rewire.itbenchmarks

Omics and molecular biologyRelease 2026-09-29

Biological model benchmark database

Find biological models, see how they were tested and inspect the evidence behind each result.

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Methods and evaluation records

Biological models and model families. Evaluated versions, configurations and pipelines are linked separately.

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54 matching models

Model · Not yet reviewed

AlphaGenome

AlphaGenome predicts regulatory activity and variant effects from long DNA sequences, with outputs for expression, splicing, chromatin and contact maps.

DNA and genomes · 4 sources

44 evaluations · 52 results

Model · Not yet reviewed

Boltz-2

Boltz predicts biomolecular complex structures; Boltz-2 also predicts binding affinity.

Molecular interactions · 7 sources

1 evaluation · 1 result

Model · Not yet reviewed

Chai-1

Chai-1 predicts the structures of biomolecular complexes containing proteins, nucleic acids and small molecules.

Proteins and complexes · Molecular interactions · 3 sources

5 evaluations · 5 results

Model · Not yet reviewed

DiffDock-L

DiffDock-L places small-molecule ligands in protein structures using a diffusion docking model.

Molecular interactions · 3 sources

1 evaluation · 1 result

Model · Not yet reviewed

ESM-2

ESM-2 is a family of protein sequence encoders that produce representations for downstream protein analyses.

Proteins and complexes · 4 sources

3 evaluations · 11 results

Model · Not yet reviewed

ESMFold

ESMFold predicts protein structures directly from amino-acid sequence using ESM-2 representations.

Proteins and complexes · 4 sources

14 evaluations · 14 results

Model · Not yet reviewed

Evo 2

Evo 2 models and generates DNA over long contexts at single-nucleotide resolution.

DNA and genomes · Microbes and communities · 5 sources

87 evaluations · 92 results

Model · Not yet reviewed

GEARS

GEARS predicts transcriptional responses to single- and multi-gene perturbations from single-cell perturbation screens.

Cells and tissues · 4 sources

1 evaluation · 2 results

Model · Not yet reviewed

Geneformer

Geneformer represents single-cell transcriptomes as ranked genes and learns contextual gene and cell representations.

Cells and tissues · 3 sources

5 evaluations · 5 results

Model · Not yet reviewed

METAGENE-1

METAGENE-1 is an autoregressive DNA/RNA sequence model trained on wastewater metagenomic data.

Microbes and communities · 5 sources

No evaluations linked in this release

How to read the evidence

Coverage: records and linked evaluations

26,126 records across 16 record types. These counts describe catalogue coverage, not model performance.

Records by kind

  • result11,307
  • evaluation8,730
  • configuration2,393
  • claim1,121
  • source974
  • task495
  • dataset subset335
  • protocol335
  • dataset138
  • pipeline124
  • model61
  • method42
  • benchmark39
  • baseline27
  • evaluator4
  • service1

Records by research area

  • RNA and transcriptomes3,773
  • Proteins and complexes3,312
  • DNA and genomes2,698
  • Cells and tissues1,430
  • Genomics1,415
  • RNA and transcriptomics1,169
  • Molecular interactions764
  • Glycomics498
  • Molecular omics489
  • Microbes and communities457

Benchmark evidence coverage

38 of 39 benchmarks have linked evaluations in this release. Zero means no evaluation is linked here, not that the benchmark has never been used.

  • NABench1,101
  • Virtual Cell Challenge 20261,048
  • mRNABench696
  • ProteinBench556
  • CAFA438
  • BEELINE384
  • Open Problems384
  • GlycanML323
  • DART-Eval316
  • SegmentNT human genome annotation294
  • GUE280
  • BEACON221
  • FLIP155
  • FLIP2149
  • PFMBench141
  • BEND105
  • CAPRI100
  • HEST-Benchmark100
  • CASP90
  • ProteinGym90
  • Gene-MTEB80
  • PerturBench76
  • scIB69
  • TDC molecular tasks66
  • ATOM3D57
  • RhoFold+ CASP15 natural RNA comparison56
  • TAPE50
  • MSAlign molecular retrieval evaluations36
  • MassSpecGym24
  • Plant Genomic Benchmark (PGB)24
  • GENEB22
  • Genomic Benchmarks18
  • CAMI16
  • scFoundation cell-type annotation comparison14
  • Genie 3 unconditional short monomer comparison13
  • ESMFold2 Runs N’ Poses comparison11
  • PLINDER7
  • MIST CANOPUS molecular retrieval6
  • PEtab benchmark collection0

Published evaluations and rewire evaluations are records in the same database, with their origin shown beside each result. This release includes 11,295 source-checked published results and 12 results from existing rewire runs.

Source checked does not mean independently reproduced. Comparisons require compatible data, protocols and metrics. Missing details stay visible.

Investigate discrepancies

Check whether the data supports replaying a metric, investigating an unexpected result or testing an explanation independently.

Readiness and investigations →

Rewire evaluations

Read the protocol, coverage and limitations behind our corrected splice-variant evaluation.

MFASS v2 evaluation →

Correction history

MFASS v1 is superseded. Its original tables and methods remain available as an archived report.

Archived MFASS v1 report →
Collection coverage and remaining gaps

This is a dated collection, not an exhaustive model census. Models, methods, evaluated configurations and pipelines are listed separately. Counts describe records, not unique checkpoints or independent experiments.

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Release 2026-09-29-06401fd5b220 · 2026-09-29

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Original literature downloads

The original 100-paper collection is retained for citation history. These files include six result rows excluded from the current omics scope; use the database release above for the reviewed collection.

Original results CSVOriginal papers JSON