UTRBERT-4mer
Published RNA language model backbone, fine-tuned per task by the BEACON authors under their protocol.
Overview
Published RNA language model backbone, fine-tuned per task by the BEACON authors under their protocol.
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.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: UTRBERT-4mer | Task: BEACON APA: Alternative polyadenylation isoform prediction Dataset subset: APARENT (BEACON split) | 72.71(0.85)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.85 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(APA) |
| Configuration: UTRBERT-4mer | Task: BEACON CMP: Contact map prediction Dataset subset: RNAcontact (BEACON split) | 44.91(27.56)% precision_at_l percent · higher Uncertainty: type: standard_deviation; value: 27.56 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(CMP) |
| Configuration: UTRBERT-4mer | Task: BEACON CRI-Off: CRISPR off-target effect prediction Dataset subset: DeepCRISPR (BEACON split) | 3.11(1.10)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 1.10 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(CRI-Off) |
| Configuration: UTRBERT-4mer | Task: BEACON CRI-On: CRISPR on-target efficiency prediction Dataset subset: DeepCRISPR (BEACON split) | 23.20(1.10)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 1.10 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(CRI-On) |
| Configuration: UTRBERT-4mer | Task: BEACON DMP: Distance map prediction Dataset subset: RNAcontact (BEACON split) | 47.77(2.08)% r2 percent · higher Uncertainty: type: standard_deviation; value: 2.08 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(DMP) |
| Configuration: UTRBERT-4mer | Task: BEACON Modif: RNA modification site prediction Dataset subset: MultiRM (BEACON split) | 95.10(0.12)% auc percent · higher Uncertainty: type: standard_deviation; value: 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(Modif) |
| Configuration: UTRBERT-4mer | Task: BEACON MRL: Mean ribosome loading prediction Dataset subset: Optimus (BEACON split) | 82.90(0.75)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.75 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(MRL) |
| Configuration: UTRBERT-4mer | Task: BEACON ncRNA: Non-coding RNA family classification Dataset subset: Noorul's ncRNA set (BEACON split) | 94.32(0.946)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.946 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(ncRNA) |
| Configuration: UTRBERT-4mer | Task: BEACON PRS: Programmable RNA switch prediction Dataset subset: Angenent-Mari's switch set (BEACON split) | 56.43(0.67)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.67 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(PRS) |
| Configuration: UTRBERT-4mer | Task: BEACON SPL: Splice site prediction Dataset subset: SpliceAI (BEACON split) | 42.04(0.53)% top_k_accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.53 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(SPL) |
| Configuration: UTRBERT-4mer | Task: BEACON SSI: Structure score imputation Dataset subset: StructureImpute (BEACON split) | 33.22(0.00)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.00 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(SSI) |
| Configuration: UTRBERT-4mer | Task: BEACON SSP: Secondary structure prediction Dataset subset: bpRNA-1m (BEACON split) | 59.41(0.45)% f1 percent · higher Uncertainty: type: standard_deviation; value: 0.45 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(SSP) |
| Configuration: UTRBERT-4mer | Task: BEACON VDP: Vaccine degradation prediction Dataset subset: OpenVaccine (BEACON split) | 0.341(0.002) mcrmse error · lower Uncertainty: type: standard_deviation; value: 0.002 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceUTRBERT-4mer 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-4mer),column(VDP) |
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Sources and history
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Release 2026-09-29-06401fd5b220 · Record review: source checked
1 source records 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-4mer
- areas
- rna-transcriptomes
- family
- pretrained
- source locator
- Table3,p.8,row(UTRBERT-4mer)
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: UTRBERT-4mer on BEACON APA: Alternative polyadenylation isoform prediction
- model: UTRBERT-4mer on BEACON CMP: Contact map prediction
- model: UTRBERT-4mer on BEACON CRI-Off: CRISPR off-target effect prediction
- model: UTRBERT-4mer on BEACON CRI-On: CRISPR on-target efficiency prediction
- model: UTRBERT-4mer on BEACON DMP: Distance map prediction
- model: UTRBERT-4mer on BEACON Modif: RNA modification site prediction
- model: UTRBERT-4mer on BEACON MRL: Mean ribosome loading prediction
- model: UTRBERT-4mer on BEACON ncRNA: Non-coding RNA family classification
- model: UTRBERT-4mer on BEACON PRS: Programmable RNA switch prediction
- model: UTRBERT-4mer on BEACON SPL: Splice site prediction
- model: UTRBERT-4mer on BEACON SSI: Structure score imputation
- model: UTRBERT-4mer on BEACON SSP: Secondary structure prediction
- model: UTRBERT-4mer on BEACON VDP: Vaccine degradation prediction