Splice-MS1024 | configuration

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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
Splice-MS1024Evaluation	BEACON MRL: Mean ribosome loading prediction, Optimus (BEACON split)	67.15(30.54) (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON APA: Alternative polyadenylation isoform prediction, APARENT (BEACON split)	60.03(3.42)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON PRS: Programmable RNA switch prediction, Angenent-Mari's switch set (BEACON split)	57.72(0.45)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON DMP: Distance map prediction, RNAcontact (BEACON split)	55.89(0.48)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON SSI: Structure score imputation, StructureImpute (BEACON split)	39.22(0.02)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON CMP: Contact map prediction, RNAcontact (BEACON split)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	47.32(3.16)%	Not reported
Splice-MS1024Evaluation	BEACON CRI-Off: CRISPR off-target effect prediction, DeepCRISPR (BEACON split)	Not reported	5.00(0.71)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON CRI-On: CRISPR on-target efficiency prediction, DeepCRISPR (BEACON split)	Not reported	27.59(4.61) (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON Modif: RNA modification site prediction, MultiRM (BEACON split)	Not reported	Not reported	Not reported	53.45(6.25)	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON ncRNA: Non-coding RNA family classification, Noorul's ncRNA set (BEACON split)	Not reported	Not reported	96.05(0.777)%	Not reported	Not reported	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON SPL: Splice site prediction, SpliceAI (BEACON split)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	48.52(0.49)%
Splice-MS1024Evaluation	BEACON SSP: Secondary structure prediction, bpRNA-1m (BEACON split)	Not reported	Not reported	Not reported	Not reported	68.26(0.20)%	Not reported	Not reported	Not reported
Splice-MS1024Evaluation	BEACON VDP: Vaccine degradation prediction, OpenVaccine (BEACON split)	Not reported	Not reported	Not reported	Not reported	Not reported	0.313(0.000)	Not reported	Not reported

All 13 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Splice-MS1024	Task: BEACON APA: Alternative polyadenylation isoform prediction Dataset subset: APARENT (BEACON split)	60.03(3.42) R² unitless · higher Uncertainty: SD 3.42 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(APA)
Configuration: Splice-MS1024	Task: BEACON CMP: Contact map prediction Dataset subset: RNAcontact (BEACON split)	47.32(3.16)% Precision at l percent · higher Uncertainty: SD 3.16 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(CMP)
Configuration: Splice-MS1024	Task: BEACON CRI-Off: CRISPR off-target effect prediction Dataset subset: DeepCRISPR (BEACON split)	5.00(0.71) Spearman unitless · higher Uncertainty: SD 0.71 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(CRI-Off)
Configuration: Splice-MS1024	Task: BEACON CRI-On: CRISPR on-target efficiency prediction Dataset subset: DeepCRISPR (BEACON split)	27.59(4.61) Spearman unitless · higher Uncertainty: SD 4.61 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(CRI-On)
Configuration: Splice-MS1024	Task: BEACON DMP: Distance map prediction Dataset subset: RNAcontact (BEACON split)	55.89(0.48) R² unitless · higher Uncertainty: SD 0.48 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(DMP)
Configuration: Splice-MS1024	Task: BEACON Modif: RNA modification site prediction Dataset subset: MultiRM (BEACON split)	53.45(6.25) AUROC unitless · higher Uncertainty: SD 6.25 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(Modif)
Configuration: Splice-MS1024	Task: BEACON MRL: Mean ribosome loading prediction Dataset subset: Optimus (BEACON split)	67.15(30.54) R² unitless · higher Uncertainty: SD 30.54 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(MRL)
Configuration: Splice-MS1024	Task: BEACON ncRNA: Non-coding RNA family classification Dataset subset: Noorul's ncRNA set (BEACON split)	96.05(0.777)% Accuracy percent · higher Uncertainty: SD 0.777 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(ncRNA)
Configuration: Splice-MS1024	Task: BEACON PRS: Programmable RNA switch prediction Dataset subset: Angenent-Mari's switch set (BEACON split)	57.72(0.45) R² unitless · higher Uncertainty: SD 0.45 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(PRS)
Configuration: Splice-MS1024	Task: BEACON SPL: Splice site prediction Dataset subset: SpliceAI (BEACON split)	48.52(0.49)% Splice top k accuracy percent · higher Uncertainty: SD 0.49 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(SPL)
Configuration: Splice-MS1024	Task: BEACON SSI: Structure score imputation Dataset subset: StructureImpute (BEACON split)	39.22(0.02) R² unitless · higher Uncertainty: SD 0.02 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(SSI)
Configuration: Splice-MS1024	Task: BEACON SSP: Secondary structure prediction Dataset subset: bpRNA-1m (BEACON split)	68.26(0.20)% F1 (base pairs; binary F1 over all position pairs pooled across the test set; threshold 0.5) percent · higher Uncertainty: SD 0.20 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),column(SSP)
Configuration: Splice-MS1024	Task: BEACON VDP: Vaccine degradation prediction Dataset subset: OpenVaccine (BEACON split)	0.313(0.000) Mean columnwise RMSE unit-unreported · lower Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Splice-MS1024 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(Splice-MS1024),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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Stable ID: beacon-model-splice-ms1024

areas: rna-transcriptomes
source locator: Table3,p.8,row(Splice-MS1024)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
family label: pretrained

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