CNN
Supervised architecture trained from scratch per task by the BEACON authors.
Overview
Supervised architecture trained from scratch per task by the BEACON authors.
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 |
|---|---|---|---|
| Method: CNN | Task: BEACON APA: Alternative polyadenylation isoform prediction Dataset subset: APARENT (BEACON split) | 50.93(0.17)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.17 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(APA) |
| Method: CNN | Task: BEACON CMP: Contact map prediction Dataset subset: RNAcontact (BEACON split) | 43.89(5.53)% precision_at_l percent · higher Uncertainty: type: standard_deviation; value: 5.53 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(CMP) |
| Method: CNN | Task: BEACON CRI-Off: CRISPR off-target effect prediction Dataset subset: DeepCRISPR (BEACON split) | 11.40(0.10)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 0.10 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(CRI-Off) |
| Method: CNN | Task: BEACON CRI-On: CRISPR on-target efficiency prediction Dataset subset: DeepCRISPR (BEACON split) | 29.69(2.52)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 2.52 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(CRI-On) |
| Method: CNN | Task: BEACON DMP: Distance map prediction Dataset subset: RNAcontact (BEACON split) | 27.76(5.00)% r2 percent · higher Uncertainty: type: standard_deviation; value: 5.00 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(DMP) |
| Method: CNN | Task: BEACON Modif: RNA modification site prediction Dataset subset: MultiRM (BEACON split) | 70.87(0.40)% auc percent · higher Uncertainty: type: standard_deviation; value: 0.40 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(Modif) |
| Method: CNN | Task: BEACON MRL: Mean ribosome loading prediction Dataset subset: Optimus (BEACON split) | 74.13(0.58)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.58 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(MRL) |
| Method: CNN | Task: BEACON ncRNA: Non-coding RNA family classification Dataset subset: Noorul's ncRNA set (BEACON split) | 88.62(0.71)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.71 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(ncRNA) |
| Method: CNN | Task: BEACON PRS: Programmable RNA switch prediction Dataset subset: Angenent-Mari's switch set (BEACON split) | 45.40(0.66)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.66 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(PRS) |
| Method: CNN | Task: BEACON SPL: Splice site prediction Dataset subset: SpliceAI (BEACON split) | 8.43(0.38)% top_k_accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.38 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(SPL) |
| Method: CNN | Task: BEACON SSI: Structure score imputation Dataset subset: StructureImpute (BEACON split) | 34.36(0.12)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(SSI) |
| Method: CNN | Task: BEACON SSP: Secondary structure prediction Dataset subset: bpRNA-1m (BEACON split) | 49.95(0.82)% f1 percent · higher Uncertainty: type: standard_deviation; value: 0.82 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(SSP) |
| Method: CNN | Task: BEACON VDP: Vaccine degradation prediction Dataset subset: OpenVaccine (BEACON split) | 0.361(0.003) mcrmse error · lower Uncertainty: type: standard_deviation; value: 0.003 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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(CNN),column(VDP) |
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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-cnn
- areas
- rna-transcriptomes
- family
- naive
- source locator
- Table3,p.8,row(CNN)
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: CNN on BEACON APA: Alternative polyadenylation isoform prediction
- model: CNN on BEACON CMP: Contact map prediction
- model: CNN on BEACON CRI-Off: CRISPR off-target effect prediction
- model: CNN on BEACON CRI-On: CRISPR on-target efficiency prediction
- model: CNN on BEACON DMP: Distance map prediction
- model: CNN on BEACON Modif: RNA modification site prediction
- model: CNN on BEACON MRL: Mean ribosome loading prediction
- model: CNN on BEACON ncRNA: Non-coding RNA family classification
- model: CNN on BEACON PRS: Programmable RNA switch prediction
- model: CNN on BEACON SPL: Splice site prediction
- model: CNN on BEACON SSI: Structure score imputation
- model: CNN on BEACON SSP: Secondary structure prediction
- model: CNN on BEACON VDP: Vaccine degradation prediction