Biological benchmarks

30 benchmark records in release 2026-09-22-f58a0f1d267f.

Broad tasks, specific protocols and evaluators have their own records. Follow each benchmark to its procedures and results.

• ATOM3D

  Molecular interactions

  ATOM3D provides molecular-structure datasets and utilities for task-specific evaluation.

• BEACON

  RNA

  BEACON compares RNA representations across structural and functional downstream tasks.

• BEELINE

  Biological networks

  BEELINE compares inferred gene-regulatory edge rankings with reference networks.

• BEND

  Genomics

  BEND evaluates DNA representations using task-specific genomic annotations and explicit split membership.

• CAFA

  Protein function

  CAFA evaluates prospective protein-function predictions against annotations that become available after prediction submission.

• CAMI

  Microbiome

  CAMI is a community benchmark program for metagenomic computational methods.

• CAPRI

  Protein structure

  CAPRI assesses blind predictions of protein-complex structures supplied before experimental publication.

• CASP

  Protein structure

  CASP assesses structure-prediction methods through blind predictions and category-specific evaluation.

• DART-Eval

  Genomics

  DART-Eval measures human regulatory-DNA representations under zero-shot, probing and fine-tuning regimes.

• FLIP

  Protein function

  FLIP evaluates protein-sequence representations using multiple deliberately defined train/test splits.

• FLIP2

  Protein function

  FLIP2 evaluates protein fitness prediction under deliberately shifted training and test distributions.

• GENEB

  Genomics

  GENEB compares frozen genomic representations across classification tasks and label-budget regimes.

• Genomic Benchmarks

  Genomics

  Genomic Benchmarks packages genomic sequence-classification datasets with explicit versions and supplied train/test folders.

• GlycanML

  Glycomics

  GlycanML evaluates glycan learning across multiple classification and interaction tasks.

• GUE

  Genomics

  GUE evaluates genome understanding across multiple datasets, task types and species.

• HEST-Benchmark

  Spatial omics

  HEST-Benchmark tests prediction of gene expression from histological image representations.

• MassSpecGym

  Metabolomics

  MassSpecGym separates spectrum-to-structure generation, candidate retrieval and structure-to-spectrum simulation.

• mRNABench

  RNA

  mRNABench assesses genomic-model embeddings on transcript-specific expression, stability and regulatory tasks.

• NABench

  RNA

  NABench compares nucleotide foundation models on measured DNA/RNA sequence effects under multiple adaptation settings.

• Open Problems

  Single cell

  Open Problems is an extensible platform hosting benchmark tasks and their datasets.

• PerturBench

  Single cell

  PerturBench evaluates predicted single-cell perturbation responses with explicit aggregation and metric choices.

• PEtab benchmark collection

  Mechanistic biology

  The PEtab collection supports evaluation of computational methods for fitting mathematical models to observations.

• PFMBench

  Protein function

  PFMBench is a configurable suite of protein-model downstream evaluations.

• PLINDER

  Molecular interactions

  PLINDER supplies annotated protein–ligand systems and evaluation resources for docking.

• ProteinBench

  Protein structure

  ProteinBench assesses multiple protein-model tasks using quality, novelty, diversity and robustness dimensions.

• ProteinGym

  Protein function

  ProteinGym separates experimental variant-effect and clinical annotation tasks under supervised and zero-shot regimes.

• scIB

  Single cell

  scIB is an atlas-level single-cell integration benchmark study covering RNA, chromatin-accessibility and simulated datasets. It compares batch removal with preservation of biological variation. The scib Python package and scib-pipeline implement its evaluation workflow.

• TAPE

  Protein function

  TAPE evaluates protein representations through five supervised downstream tasks.

• TDC molecular tasks

  Molecular interactions

  TDC organizes molecular prediction tasks into datasets and benchmark groups with explicit splitting and evaluation interfaces.

• Virtual Cell Challenge 2026

  Single cell

  The 2026 Virtual Cell Challenge evaluates perturbation-response prediction in unseen cellular contexts.

This index reflects a dated catalogue, not an exhaustive census. Source checking does not mean independent reproduction; compare results only under compatible protocols, datasets and metrics.