BEACON
A 13-task RNA representation benchmark covering structure, function, processing, modification, translation, degradation, programmable switches, and CRISPR activity.
Scientific domain
Transcriptomics
Bulk and other transcriptome-level measurements and analyses.
转录组学
27 registered benchmarks and tracks
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 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 CRISPR On-Target Prediction
Regression of CRISPR guide on-target activity from an RNA sequence, evaluated with Spearman rank correlation.
Biology-Instructions RNA Modification Prediction
Multi-label prediction of RNA chemical modifications, evaluated with macro area under the ROC curve.
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.
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 Programmable RNA Switches
Three-output regression of ON, OFF, and ON/OFF programmable RNA-switch values, aggregated as their mean squared Pearson correlation.
Biology-Instructions RNA-Protein Interaction Prediction
Binary interaction prediction for an RNA and protein sequence pair, evaluated with Matthews correlation coefficient.
Biology-Instructions siRNA Efficiency Prediction
Regression of siRNA efficiency from paired sequence context, evaluated with the SAIS-inspired mixed score.
BioMysteryBench
An agentic bioinformatics benchmark of objective, expert-authored mysteries over anonymized real-world biological data, scored on final answers rather than prescribed analysis paths.
BixBench
A containerized benchmark of long-horizon bioinformatics analysis over real published notebooks and associated data, with open-answer and multiple-choice evaluation modes.
CompBioBench
A 100-task agent benchmark of objectively gradable computational-biology problems requiring multi-step reasoning, bespoke code, tools, and real-world external resources.
Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing
A reusable benchmark for comparing differential transcript usage detection tools across simulated and real transcriptomics data.
crafted experiments
Real single-cell RNA-seq data augmented with known gene perturbations for comparing feature-selection methods.
GeneBench-Pro
A research-level agent benchmark of 129 synthetic, multistage computational-biology analyses that require iterative QC, statistical modeling, diagnostics, and decision-relevant judgment.
LAB-Bench
A practical biology-research suite of 2,457 multiple-choice questions across eight broad categories and 31 versioned task files, with public and private contamination-monitoring splits.
LAB-Bench DbQA
Database-retrieval category spanning 10 genomics, clinical, protein, regulatory, vaccine-response, and viral-PPI tasks.
LAB-Bench DbQA — miRNA targets
Retrieves computationally predicted human miRNA targets from miRDB.
LAB-Bench DbQA — Vaccine response gene sets
Retrieves membership in MSigDB vaccine-response gene sets.
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 — Translation efficiency
Selects an RNA sequence whose ORF context is most likely to yield high translation efficiency.
LifeSciBench
Expert-authored, artifact-rich free-response tasks that evaluate realistic research judgment across applied life-science workflows.
scBench
Agentic evaluation suite for data-grounded single-cell analysis across diverse sequencing technologies and workflow stages.
scIB
A 13-task benchmark of single-cell data integration across simulated, scRNA-seq, and scATAC-seq settings, evaluated with 14 batch-removal and biological-conservation metrics.
Single-cell Omics Arena
A benchmark for evaluating LLM cell-type annotation across scRNA-seq and single-cell multiomics data.
SpatialBench
A benchmark of deterministic, verifiable agentic problems derived from real spatial-transcriptomics workflows, testing whether agents can manipulate data and recover key biological results.
Capability coverage
Registry records tagged Transcriptomics, counted by capability.
Accessible data table
| Capability | Records |
|---|---|
| Knowledge | 4 |
| Evidence synthesis | 2 |
| Retrieval | 6 |
| Prediction | 15 |
| Classification | 8 |
| Regression | 7 |
| Design | 3 |
| Generation | 1 |
| Optimization | 1 |
| Data analysis | 12 |
| Coding | 6 |
| Tool use | 8 |
| Experiment planning | 2 |
| Troubleshooting | 2 |
| Scientific reasoning | 13 |
| Scientific communication | 1 |
Scientific Tasks in this domain
Task mappings are evidence-backed and may be partial for mixed suites.
Coverage-gap reading: zero counts indicate a gap in this registry, not proof that no benchmark exists. Propose a primary source through the contribution form.