BEACON
A 13-task RNA representation benchmark covering structure, function, processing, modification, translation, degradation, programmable switches, and CRISPR activity.
Scientific task · Sequence and regulation
DNA regulation and perturbation
Predict DNA regulatory elements
DNA调控与扰动
Nucleic-acid result atlas: T24 results (narrower_than_registry) · T26 results (narrower_than_registry)
Definition and search aliases
- Permanent ID
dna-regulation-perturbation- Aliases
- regulatory genomics
- Deprecated aliases
- None
- Hierarchy
- Parent task; benchmark coverage below includes its leaf tasks.
Coverage
4 benchmark families cover this task
Biology-Instructions
A multi-omics sequence-instruction suite with 21 formal predictive tasks across DNA, RNA, protein, and multi-molecule inputs; the final paper reports task-specific held-out evaluations rather than a single aggregate score.
Biology-Instructions CRISPR On-Target Prediction
Regression of CRISPR guide on-target activity from an RNA sequence, evaluated with Spearman rank correlation.
Genomic Benchmarks
A versioned collection of nine DNA sequence-classification datasets covering regulatory elements, promoters, enhancers, open chromatin, species, and coding-context discrimination.
LAB-Bench SeqQA — Primers-to-restriction enzymes
Infers restriction enzymes from a gene name and primer pair.
LAB-Bench SeqQA — Primers to amplicon length
Calculates expected amplicon length from a primer pair and DNA template.
LAB-Bench SeqQA — GC percentage
Calculates the rounded GC percentage of a DNA sequence.
LAB-Bench SeqQA — Restriction-fragment lengths
Calculates fragment lengths after restriction digestion of a DNA sequence.
LAB-Bench SeqQA — Restriction-fragment count
Calculates the number of fragments after restriction digestion of a DNA sequence.
LAB-Bench SeqQA
Sequence-comprehension and manipulation category spanning 15 formal tasks involving PCR, restriction digestion, ORFs, translation, GC content, and DNA–protein relationships.
LAB-Bench SeqQA — Gene-to-restriction primers
Selects restriction-cloning primers from a named gene and enzyme pair.
LAB-Bench SeqQA — Gene-to-Gibson primers (HindIII)
Selects primers for Gibson assembly into a HindIII-linearized vector.
LAB-Bench SeqQA — Gene-to-Gibson primers (SmaI)
Selects primers for Gibson assembly into a SmaI-linearized vector.
LAB-Bench SeqQA — Amplicon length to primers
Selects primers that produce a requested amplicon length from a DNA template.
LAB-Bench SeqQA — Sequence-to-restriction primers
Selects restriction-cloning primers from an explicit gene sequence and enzyme pair.
LAB-Bench SeqQA — Amplicon sequence to primers
Selects primers that produce a requested amplicon sequence from a DNA template.
Biology-Instructions Enhancer Activity Prediction
Two-output regression of housekeeping and developmental enhancer activity from a DNA sequence, evaluated with separate Pearson correlations.
Biology-Instructions Enhancer-Promoter Interaction Prediction
Binary interaction prediction for enhancer and promoter DNA sequences, evaluated with Matthews correlation coefficient.
Biology-Instructions Epigenetic Marks Prediction
Binary prediction of whether a DNA sequence carries an epigenetic mark, evaluated with Matthews correlation coefficient.
Biology-Instructions Core Promoter Detection
Binary detection of a core promoter in a short DNA sequence, evaluated with Matthews correlation coefficient.
Biology-Instructions Promoter Detection 300
Binary promoter detection in a 300-base-pair DNA context, evaluated with Matthews correlation coefficient.
Biology-Instructions Human Transcription Binding Sites Detection
Binary detection of transcription-factor binding sites in human DNA sequences, evaluated with Matthews correlation coefficient.
Biology-Instructions Mouse Transcription Binding Sites Detection
Binary detection of transcription-factor binding sites in mouse DNA sequences, evaluated with Matthews correlation coefficient.
LAB-Bench DbQA — GTRD transcription-factor binding sites
Retrieves promoter-region transcription-factor binding-site annotations from GTRD.
Evidence-backed count claims
Each row keeps its original unit and basis. Rows with different units or overlapping mappings are never added.
| Benchmark | Mapped task | Coverage | Count | Version | Evidence |
|---|---|---|---|---|---|
| BEACON root: beacon-rna | CRISPR guide activity prediction official-taxonomy · high | explicitly-in-scope | 1 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | CRISPR guide activity prediction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (CRISPR On-Target Prediction). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions CRISPR On-Target Prediction root: bioinstruction | CRISPR guide activity prediction official-track · high | explicitly-in-scope | 2076 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-crispr-on-target-evidence-paper |
| BEACON root: beacon-rna | CRISPR off-target prediction official-taxonomy · high | explicitly-in-scope | 1 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| Genomic Benchmarks root: genomic-benchmarks | DNA sequence analysis official-taxonomy · high | explicitly-in-scope | 3 tasks Benchmark dataset classification tasks. | package-1.0.0-snapshot as of 2026-07-22 | genomic-benchmarks-paper-definition-evidence |
| LAB-Bench SeqQA — Primers-to-restriction enzymes root: lab-bench | DNA sequence analysis official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-geneprimers-enz-evidence-paper |
| LAB-Bench SeqQA — Primers to amplicon length root: lab-bench | DNA sequence analysis official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-primers-len-evidence-paper |
| LAB-Bench SeqQA — GC percentage root: lab-bench | DNA sequence analysis official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-prop-seq-gcpercent-evidence-paper |
| LAB-Bench SeqQA — Restriction-fragment lengths root: lab-bench | DNA sequence analysis official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-re-seq-lenfrags-evidence-paper |
| LAB-Bench SeqQA — Restriction-fragment count root: lab-bench | DNA sequence analysis official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-re-seq-numfrags-evidence-paper |
| LAB-Bench SeqQA root: lab-bench | DNA sequence design official-track · high | explicitly-in-scope | Not reported Primer-design questions across formal SeqQA child tracks. | repository-998a8e0 | lab-bench-seqqa-evidence-paper |
| LAB-Bench SeqQA — Gene-to-restriction primers root: lab-bench | DNA sequence design official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-gene-enzprimers-evidence-paper |
| LAB-Bench SeqQA — Gene-to-Gibson primers (HindIII) root: lab-bench | DNA sequence design official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-gene-gibshindprimers-evidence-paper |
| LAB-Bench SeqQA — Gene-to-Gibson primers (SmaI) root: lab-bench | DNA sequence design official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-gene-gibssmaprimers-evidence-paper |
| LAB-Bench SeqQA — Amplicon length to primers root: lab-bench | DNA sequence design official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-len-primers-evidence-paper |
| LAB-Bench SeqQA — Sequence-to-restriction primers root: lab-bench | DNA sequence design official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-seq-enzprimers-evidence-paper |
| LAB-Bench SeqQA — Amplicon sequence to primers root: lab-bench | DNA sequence design official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-pcr-seq-primers-evidence-paper |
| Biology-Instructions root: bioinstruction | Enhancer activity prediction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (Enhancer Activity Prediction). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Enhancer Activity Prediction root: bioinstruction | Enhancer activity prediction official-track · high | explicitly-in-scope | 484052 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-ea-evidence-paper |
| Genomic Benchmarks root: genomic-benchmarks | Enhancer activity prediction official-taxonomy · high | explicitly-in-scope | 4 tasks Benchmark dataset classification tasks. | package-1.0.0-snapshot as of 2026-07-22 | genomic-benchmarks-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | Enhancer-promoter interaction prediction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (Enhancer-Promoter Interaction Prediction). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Enhancer-Promoter Interaction Prediction root: bioinstruction | Enhancer-promoter interaction prediction official-track · high | explicitly-in-scope | 16368 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-epi-evidence-paper |
| Biology-Instructions root: bioinstruction | Epigenetic-mark prediction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (Epigenetic Marks Prediction). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Epigenetic Marks Prediction root: bioinstruction | Epigenetic-mark prediction official-track · high | explicitly-in-scope | 287367 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-emp-evidence-paper |
| Genomic Benchmarks root: genomic-benchmarks | Epigenetic-mark prediction official-taxonomy · high | explicitly-in-scope | 1 tasks Benchmark dataset classification tasks. | package-1.0.0-snapshot as of 2026-07-22 | genomic-benchmarks-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | Promoter detection official-track · high | explicitly-in-scope | 2 tracks Formal evaluation tracks (Core Promoter Detection and Promoter Detection 300). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Core Promoter Detection root: bioinstruction | Promoter detection official-track · high | explicitly-in-scope | 118392 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-cpd-evidence-paper |
| Biology-Instructions Promoter Detection 300 root: bioinstruction | Promoter detection official-track · high | explicitly-in-scope | 118392 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-pd300-evidence-paper |
| Genomic Benchmarks root: genomic-benchmarks | Promoter detection official-taxonomy · high | explicitly-in-scope | 1 tasks Benchmark dataset classification tasks. | package-1.0.0-snapshot as of 2026-07-22 | genomic-benchmarks-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | Transcription-factor binding-site prediction official-track · high | explicitly-in-scope | 2 tracks Formal evaluation tracks (Human and mouse Transcription Binding Sites Detection). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Human Transcription Binding Sites Detection root: bioinstruction | Transcription-factor binding-site prediction official-track · high | explicitly-in-scope | 138344 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-tb-human-evidence-paper |
| Biology-Instructions Mouse Transcription Binding Sites Detection root: bioinstruction | Transcription-factor binding-site prediction official-track · high | explicitly-in-scope | 100028 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-tb-mouse-evidence-paper |
| LAB-Bench DbQA — GTRD transcription-factor binding sites root: lab-bench | Transcription-factor binding-site prediction official-track · high | observed | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-dbqa-tfbs-gtrd-evidence-paper |
Official evaluations connected to these benchmarks
Runs are included only for benchmark records mapped here (and formal child tracks when a mapped suite is the root). A task mapping does not imply that every run isolates this task.