All Competitors

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

Showing 124 of 163 filtered models

  • SQUALL

    Peking UniversityJune 3, 2026biomarker_discoveryfoundation_modelgene_expression+6

    Multimodal foundation model pretrained on 1.76 billion paired histology-spatial transcriptomics spots, linking whole-slide images to spatial molecular programs.

    PathologySpatial omics
    6Openness
  • miDGD

    Aarhus UniversityJune 2, 2026autoencoderdeep_generative_decodergene_expression+6

    A deep generative decoder that infers microRNA expression directly from bulk or single-cell mRNA gene expression via a shared mRNA/miRNA latent space.

    RNASingle-cell
    8Openness
  • TARIO-2

    NoetikJune 1, 2026foundation_modelgene_expressionhistology+4

    Multimodal tumor foundation model trained on paired H&E histology and spatial transcriptomics to infer whole-transcriptome and tumor-microenvironment signal from routine H&E alone.

    PathologySpatial omics
    6Openness
  • Vermeer

    2
    Microsoft Research +2 othersJune 1, 2026autoregressivecell_biologyfluorescence_microscopy+7

    Channel-adaptive autoregressive generative model that synthesizes in-silico fluorescence microscopy of protein subcellular localization from amino-acid sequence and cellular landmark stains.

    ImagingProtein
    17Openness
  • AMix-2

    Shanghai AI Laboratory +4 othersMay 30, 2026diffusionfold_classificationfoundation_model+6

    A protein-text foundation model embedding sequences and natural language in a shared token space, enabling protein understanding and de novo design from one checkpoint.

    ProteinLanguage model
    10Openness
  • Nanjing University +2 othersMay 30, 2026foundation_modelgene_expression_predictionhistology+7

    A tri-modal foundation model unifying histology images, spatial transcriptomics, and biological language for zero-shot spatial biology and pathology reasoning.

    PathologySpatial omics
    65Openness
  • STMDiT

    ETH Zurich +1 otherMay 29, 2026diffusion_transformergenerativehistology+5

    A diffusion transformer that synthesizes H&E histopathology image patches conditioned jointly on spatial transcriptomics gene expression and morphological embeddings.

    PathologySpatial omics
    44Openness
  • University of FloridaMay 18, 2026bertbilstmcnn+11

    Multimodal deep-learning framework that detects and localizes DNA lesions directly from native nanopore sequencing, built on the damage-aware LesionBERT foundation model.

    DNA & Gene
    45Openness
  • Bio-BLIP

    Stanford UniversityMay 15, 2026foundation_modelgenomicsmendelian_disease+7

    A multimodal Q-former that fuses DNA sequence, gene context, protein function, and text into a prefix for a frozen LLM, enabling zero-shot genetic variant interpretation.

    DNA & GeneLanguage model
    23Openness
  • ProtLiD

    4
    National University of SingaporeMay 15, 2026de_novo_designdiffusiongenerative+6

    A ligand-conditioned masked discrete diffusion model that co-designs protein sequence and structure under explicit small-molecule constraints.

    Protein
    5Openness
  • SpaRank

    Guangxi UniversityMay 13, 2026cell_type_deconvolutionfoundation_modelmultimodal+3

    A transferable spatial-transcriptomics deconvolution model whose rank-based spot encoding lets one pretrained model generalize across tissues, disease states, and platforms without retraining.

    Spatial omics
    8Openness
  • OmniGene-4

    Huazhong University of Science and TechnologyMay 12, 2026dnafoundation_modelinstruction_following+7

    A unified bio-language Mixture-of-Experts foundation model spanning DNA, protein sequence and structure, and biological text, applied across eight task families from a single checkpoint.

    Language modelDNA & GeneProtein
    7Openness
  • BRIDGE

    The University of Hong KongMay 8, 2026contrastive_learningfoundation_modelgene_expression_prediction+8

    A multi-organ foundation model aligning histology image features with spatial-transcriptomics gene expression across 13 organs for zero-shot virtual ST and survival prediction.

    PathologySpatial omics
    31Openness
  • A-CODE

    University of Illinois Urbana-Champaign +1 otherMay 5, 2026binder_designde_novo_designdiffusion+4

    A fully atomic protein co-design model using unified multimodal diffusion to jointly refine atom types and coordinates in a single stage, with support for non-canonical amino acids.

    Protein
    8Openness
  • DoFormer

    Columbia University +1 otherMay 4, 2026causal_inferencefoundation_modelgene_expression+3

    A causal multimodal Transformer that embeds the do-operator within attention to predict single-cell responses to gene perturbations, including unseen ones.

    Single-cell
    8Openness
  • University of KentuckyMay 4, 2026contrastive_learningintrinsic_disorder_predictionmolecular_dynamics+6

    A protein language model that aligns ESM sequence embeddings with molecular-dynamics trajectory embeddings via contrastive learning for zero-shot mutation-effect prediction.

    Protein
    10Openness
  • Proteo-R1

    492115
    Stanford University +3 othersMay 1, 2026antibodyde_novo_designdiffusion+5

    A reasoning-guided foundation model for de novo antibody CDR design, pairing a multimodal-LLM understanding expert with a Boltz-1-based diffusion generation expert.

    Protein
    53Openness
  • scPert

    Zhejiang University School of MedicineApril 28, 2026drug_discoveryfoundation_modelgene_expression+4

    A multi-modal Transformer that fuses LLM gene embeddings with biological knowledge graphs to predict single-cell transcriptomic responses to genetic perturbations.

    Single-cell
    14Openness
  • MIMIC

    30
    Polymathic AIApril 27, 2026foundation_modelgenerativegenomics+6

    Generative multimodal foundation model that jointly models DNA, RNA, protein, and cellular context across six biological modalities, with SOTA splicing prediction.

    RNAProteinDNA & Gene
    16Openness
  • GenNA

    Zhejiang UniversityApril 24, 2026de_novo_designfoundation_modelgenerative+5

    An autoregressive nucleotide-and-text foundation model pretrained on ~416B characters from 2,221 eukaryotic species for natural-language-guided conditional generation of DNA and RNA sequences.

    DNA & GeneRNA
    16Openness
  • H2O

    Tencent AI for Life Science Lab +2 othersApril 24, 2026contrastive_learningfoundation_modelgene_expression+6

    A foundation model that predicts spatial transcriptomics and proteomics directly from routine H&E whole-slide images using a vision transformer aligned with a language model.

    PathologySpatial omics
    7Openness
  • Stanford UniversityApril 24, 2026bertde_novo_designdiffusion+6

    A 110M-parameter multimodal RNA language model that designs RNA sequences from secondary structure, consensus, and Gene Ontology constraints via discrete diffusion.

    RNA
    48Openness
  • Aiki-XP

    AikiumApril 23, 2026foundation_modelgenomicsmultimodal+5

    Leakage-controlled multimodal model predicting within-species relative protein expression across 385 bacterial species, with transfer to unseen phyla.

    Protein
    96Openness
  • RVQ-Alpha

    Guangzhou National LaboratoryApril 23, 2026cell_type_annotationlanguage_modelmultimodal+5

    A Qwen3-4B language model that reads and reasons over single cells by tokenizing scRNA-seq with residual vector quantization and training with verifiable reinforcement learning.

    Single-cell
    4Openness