Biological benchmarks

39 benchmark records in release 2026-09-29-06401fd5b220.

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.

• ESMFold2 Runs N’ Poses comparison

  Proteins and complexes

  Bounded complete Figure 2C Runs N’ Poses subpanel: all eleven printed labels, separated into single-sequence and MSA comparisons.

• 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.

• Gene-MTEB

  Genomics

  Genomic embedding evaluations covering sequence classification and clustering. Accuracy and V-measure remain separate metrics and each source task retains its own comparison.

• GENEB

  Genomics

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

• Genie 3 unconditional short monomer comparison

  Proteins and complexes

  Bounded complete Table 3 comparison across 13 method/version rows. Five directional metrics are included; secondary-structure composition is retained separately without ranking.

• 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.

• MIST CANOPUS molecular retrieval

  Metabolomics

  Molecular candidate retrieval from mass spectra, as evaluated in DreaMS Extended Data Table 1. Inputs and extra training data differ across the reported methods.

• mRNABench

  RNA

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

• MSAlign molecular retrieval evaluations

  Metabolomics

  Spectrum-to-molecule retrieval comparisons on NPLIB1, Spectraverse and two MassSpecGym splits, reported in MSAlign Table 3. Formula availability and candidate pools remain separate.

• 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.

• Plant Genomic Benchmark (PGB)

  Genomics

  Plant genomic evaluations introduced with AgroNT. This release contains the complete promoter and terminator comparison tables from Figure 3e and 3f; other tasks remain unextracted.

• 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.

• RhoFold+ CASP15 natural RNA comparison

  RNA and transcriptomics

  Complete Figure 2h source table: ten configurations, six natural CASP15 RNA targets, RMSD and cumulative GDT-TS/TM Z-score. Retrospective best-of-five comparison; eight unavailable entries retained in extraction receipts.

• scFoundation cell-type annotation comparison

  Cells spatial multiomics

  Source-specific reported comparison. Protocol details, fitted configurations and limitations are retained separately from other evaluations.

• 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.

• SegmentNT human genome annotation

  Genomics

  Fourteen genomic-element annotation tasks from the SegmentNT study, with complete per-nucleotide MCC and auPRC comparisons from Supplementary Tables 2 and 3. Each element and metric remains a separate comparison.

• 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.