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.
Scientific task · Sequence and regulation
RNA function and design
Predict or design RNA structure
RNA功能与设计
Definition and search aliases
- Permanent ID
rna-function-design- Aliases
- RNA tasks
- Deprecated aliases
- None
- Hierarchy
- Parent task; benchmark coverage below includes its leaf tasks.
Coverage
4 benchmark families cover this task
Biology-Instructions Programmable RNA Switches
Three-output regression of ON, OFF, and ON/OFF programmable RNA-switch values, aggregated as their mean squared Pearson correlation.
BEACON
A 13-task RNA representation benchmark covering structure, function, processing, modification, translation, degradation, programmable switches, and CRISPR activity.
Biology-Instructions Non-coding RNA Function Classification
Thirteen-class functional classification of a non-coding RNA sequence, evaluated with exact extracted-label accuracy.
Biology-Instructions RNA Modification Prediction
Multi-label prediction of RNA chemical modifications, evaluated with macro area under the ROC curve.
Biology-Instructions APA Isoform Prediction
Regression of alternative-polyadenylation isoform usage from an RNA sequence, reported as squared Pearson correlation under the paper's R2 label.
Biology-Instructions Mean Ribosome Loading Prediction
Regression of mean ribosome loading from an RNA sequence, reported as squared Pearson correlation under the paper's R2 label.
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 — ORF amino-acid position
Finds the amino acid encoded at a specified position in the longest ORF of a DNA sequence.
LAB-Bench SeqQA — ORF amino-acid sequence
Translates the longest ORF in a DNA sequence to its amino-acid sequence.
LAB-Bench SeqQA — ORF count above length
Counts open reading frames encoding proteins above a specified amino-acid length.
LAB-Bench SeqQA — Translation efficiency
Selects an RNA sequence whose ORF context is most likely to yield high translation efficiency.
ATOM3D
A living collection of eight curated 3D molecular-learning tasks spanning small molecules, protein interactions and mutations, ligand binding, and protein/RNA structure ranking.
Biology-Instructions siRNA Efficiency Prediction
Regression of siRNA efficiency from paired sequence context, evaluated with the SAIS-inspired mixed score.
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 |
|---|---|---|---|---|---|
| Biology-Instructions root: bioinstruction | RNA design official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (Programmable RNA Switches). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Programmable RNA Switches root: bioinstruction | RNA design official-track · high | explicitly-in-scope | 93399 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-prs-evidence-paper |
| BEACON root: beacon-rna | RNA function classification official-taxonomy · high | explicitly-in-scope | 1 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | RNA function classification official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (Non-coding RNA Function Classification). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions Non-coding RNA Function Classification root: bioinstruction | RNA function classification official-track · high | explicitly-in-scope | 11160 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-ncrna-evidence-paper |
| BEACON root: beacon-rna | RNA modification prediction official-taxonomy · high | explicitly-in-scope | 1 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | RNA modification prediction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (RNA Modification Prediction). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions RNA Modification Prediction root: bioinstruction | RNA modification prediction official-track · high | explicitly-in-scope | 309460 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-modification-evidence-paper |
| BEACON root: beacon-rna | RNA processing and translation prediction official-taxonomy · high | explicitly-in-scope | 3 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | RNA processing and translation prediction official-track · high | explicitly-in-scope | 2 tracks Formal evaluation tracks (APA Isoform Prediction and Mean Ribosome Loading). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions APA Isoform Prediction root: bioinstruction | RNA processing and translation prediction official-track · high | explicitly-in-scope | 1658482 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-apa-evidence-paper |
| Biology-Instructions Mean Ribosome Loading Prediction root: bioinstruction | RNA processing and translation prediction official-track · high | explicitly-in-scope | 91519 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-mrl-evidence-paper |
| LAB-Bench SeqQA root: lab-bench | RNA processing and translation prediction official-track · high | explicitly-in-scope | 200 questions Four 50-question ORF and translation formal child tracks. | repository-998a8e0 | lab-bench-seqqa-evidence-paper |
| LAB-Bench SeqQA — ORF amino-acid position root: lab-bench | RNA processing and translation prediction official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-orf-seq-aaid-evidence-paper |
| LAB-Bench SeqQA — ORF amino-acid sequence root: lab-bench | RNA processing and translation prediction official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-orf-seq-aaseq-evidence-paper |
| LAB-Bench SeqQA — ORF count above length root: lab-bench | RNA processing and translation prediction official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-orf-seq-numlen-evidence-paper |
| LAB-Bench SeqQA — Translation efficiency root: lab-bench | RNA processing and translation prediction official-track · high | explicitly-in-scope | 50 questions questions across public and private splits | repository-998a8e0 | lab-bench-seqqa-orf-transeff-evidence-paper |
| BEACON root: beacon-rna | RNA stability and degradation prediction official-taxonomy · high | explicitly-in-scope | 1 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| BEACON root: beacon-rna | RNA structure prediction official-taxonomy · high | explicitly-in-scope | 4 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| ATOM3D root: atom3d | RNA structure quality assessment official-track · high | explicitly-in-scope | 1 tasks Curated 3D benchmark datasets. | v0.2.6 as of 2026-07-22 | atom3d-paper-definition-evidence |
| BEACON root: beacon-rna | Programmable RNA-switch activity prediction official-taxonomy · high | explicitly-in-scope | 1 tasks Formal RNA benchmark tasks. | neurips-2024 | beacon-paper-definition-evidence |
| Biology-Instructions root: bioinstruction | siRNA efficacy prediction official-track · high | explicitly-in-scope | 1 tracks Formal evaluation tracks (siRNA Efficiency Prediction). | emnlp-2025 | bioinstruction-evidence-paper |
| Biology-Instructions siRNA Efficiency Prediction root: bioinstruction | siRNA efficacy prediction official-track · high | explicitly-in-scope | 66987 examples distinct examples across the published train, validation, and test splits | emnlp-2025 | bioinstruction-sirna-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.