AlphaGenome
AlphaGenome predicts regulatory activity and variant effects from long DNA sequences, with outputs for expression, splicing, chromatin and contact maps.
dna-genomes · 4 linked sources
Omics and molecular biology
Biological model benchmark database
Find models, understand how they are tested, and inspect the evidence behind their results.
Methods and evaluation records
Biological models and model families. Evaluated versions, configurations and pipelines are linked separately.
59 matching records · Release 2026-09-17-d277315f7d76
Boltz-2
Boltz predicts biomolecular complex structures; Boltz-2 also predicts binding affinity.
molecular-interactions · 7 linked sources
Chai-1
Chai-1 predicts the structures of biomolecular complexes containing proteins, nucleic acids and small molecules.
proteins-complexes · molecular-interactions · 3 linked sources
DiffDock-L
DiffDock-L places small-molecule ligands in protein structures using a diffusion docking model.
molecular-interactions · 3 linked sources
DNABERT-2
DNABERT-2 learns DNA representations that can be adapted to genomic prediction tasks.
dna-genomes · 6 linked sources
ESM-2
ESM-2 is a family of protein sequence encoders that produce representations for downstream protein analyses.
proteins-complexes · 4 linked sources
ESMFold
ESMFold predicts protein structures directly from amino-acid sequence using ESM-2 representations.
proteins-complexes · 4 linked sources
Evo 2
Evo 2 models and generates DNA over long contexts at single-nucleotide resolution.
dna-genomes · microbes-communities · 5 linked sources
GEARS
GEARS predicts transcriptional responses to single- and multi-gene perturbations from single-cell perturbation screens.
cells-tissues · 4 linked sources
Geneformer
Geneformer represents single-cell transcriptomes as ranked genes and learns contextual gene and cell representations.
cells-tissues · 3 linked sources
METAGENE-1
METAGENE-1 is an autoregressive DNA/RNA sequence model trained on wastewater metagenomic data.
microbes-communities · 5 linked sources
MIMIC
MIMIC represents DNA, RNA, protein and associated molecular measurements in a shared multimodal model.
rna-transcriptomes · proteins-complexes · 5 linked sources
mRNA-FM
mRNA-FM encodes coding RNA with codon-level tokens to produce representations for downstream analysis.
rna-transcriptomes · 3 linked sources
Nucleotide Transformer v2
Nucleotide Transformer v2 represents DNA using an encoder pretrained on multiple species.
dna-genomes · 8 linked sources
Pangolin
Pangolin predicts splice-site strength and changes caused by genetic variants.
dna-genomes · 3 linked sources
ProkBERT
ProkBERT is a family of microbial DNA encoders used for sequence representation, promoter prediction and phage identification.
microbes-communities · 5 linked sources
ProteinMPNN
ProteinMPNN designs amino-acid sequences for a supplied protein backbone.
proteins-complexes · 6 linked sources
RhoFold+
RhoFold+ predicts RNA three-dimensional structures from RNA sequence with alignment information.
rna-transcriptomes · 4 linked sources
RNA-FM
RNA-FM learns contextual representations of RNA nucleotides for downstream RNA analyses.
rna-transcriptomes · 4 linked sources
scFoundation
scFoundation produces contextual cell and gene representations from gene-expression measurements.
cells-tissues · 4 linked sources
About the evidence
Published evaluations and rewire evaluations are records in the same database, with their origin shown beside each result. This release includes 1422 source-checked literature result rows and 12 metric rows from existing rewire runs.
Source checked does not mean independently reproduced. Comparisons require compatible data, protocols and metrics. Missing details stay visible.
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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}Download the database
Release 2026-09-17-d277315f7d76 · 2026-09-17
JSONLCSVEvidence table (CSV)Evidence table (JSONL)Evidence and review methodsChecksums and release manifest
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.