All Competitors
Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 313–336 of 518 filtered models
PLMNovo
—1—De novo peptide sequencing model that aligns tandem mass spectra with protein language model embeddings through constrained optimization.
Protein19OpennessKidney-specialized single-cell foundation model trained across four mammalian species for zero-shot cell-type annotation and batch integration.
Single-cellSpatial omics22OpennessBioVERSE
—2—Multimodal biomedical framework aligning frozen single-cell and protein model encoders to an LLM's embedding space for zero-shot reasoning.
Language modelSingle-cellProtein23OpennessGCP-VQVAE
432—Protein structure tokenizer that maps 3D backbones to discrete tokens with an SE(3)-equivariant encoder preserving orientation and chirality.
Protein86OpennessScooby
6912359Technical University of Munich +4 othersOctober 1, 2025chromatinchromatin_accessibility_predictionconvolutional_neural_network+5Predicts single-cell scRNA-seq coverage and scATAC-seq insertion profiles from DNA sequence, adapting the Borzoi trunk with a cell-specific decoder.
Single-cell70OpennessSciReasoner
90—49Multimodal scientific foundation model unifying protein, DNA/RNA, and small-molecule structure in one token vocabulary for cross-domain reasoning.
ProteinDNA & GeneSmall molecule66OpennessEiRA
—2—Protein binder design model post-trained from a multimodal protein language model to bind proteins, peptides, small molecules, and nucleic acids.
Protein13OpennessscYeast
51—Single-cell foundation model for yeast that injects regulatory network priors into transformer attention for zero-shot and fine-tuned analysis.
Single-cell68OpennessrBio
14616—Reasoning language model post-trained on virtual cell simulations, answering questions about gene perturbations and their effects in natural language.
Language model60OpennessChromnitron
261—Multimodal foundation model predicting genome-wide binding of chromatin-associated proteins from protein sequence, DNA sequence, and chromatin state.
DNA & GeneProtein25OpennessAVES2-BEATs
396—Self-supervised bioacoustic audio encoder that turns animal-sound recordings into transferable embeddings for species classification and detection.
Biosignals59OpennessCLASP
44—Tri-modal contrastive model aligning protein structure, sequence, and text in a shared space for zero-shot cross-modal retrieval and classification.
Protein42OpennessstructRFM
36329RNA foundation model pretrained jointly on sequences and secondary structures for structure prediction, homology and splice site classification.
RNA92OpennessPoET-2
2710—Multimodal, retrieval-augmented protein foundation model that learns family-specific evolutionary constraints with optional structure conditioning.
Protein37OpennessOpenMed NER
4.7K2—Biomedical named entity recognition transformers, with task-specialized checkpoints for chemicals, diseases, genes, proteins, species, and anatomy.
Language model71OpennessProteomeLM
363237EPFLAugust 1, 2025foundation_modelgene_essentiality_predictionprotein_protein_interaction_prediction+4Proteome-scale protein language model whose representations enable zero-shot protein-protein interaction and gene essentiality prediction.
Protein64OpennessGREmLN
38——Single-cell transcriptomics foundation model that encodes gene regulatory network structure into self-attention through graph signal processing.
Single-cell80OpennessZebraformer
—1—Zebrafish single-cell foundation model built on the Geneformer framework, producing frozen gene and cell embeddings for developmental analysis.
Single-cell46OpennessMedGemma
1.6K375118.8KOpen medical multimodal models from Google, built on Gemma 3 with a medically tuned SigLIP vision encoder for clinical text and image understanding.
Language modelImaging41OpennessPLMDA-PPI
101—Huazhong University of Science and TechnologyJuly 4, 2025graph_neural_networkinterface_contact_predictionprotein_protein_interaction+4Protein-protein interaction predictor that adds contact-guided dual attention and a geometric encoder to frozen protein language model embeddings.
Protein77Openness- University of Oxford +5 othersJuly 1, 2025clinical_outcome_predictioncross_modality_generationdiagnosis+8
Multimodal foundation model for cardiac biosignals, pretrained by masked modeling on ECG, PPG, and clinical text from ~1.7 million individuals.
BiosignalsLanguage model26Openness SigPhi-Med
594Chongqing University of TechnologyJuly 1, 2025histologyinstruction_tuningmedical_image_understanding+5Biomedical vision-language assistant for medical visual question answering, pairing Phi-2 with a vision encoder in a 4.2B-parameter model.
ImagingLanguage model15OpennessMELP
311817Multi-scale ECG-language model that aligns 12-lead ECG signals with clinical text at token, beat, and rhythm levels for zero-shot cardiac diagnosis.
BiosignalsLanguage model68Openness