All Competitors

Every biological foundation model, evaluated and ranked by the bio.rodeo team

Showing 313336 of 518 filtered models

  • PLMNovo

    1
    Duke UniversityOctober 3, 2025de_novo_peptide_sequencingmass_spectrometryprotein_sequencing+4

    De novo peptide sequencing model that aligns tandem mass spectra with protein language model embeddings through constrained optimization.

    Protein
    19Openness
  • University of PennsylvaniaOctober 1, 2025batch_integrationcell_type_annotationfoundation_model+5

    Kidney-specialized single-cell foundation model trained across four mammalian species for zero-shot cell-type annotation and batch integration.

    Single-cellSpatial omics
    22Openness
  • BioVERSE

    2
    IBM ResearchOctober 1, 2025cell_biologycell_type_annotationcross_modal_question_answering+5

    Multimodal biomedical framework aligning frozen single-cell and protein model encoders to an LLM's embedding space for zero-shot reasoning.

    Language modelSingle-cellProtein
    23Openness
  • GCP-VQVAE

    432
    University of MissouriOctober 1, 2025graph_neural_networkprotein_structurerepresentation_learning+4

    Protein structure tokenizer that maps 3D backbones to discrete tokens with an SE(3)-equivariant encoder preserving orientation and chirality.

    Protein
    86Openness
  • Scooby

    6912359
    Technical University of Munich +4 othersOctober 1, 2025chromatinchromatin_accessibility_predictionconvolutional_neural_network+5

    Predicts single-cell scRNA-seq coverage and scATAC-seq insertion profiles from DNA sequence, adapting the Borzoi trunk with a cell-specific decoder.

    Single-cell
    70Openness
  • Shanghai AI LaboratorySeptember 25, 2025foundation_modelmultimodalprotein_function_prediction+2

    Multimodal scientific foundation model unifying protein, DNA/RNA, and small-molecule structure in one token vocabulary for cross-domain reasoning.

    ProteinDNA & GeneSmall molecule
    66Openness
  • EiRA

    2
    Hunan UniversitySeptember 2, 2025binder_designdnagenerative+6

    Protein binder design model post-trained from a multimodal protein language model to bind proteins, peptides, small molecules, and nucleic acids.

    Protein
    13Openness
  • OwkinZero

    1
    OwkinAugust 22, 2025drug_discoveryfoundation_modelreinforcement_learning+2

    Biological reasoning language model that post-trains Qwen3 with reinforcement learning from verifiable rewards for drug-discovery tasks.

    Language model
    15Openness
  • scYeast

    51
    Shanghai Jiao Tong UniversityAugust 20, 2025cell_type_annotationfoundation_modeltransformer+1

    Single-cell foundation model for yeast that injects regulatory network priors into transformer attention for zero-shot and fine-tuned analysis.

    Single-cell
    68Openness
  • rBio

    14616
    Chan Zuckerberg InitiativeAugust 18, 2025cell_biologyfoundation_modelreinforcement_learning+2

    Reasoning language model post-trained on virtual cell simulations, answering questions about gene perturbations and their effects in natural language.

    Language model
    60Openness
  • Broad InstituteAugust 17, 2025chromatinfoundation_modelgene_regulation+7

    Multimodal foundation model predicting genome-wide binding of chromatin-associated proteins from protein sequence, DNA sequence, and chromatin state.

    DNA & GeneProtein
    25Openness
  • Earth Species ProjectAugust 15, 2025beatsbioacousticsfoundation_model+4

    Self-supervised bioacoustic audio encoder that turns animal-sound recordings into transferable embeddings for species classification and detection.

    Biosignals
    59Openness
  • CLASP

    44
    McGill UniversityAugust 10, 2025contrastive_learningcross_modal_retrievalgraph_neural_network+7

    Tri-modal contrastive model aligning protein structure, sequence, and text in a shared space for zero-shot cross-modal retrieval and classification.

    Protein
    42Openness
  • University of Science and Technology of ChinaAugust 7, 2025bertfoundation_modellanguage_model+8

    RNA foundation model pretrained jointly on sequences and secondary structures for structure prediction, homology and splice site classification.

    RNA
    92Openness
  • PoET-2

    2710
    OpenProtein.AIAugust 5, 2025foundation_modellanguage_modelprotein_design+5

    Multimodal, retrieval-augmented protein foundation model that learns family-specific evolutionary constraints with optional structure conditioning.

    Protein
    37Openness
  • OpenMed NER

    4.7K2
    OpenMedAugust 3, 2025biomedical_literatureinformation_extractionnamed_entity_recognition+2

    Biomedical named entity recognition transformers, with task-specialized checkpoints for chemicals, diseases, genes, proteins, species, and anatomy.

    Language model
    71Openness
  • EPFLAugust 1, 2025foundation_modelgene_essentiality_predictionprotein_protein_interaction_prediction+4

    Proteome-scale protein language model whose representations enable zero-shot protein-protein interaction and gene essentiality prediction.

    Protein
    64Openness
  • GREmLN

    38
    Chan Zuckerberg Initiative +2 othersJuly 9, 2025cell_type_annotationchromatinfoundation_model+6

    Single-cell transcriptomics foundation model that encodes gene regulatory network structure into self-attention through graph signal processing.

    Single-cell
    80Openness
  • MNCN-CSICJuly 9, 2025bertembeddingsfoundation_model+4

    Zebrafish single-cell foundation model built on the Geneformer framework, producing frozen gene and cell embeddings for developmental analysis.

    Single-cell
    46Openness
  • MedGemma

    1.6K375118.8K
    Google Research +1 otherJuly 9, 2025clinical_reasoningelectronic_health_recordsfine_tuning+8

    Open medical multimodal models from Google, built on Gemma 3 with a medically tuned SigLIP vision encoder for clinical text and image understanding.

    Language modelImaging
    41Openness
  • PLMDA-PPI

    101
    Huazhong University of Science and TechnologyJuly 4, 2025graph_neural_networkinterface_contact_predictionprotein_protein_interaction+4

    Protein-protein interaction predictor that adds contact-guided dual attention and a geometric encoder to frozen protein language model embeddings.

    Protein
    77Openness
  • 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 model
    26Openness
  • Chongqing University of TechnologyJuly 1, 2025histologyinstruction_tuningmedical_image_understanding+5

    Biomedical vision-language assistant for medical visual question answering, pairing Phi-2 with a vision encoder in a 4.2B-parameter model.

    ImagingLanguage model
    15Openness
  • MELP

    311817
    The University of Hong KongJune 27, 2025contrastive_learningecg_classificationelectrocardiogram+4

    Multi-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 model
    68Openness