suite · audited · verified 2026-07-22

BEACON

A 13-task RNA representation benchmark covering structure, function, processing, modification, translation, degradation, programmable switches, and CRISPR activity.

+5 more
Nucleic-acid result atlas: B09 results (same_entity)

Benchmark definition

What is counted

Version
neurips-2024
Total
13 (formal RNA benchmark tasks)
Task formats
sequence classification; nucleotide-level classification; sequence regression; nucleotide-level regression
Capabilities
PredictionClassificationRegression
Modalities
DNA or RNA sequence

Version history

VersionStatusRelease / as-ofTotalFormal tracks
neurips-2024
beacon-neurips-2024
current2024-06-1413 (formal RNA benchmark tasks)None registered

Tracks and subsets

IDCountBasisPartition?Notes
Structure tasks
beacon-structure
4formal RNA benchmark tasksExclusive & exhaustiveSSP, CMP, DMP, and SSI.
Function tasks
beacon-function
5formal RNA benchmark tasksExclusive & exhaustiveSPL, APA, ncRNA, Modif, and MRL.
Engineering tasks
beacon-engineering
4formal RNA benchmark tasksExclusive & exhaustiveVDP, PRS, CRI-On, and CRI-Off.

Scientific Task Atlas

Scientific task classification

complete for neurips-2024. All thirteen tasks are assigned once using the structure, function, and engineering groupings in the creator paper.

Scientific taskCoverageCountMappingEvidence
RNA structure predictionexplicitly-in-scope4 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
Secondary structure, structural score, distance-map, and tertiary-structure tasks.
RNA processing and translation predictionexplicitly-in-scope3 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
Splice-site prediction, alternative polyadenylation, and mean ribosome loading.
RNA function classificationexplicitly-in-scope1 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
Non-coding RNA functional classification.
RNA modification predictionexplicitly-in-scope1 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
RNA modification-site prediction.
RNA stability and degradation predictionexplicitly-in-scope1 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
Condition-specific RNA degradation prediction.
Programmable RNA-switch activity predictionexplicitly-in-scope1 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
Programmable RNA-switch activity prediction.
CRISPR guide activity predictionexplicitly-in-scope1 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
CRISPR on-target efficiency prediction.
CRISPR off-target predictionexplicitly-in-scope1 tasks
Formal RNA benchmark tasks.
official-taxonomy
high confidence
beacon-paper-definition-evidence
CRISPR off-target interaction prediction.

Scientific coverage notes

DomainCoverageCountInterpretation
Transcriptomicsexplicitly-in-scope13All tasks consume RNA sequence and evaluate RNA structural, functional, or engineering outcomes.
Genomicsexplicitly-in-scope2CRISPR on-target and off-target tasks involve guide and target sequence activity.

Evaluation registry

Works and run settings

A setting change—scope, prompt, tools, budget, grader, or repeats—creates a separate run. Charts never cross a comparability group.

beacon-creator-task-nativevneurips-2024
Scopefull · n=13
ShotsNot applicable
TurnsNot applicable
System prompt publicNot applicable
Reasoning / effortNot applicable
BrowserNot applicable
InternetNot applicable
DatabasesNot applicable
Code executionNot applicable
ContainerNot reported
External toolstask-specific fine-tuning scripts over CNN/ResNet/LSTM and RNA language models
Token budgetNot applicable
Time / cost budgetNot reported
TemperatureNot applicable
SeedNot reported
Repeats3
Graderdeterministic task-specific scorer · human review: no
StatisticsTask-level mean and variation over three seeds; no cross-task total score.
ContaminationTask-specific source datasets and prescribed train/validation/test partitions.
Metrics, results, and full protocol

Metrics

MetricKind / baselineUnitAggregationThreshold / tolerance
F1absolutepercenttask-specificNot reported
Top L Precisionabsolutepercentcontact-map taskNot reported
R2absolutepercenttask-specific regressionNot reported
Top-k ACCabsolutepercentsplice-site taskNot reported
ACCabsolutepercentsequence classificationNot reported
AUCabsolutepercentmodification predictionNot reported
MCRMSEabsoluteerrormean columnwise RMSENot reported
Spearman Corrabsolutepercent correlationCRISPR task examplesNot reported

No numeric result rows are published yet; the verified protocol remains useful.

Evidence

  • table: Tables 1 and 3; Sections 5.1-5.2; Appendix A.1 (Gives split sizes, task metrics, model families, three random seeds, and task-specific training settings.) — supports /scope, /protocol, /metrics

Evidence and change history

Source locators remain visible; expand an item to inspect the exact Registry fields it supports.

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models · table: pp. 1-7, Figure 1 and Tables 1-3; Appendix A.1 and Table 22 (Defines all 13 tasks, split sizes, metrics, three-seed evaluation, and dataset-specific licenses.) · Supports 31 fields

Open source →

  • /name
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  • /task_formats
  • /task_counts/total
  • /task_counts/basis
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  • /coverage_notes
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  • /versions/0/release_date
  • /versions/0/task_counts/total
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beacon-repository-resource · repository-path: README.md; downstream/*; scripts/* at da7f9c7ac3f39605af27e1dfcdf879adba963d79 (Confirms exact task names, public implementation, task-specific scorers, and Apache-2.0 code license.) · Supports 7 fields

Open source →

  • /access/tasks
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  • /versions/0/formal_tracks

View source-level modification history on GitHub →