utrbert-3mer
Linear probe, trained per mRNABench task, on frozen embeddings averaged over nucleotides from utrbert-3mer, a 3'UTRBERT checkpoint with a 3-mer tokenizer; 3'UTRBERT is a Transformer mRNA model pretrained on the 3' UTRs of 100,000 human mRNAs.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
8 evaluations · 8 results. Different protocols are not a single leaderboard.
Sorted by AUPRC (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 8 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes eCLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 0.296 ± 0.002 AUPRC fraction · higher Uncertainty: 95% CI ± 0.002 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer 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 45, XML tr 47, column 4 (eCLIP | AUPRC), model utrbert-3mer |
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes GO: Gene Ontology term prediction Dataset subset: mRNABench GO (mRNABench split) | 0.265 ± 0.004 AUPRC fraction · higher Uncertainty: 95% CI ± 0.004 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer on mRNABench variant probes GO: Gene Ontology term 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 6 (XML T3), data row 45, XML tr 47, column 5 (GO | AUPRC), model utrbert-3mer |
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes HL: mRNA half life Dataset subset: mRNABench HL (mRNABench split) | 0.407 ± 0.011 Pearson unitless · higher Uncertainty: 95% CI ± 0.011 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer on mRNABench variant probes HL: mRNA half life 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 6 (XML T3), data row 45, XML tr 47, column 2 (HL | Pearson R), model utrbert-3mer |
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes MRL-HL-Pair: Paired mean ribosome load and half life Dataset subset: mRNABench MRL-HL-Pair (mRNABench split) | 0.502 ± 0.056 Pearson unitless · higher Uncertainty: 95% CI ± 0.056 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer on mRNABench variant probes MRL-HL-Pair: Paired mean ribosome load and half life 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 6 (XML T3), data row 45, XML tr 47, column 3 (MRL-HL-Pair | Pearson R), model utrbert-3mer |
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes MRL-MPRA: Mean ribosome load on an MPRA library Dataset subset: mRNABench MRL MPRA (mRNABench split) | 0.556 ± 0.001 Pearson unitless · higher Uncertainty: 95% CI ± 0.001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer on mRNABench variant probes MRL-MPRA: Mean ribosome load on an MPRA library 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 6 (XML T3), data row 45, XML tr 47, column 4 (MRL-MPRA | Pearson R), model utrbert-3mer |
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes MRL: Mean ribosome load Dataset subset: mRNABench MRL (mRNABench split) | 0.157 ± 0.014 Pearson unitless · higher Uncertainty: 95% CI ± 0.014 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer on mRNABench variant probes MRL: Mean ribosome load 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 45, XML tr 47, column 5 (MRL | Pearson R), model utrbert-3mer |
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes Prot-Loc: Protein localisation Dataset subset: mRNABench Prot Loc (mRNABench split) | 0.265 ± 0.005 AUPRC fraction · higher Uncertainty: 95% CI ± 0.005 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer on mRNABench variant probes Prot-Loc: Protein localisation 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 6 (XML T3), data row 45, XML tr 47, column 6 (Prot-Loc | AUPRC), model utrbert-3mer |
| Pipeline: utrbert-3mer | Protocol: mRNABench variant probes VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 0.300 ± 0.035 AUPRC fraction · higher Uncertainty: 95% CI ± 0.035 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceutrbert-3mer 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 45, XML tr 47, column 6 (VEP | AUPRC), model utrbert-3mer |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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Evidence
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Evidence table
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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 |
|---|---|---|
| Description Linear probe, trained per mRNABench task, on frozen embeddings averaged over nucleotides from utrbert-3mer, a 3'UTRBERT checkpoint with a 3-mer tokenizer; 3'UTRBERT is a Transformer mRNA model pretrained on the 3' UTRs of 100,000 human mRNAs. Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction expansion-p3-mrnabench-2025: Appendix A, Overview of Evaluated Models (family and variant rows; naive baselines paragraph); Section 4.3, Linear Probing ('training a linear classifier on frozen embeddings'; 'averaging over per-nucleotide embeddings') Version: preprint archived 2025-07-08 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the 10 method and model descriptions against their sources (EVmutation, GEMME and RSALOR abstracts, the FramePool k-mer random forests, the RhoMax BLASSO text) and spot-checked the 49 mRNABench rows against Appendix A; all accurate. Licences on the 3 new sources match their Europe PMC records. At the reviewer's suggestion, the en dash printed in some checkpoint names is written as a hyphen in the descriptions. Field: Claim: metadata-correction-e03178fe1ae2e8f7660c Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record 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-method-utrbert-3mer
- areas
- rna-transcriptomes
- source locator
- Tables 5/6, row utrbert-3mer; Appendix A (APP1), C (APP3), D (APP4)
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
Related records
- subject: utrbert-3mer: description
- system: utrbert-3mer on mRNABench variant probes eCLIP: eCLIP binding site prediction
- system: utrbert-3mer on mRNABench variant probes GO: Gene Ontology term prediction
- system: utrbert-3mer on mRNABench variant probes HL: mRNA half life
- system: utrbert-3mer on mRNABench variant probes MRL: Mean ribosome load
- system: utrbert-3mer on mRNABench variant probes MRL-HL-Pair: Paired mean ribosome load and half life
- system: utrbert-3mer on mRNABench variant probes MRL-MPRA: Mean ribosome load on an MPRA library
- system: utrbert-3mer on mRNABench variant probes Prot-Loc: Protein localisation
- system: utrbert-3mer on mRNABench variant probes VEP: Variant effect prediction