UTRBERT-6mer
Published RNA language model backbone, fine-tuned per task by the BEACON authors under their protocol.
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
13 evaluations · 13 results. Different protocols are not a single leaderboard.
Sorted by R² (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.
| Tested configuration | Protocol and dataset | R² | Spearman | Accuracy | AUROC | F1 (base pairs; binary F1 over all position pairs pooled across the test set; threshold 0.5) | Mean columnwise RMSE | Precision at l | Splice top k accuracy |
|---|---|---|---|---|---|---|---|---|---|
| UTRBERT-6merEvaluation | BEACON MRL: Mean ribosome loading prediction, Optimus (BEACON split) | 83.60(0.39) (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON APA: Alternative polyadenylation isoform prediction, APARENT (BEACON split) | 71.17(2.30) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON PRS: Programmable RNA switch prediction, Angenent-Mari's switch set (BEACON split) | 57.14(0.12) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON DMP: Distance map prediction, RNAcontact (BEACON split) | 50.02(1.05) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON SSI: Structure score imputation, StructureImpute (BEACON split) | 29.93(0.17) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON CMP: Contact map prediction, RNAcontact (BEACON split) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 51.56(20.30)% | Not reported |
| UTRBERT-6merEvaluation | BEACON CRI-Off: CRISPR off-target effect prediction, DeepCRISPR (BEACON split) | Not reported | 4.90(0.57) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON CRI-On: CRISPR on-target efficiency prediction, DeepCRISPR (BEACON split) | Not reported | 28.60(1.55) (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON Modif: RNA modification site prediction, MultiRM (BEACON split) | Not reported | Not reported | Not reported | 95.08(0.17) | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON ncRNA: Non-coding RNA family classification, Noorul's ncRNA set (BEACON split) | Not reported | Not reported | 93.12(0.168)% | Not reported | Not reported | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON SPL: Splice site prediction, SpliceAI (BEACON split) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 38.58(2.72)% |
| UTRBERT-6merEvaluation | BEACON SSP: Secondary structure prediction, bpRNA-1m (BEACON split) | Not reported | Not reported | Not reported | Not reported | 38.56(28.76)% | Not reported | Not reported | Not reported |
| UTRBERT-6merEvaluation | BEACON VDP: Vaccine degradation prediction, OpenVaccine (BEACON split) | Not reported | Not reported | Not reported | Not reported | Not reported | 0.340(0.001) | Not reported | Not reported |
All 13 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: UTRBERT-6mer | Task: BEACON APA: Alternative polyadenylation isoform prediction Dataset subset: APARENT (BEACON split) | 71.17(2.30) R² unitless · higher Uncertainty: SD 2.30 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON APA: Alternative polyadenylation isoform prediction BEACON harness, fixed downstream head per task. Train/validation/test 145,463/33,170/49,755; dataset APARENT. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(APA) |
| Configuration: UTRBERT-6mer | Task: BEACON CMP: Contact map prediction Dataset subset: RNAcontact (BEACON split) | 51.56(20.30)% Precision at l percent · higher Uncertainty: SD 20.30 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON CMP: Contact map prediction BEACON harness, fixed downstream head per task. Train/validation/test 188/23/80; dataset RNAcontact. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(CMP) |
| Configuration: UTRBERT-6mer | Task: BEACON CRI-Off: CRISPR off-target effect prediction Dataset subset: DeepCRISPR (BEACON split) | 4.90(0.57) Spearman unitless · higher Uncertainty: SD 0.57 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON CRI-Off: CRISPR off-target effect prediction BEACON harness, fixed downstream head per task. Train/validation/test 14,223/2,032/4,064; dataset DeepCRISPR. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(CRI-Off) |
| Configuration: UTRBERT-6mer | Task: BEACON CRI-On: CRISPR on-target efficiency prediction Dataset subset: DeepCRISPR (BEACON split) | 28.60(1.55) Spearman unitless · higher Uncertainty: SD 1.55 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON CRI-On: CRISPR on-target efficiency prediction BEACON harness, fixed downstream head per task. Train/validation/test 1,453/207/416; dataset DeepCRISPR. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(CRI-On) |
| Configuration: UTRBERT-6mer | Task: BEACON DMP: Distance map prediction Dataset subset: RNAcontact (BEACON split) | 50.02(1.05) R² unitless · higher Uncertainty: SD 1.05 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON DMP: Distance map prediction BEACON harness, fixed downstream head per task. Train/validation/test 188/23/80; dataset RNAcontact. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(DMP) |
| Configuration: UTRBERT-6mer | Task: BEACON Modif: RNA modification site prediction Dataset subset: MultiRM (BEACON split) | 95.08(0.17) AUROC unitless · higher Uncertainty: SD 0.17 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON Modif: RNA modification site prediction BEACON harness, fixed downstream head per task. Train/validation/test 304,661/3,599/1,200; dataset MultiRM. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(Modif) |
| Configuration: UTRBERT-6mer | Task: BEACON MRL: Mean ribosome loading prediction Dataset subset: Optimus (BEACON split) | 83.60(0.39) R² unitless · higher Uncertainty: SD 0.39 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON MRL: Mean ribosome loading prediction BEACON harness, fixed downstream head per task. Train/validation/test 76,319/7,600/7,600; dataset Optimus. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(MRL) |
| Configuration: UTRBERT-6mer | Task: BEACON ncRNA: Non-coding RNA family classification Dataset subset: Noorul's ncRNA set (BEACON split) | 93.12(0.168)% Accuracy percent · higher Uncertainty: SD 0.168 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON ncRNA: Non-coding RNA family classification BEACON harness, fixed downstream head per task. Train/validation/test 5,679/650/2,400; dataset Noorul's ncRNA set. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(ncRNA) |
| Configuration: UTRBERT-6mer | Task: BEACON PRS: Programmable RNA switch prediction Dataset subset: Angenent-Mari's switch set (BEACON split) | 57.14(0.12) R² unitless · higher Uncertainty: SD 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON PRS: Programmable RNA switch prediction BEACON harness, fixed downstream head per task. Train/validation/test 73,227/9,153/9,154; dataset Angenent-Mari's switch set. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(PRS) |
| Configuration: UTRBERT-6mer | Task: BEACON SPL: Splice site prediction Dataset subset: SpliceAI (BEACON split) | 38.58(2.72)% Splice top k accuracy percent · higher Uncertainty: SD 2.72 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON SPL: Splice site prediction BEACON harness, fixed downstream head per task. Train/validation/test 144,628/18,078/16,505; dataset SpliceAI. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(SPL) |
| Configuration: UTRBERT-6mer | Task: BEACON SSI: Structure score imputation Dataset subset: StructureImpute (BEACON split) | 29.93(0.17) R² unitless · higher Uncertainty: SD 0.17 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON SSI: Structure score imputation BEACON harness, fixed downstream head per task. Train/validation/test 14,049/1,756/3,095; dataset StructureImpute. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(SSI) |
| Configuration: UTRBERT-6mer | Task: BEACON SSP: Secondary structure prediction Dataset subset: bpRNA-1m (BEACON split) | 38.56(28.76)% F1 (base pairs; binary F1 over all position pairs pooled across the test set; threshold 0.5) percent · higher Uncertainty: SD 28.76 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON SSP: Secondary structure prediction BEACON harness, fixed downstream head per task. Train/validation/test 10,814/1,300/1,305; dataset bpRNA-1m. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(SSP) |
| Configuration: UTRBERT-6mer | Task: BEACON VDP: Vaccine degradation prediction Dataset subset: OpenVaccine (BEACON split) | 0.340(0.001) Mean columnwise RMSE unit-unreported · lower Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-6mer on BEACON VDP: Vaccine degradation prediction BEACON harness, fixed downstream head per task. Train/validation/test 2,155/245/629; dataset OpenVaccine. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(UTRBERT-6mer),column(VDP) |
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Evidence
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Evidence table
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Original source · v2, 12 December 2024
Technical metadata and extraction receipts
Stable ID: beacon-model-utrbert-6mer
- areas
- rna-transcriptomes
- source locator
- Table3,p.8,row(UTRBERT-6mer)
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
- family label
- pretrained
Related records
- system: UTRBERT-6mer on BEACON APA: Alternative polyadenylation isoform prediction
- system: UTRBERT-6mer on BEACON CMP: Contact map prediction
- system: UTRBERT-6mer on BEACON CRI-Off: CRISPR off-target effect prediction
- system: UTRBERT-6mer on BEACON CRI-On: CRISPR on-target efficiency prediction
- system: UTRBERT-6mer on BEACON DMP: Distance map prediction
- system: UTRBERT-6mer on BEACON Modif: RNA modification site prediction
- system: UTRBERT-6mer on BEACON MRL: Mean ribosome loading prediction
- system: UTRBERT-6mer on BEACON ncRNA: Non-coding RNA family classification
- system: UTRBERT-6mer on BEACON PRS: Programmable RNA switch prediction
- system: UTRBERT-6mer on BEACON SPL: Splice site prediction
- system: UTRBERT-6mer on BEACON SSI: Structure score imputation
- system: UTRBERT-6mer on BEACON SSP: Secondary structure prediction
- system: UTRBERT-6mer on BEACON VDP: Vaccine degradation prediction