-auprc; mrnabench-variants-2025-result-nt-v2-50m-multi-species-eclip-auprc; mrnabench-variants-2025-result-orthrus-base-4-eclip-auprc; mrnabench-variants-2025-result-orthrus-large-6-eclip-auprc; mrnabench-variants-2025-result-orthrus-mlm-eclip-auprc; mrnabench-variants-2025-result-rinalmo-eclip-auprc; mrnabench-variants-2025-result-rna-fm-eclip-auprc; mrnabench-variants-2025-result-rnabert-eclip-auprc; mrnabench-variants-2025-result-rnaernie-eclip-auprc; mrnabench-variants-2025-result-rnamsm-eclip-auprc; mrnabench-variants-2025-result-splicebert-h-510nt-eclip-auprc; mrnabench-variants-2025-result-splicebert-v-1024nt-eclip-auprc; mrnabench-variants-2025-result-splicebert-v-510nt-eclip-auprc; mrnabench-variants-2025-result-supervised-cnn-eclip-auprc; mrnabench-variants-2025-result-utrbert-3mer-eclip-auprc; mrnabench-variants-2025-result-utrbert-4mer-eclip-auprc; mrnabench-variants-2025-result-utrbert-5mer-eclip-auprc; mrnabench-variants-2025-result-utrbert-6mer-eclip-auprc; mrnabench-variants-2025-result-utrlm-mrl-eclip-auprc; mrnabench-variants-2025-result-utrlm-te-el-eclip-auprc; source ids: expansion-p3-mrnabench-2025; source locator: Table 5 (XML T2), eCLIP column; Methods S17/S18; Appendix C (APP3); context: Every method mRNABench variant probes reports on eCLIP binding site prediction, scored with AUPRC on mRNABench eCLIP (mRNABench split).; caveats: These are configuration-level details of the experiment set summarized by the paper’s Table 2; they are not new independent experiments.; Tables report means over ten splits and 95% confidence intervals. Appendix C lists only nine seeds; the missing seed is not inferred.; Two localization columns are excluded because Table 2 and Table 5 disagree about their metric.; Supervised CNN and naive feature controls are retained; not every method is a pretrained model.; 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.; review: method: automated_source_review; date: 2026-09-23
- entity level
- protocol
Related records
- part of: mRNABench
- subject: mRNABench variant probes eCLIP: part of discovery-benchmark-mrnabench
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