All Competitors
Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 121–144 of 552 filtered models
ATOMICA
—3—Geometric deep learning model that learns atomic-scale representations of molecular interfaces across proteins, small molecules, and nucleic acids.
ProteinSmall moleculeRNA88OpennessSpatialFusion
40——Multimodal foundation model integrating spatial transcriptomics, H&E histopathology, and pathway scores for single-cell niche discovery.
Spatial omicsSingle-cellPathology71OpennessAnewOmni
842—All-atom generative foundation model that designs small molecules, peptides, and nanobodies against a target binding site from a single checkpoint.
ProteinSmall molecule63OpennessAetherCell
202—Generative virtual-cell model predicting whole-transcriptome responses to unseen compounds and genetic perturbations, from cell lines to organoids.
Single-cellSmall molecule29OpennessCDS-BART
——9Coding-sequence foundation model for mRNA design, pretrained as a BART denoising encoder-decoder on mRNA from nine taxonomic groups.
RNA63OpennessmnDINO
———Vision transformer trained with DINO self-supervision to segment micronuclei in DNA-stained fluorescence images across cell lines and microscopes.
Imaging32OpennessPatchDNA
—2—DNA language model that replaces fixed tokenization with conservation-guided patching, letting models up to 10x smaller match top genomic benchmarks.
DNA & Gene33OpennessCell-centric microscopy foundation model that distills morphology and microenvironment views into a unified embedding for virtual spatial omics.
Spatial omicsImagingPathology15OpennessPaired-sequence protein language model that jointly encodes two interacting chains to predict interactions, binding affinity, and interface contacts.
Protein27OpennessFishMamba-1
——11Institute of Hydrobiology, Chinese Academy of SciencesMarch 9, 2026dnafoundation_modelgenome_annotation+4Genomic foundation model for Cypriniformes fish, built on a Mamba-2 state space model with a 32 kb context window for long-range genome modeling.
DNA & Gene50OpennessBacPT
—1—Bacterial proteome foundation model that learns contextualized gene and whole-genome representations from tens of thousands of complete genomes.
Protein10OpennessEEG-to-text foundation model that turns raw recordings into clinically grounded natural-language narratives instead of fixed-label classifications.
Biosignals18OpennessPopformer
———Self-supervised transformer for population genetics, pretrained on 1000 Genomes data, that detects positive selection via haplotype-wise attention.
DNA & Gene19OpennessPerturbGen
25——Generative single-cell foundation model trained on 100M+ transcriptomes that predicts how genetic perturbations reshape cell trajectories over time.
Single-cell72OpennessSmall-molecule drug discovery foundation model covering ADMET, retrosynthesis, drug-target activity, and molecular optimization in a 2.6B checkpoint.
Small moleculeLanguage model7OpennessD3LM
—142DNA foundation model using masked discrete diffusion to unify bidirectional sequence understanding and de novo generation in one architecture.
DNA & Gene58OpennessMolX
—1—Monash UniversityMarch 1, 2026antibody_drug_conjugate_designbinding_affinity_predictiondrug_discovery+10Graph-transformer foundation model pretrained on 3M protein pockets and 5M molecules as E(3)-equivariant graphs for protein-ligand representation.
Protein11OpennessMultiPUFFIN
———Multimodal foundation model pretrained on ~500K unlabeled PubChem molecules that jointly predicts nine thermophysical properties of small molecules.
Small molecule10OpennessLarge language model trained on functional genomics data to prioritize novel therapeutic targets from genome-wide CRISPR knockout screens.
DNA & GeneLanguage model12OpennessARCH3D
———Foundation model for 3D genome architecture, using masked locus modeling over genome-wide contact profiles to capture chromosome-scale organization.
DNA & Gene19OpennessBOTANIC-0
—1177Plant genomic foundation models from 0.1B to 1B parameters, pretrained on 43 phylogenetically diverse plant genomes for variant effect prediction.
DNA & Gene19OpennessCellAwareGNN
—1—Vanderbilt University Medical CenterFebruary 23, 2026drug_discoveryfoundation_modelgraph_neural_network+4Knowledge-graph foundation model for drug repurposing, grounding a biomedical graph in cell-type-specific genetic associations to rank indications.
Single-cellSmall molecule11OpennessMACE-POLAR-1
—16—Polarizable machine-learning interatomic potential extending MACE with long-range electrostatics, trained on 100M OMol25 DFT calculations.
Small moleculeProtein19OpennessSingle-cell foundation model applying discrete diffusion directly to scRNA-seq counts, generating unconditional and perturbation-conditioned profiles.
Single-cell10Openness