ResNet | method

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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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: ResNet	Task: BEACON APA: Alternative polyadenylation isoform prediction Dataset subset: APARENT (BEACON split)	56.45(0.94)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.94 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(APA)
Method: ResNet	Task: BEACON CMP: Contact map prediction Dataset subset: RNAcontact (BEACON split)	59.59(0.68)% precision_at_l percent · higher Uncertainty: type: standard_deviation; value: 0.68 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(CMP)
Method: ResNet	Task: BEACON CRI-Off: CRISPR off-target effect prediction Dataset subset: DeepCRISPR (BEACON split)	11.50(0.22)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 0.22 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(CRI-Off)
Method: ResNet	Task: BEACON CRI-On: CRISPR on-target efficiency prediction Dataset subset: DeepCRISPR (BEACON split)	28.55(2.42)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 2.42 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(CRI-On)
Method: ResNet	Task: BEACON DMP: Distance map prediction Dataset subset: RNAcontact (BEACON split)	30.26(1.81)% r2 percent · higher Uncertainty: type: standard_deviation; value: 1.81 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(DMP)
Method: ResNet	Task: BEACON Modif: RNA modification site prediction Dataset subset: MultiRM (BEACON split)	71.03(0.32)% auc percent · higher Uncertainty: type: standard_deviation; value: 0.32 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(Modif)
Method: ResNet	Task: BEACON MRL: Mean ribosome loading prediction Dataset subset: Optimus (BEACON split)	74.34(0.22)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.22 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(MRL)
Method: ResNet	Task: BEACON ncRNA: Non-coding RNA family classification Dataset subset: Noorul's ncRNA set (BEACON split)	88.33(1.22)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 1.22 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(ncRNA)
Method: ResNet	Task: BEACON PRS: Programmable RNA switch prediction Dataset subset: Angenent-Mari's switch set (BEACON split)	55.21(0.28)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.28 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(PRS)
Method: ResNet	Task: BEACON SPL: Splice site prediction Dataset subset: SpliceAI (BEACON split)	21.15(1.56)% top_k_accuracy percent · higher Uncertainty: type: standard_deviation; value: 1.56 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(SPL)
Method: ResNet	Task: BEACON SSI: Structure score imputation Dataset subset: StructureImpute (BEACON split)	37.74(0.16)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.16 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(SSI)
Method: ResNet	Task: BEACON SSP: Secondary structure prediction Dataset subset: bpRNA-1m (BEACON split)	57.26(3.14)% f1 percent · higher Uncertainty: type: standard_deviation; value: 3.14 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(SSP)
Method: ResNet	Task: BEACON VDP: Vaccine degradation prediction Dataset subset: OpenVaccine (BEACON split)	0.349(0.003) mcrmse error · lower Uncertainty: type: standard_deviation; value: 0.003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet 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(ResNet),column(VDP)

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BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Original source · v2, 12 December 2024

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Technical metadata and extraction receipts

Stable ID: beacon-model-resnet

areas: rna-transcriptomes
family: naive
source locator: Table3,p.8,row(ResNet)
missing metadata: checkpoint revision: unreported; parameters: unextracted

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