All Competitors

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

Showing 124 of 27 filtered models

  • Cellpin

    Technical University of MunichJune 5, 2026denoisinggene_imputationsingle_cell+4

    A VAE trained on scRNA-seq reference data and applied frozen at inference to impute unmeasured genes and denoise spatial transcriptomics profiles.

    Spatial omicsSingle-cell
    22Openness
  • 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
  • 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
  • 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
  • GEARS

    University of Central Florida +2 othersMay 27, 2026cell_localizationdiffusion_modeldomain_adaptation+8

    Geometry-first generative framework that reconstructs single-cell spatial coordinates by integrating scRNA-seq with spatial transcriptomics, without cell-type labels.

    Single-cell
    22Openness
  • TMEformer

    Sichuan UniversityMay 20, 2026cancerfoundation_modelin_silico_perturbation+8

    A spatial-transcriptomics foundation model for the tumor microenvironment that produces TME-aware embeddings and enables in silico perturbation from a fixed pretrained checkpoint.

    Spatial omics
    10Openness
  • 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
  • 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
  • Phoenix

    Helmholtz Munich +1 otherApril 29, 2026cell_type_annotationflow_matchingfoundation_model+6

    Latent flow-matching foundation model that predicts pan-cancer spatially-resolved single-cell gene expression directly from routine H&E histology slides.

    PathologySpatial omics
    8Openness
  • 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
  • xVERSE

    Duke UniversityApril 14, 2026batch_effect_correctionfoundation_modelgenerative+5

    A transcriptomics-native single-cell foundation model that couples batch-invariant representation learning with probabilistic virtual-cell generation.

    Single-cell
    10Openness
  • Halo

    Duke University School of MedicineApril 6, 2026cell_segmentationcellpose_sammultimodal+5

    A pretrained whole-cell segmentation model for spatial transcriptomics that fuses DAPI nuclear images with RNA transcript density to recover cell boundaries.

    Spatial omics
    63Openness
  • MuPD

    Stanford UniversityApril 4, 2026data_augmentationdiffusion_transformerfoundation_model+7

    A generative diffusion-transformer foundation model that embeds H&E histology, RNA profiles, and clinical text in a shared latent space for zero-shot cross-modal synthesis.

    PathologySpatial omics
    15Openness
  • STORM

    1
    Stanford UniversityApril 4, 2026clinical_outcome_predictionfoundation_modelgene_expression_prediction+7

    A hierarchical multimodal foundation model integrating spatial transcriptomics and H&E histology for biological discovery and platform-agnostic clinical prediction.

    Spatial omicsPathology
    17Openness
  • MIT +1 otherMarch 16, 2026cancer_microenvironment_analysisfoundation_modelhistopathology+8

    Lightweight multimodal foundation model integrating spatial transcriptomics and H&E histopathology with pathway activity scores for biologically grounded spatial niche discovery at single-cell resolution.

    Spatial omicsSingle-cell
    71Openness
  • MIT +1 otherMarch 11, 2026cell_type_annotationfoundation_modelgene_expression_prediction+7

    A self-supervised, cell-centric pretraining strategy that distills morphology and microenvironment views of each cell into a unified embedding for virtual spatial omics from microscopy.

    Spatial omicsImagingPathology
    15Openness
  • STPAINTER

    University of Science and Technology of China +2 othersFebruary 13, 2026cancerdiffusionfoundation_model+4

    A pan-cancer pretrained latent diffusion model that enhances spatial transcriptomics, imputing genome-wide expression from sparse panels with zero-shot generalization.

    Spatial omicsSingle-cell
    4Openness
  • MoLF

    National Center for Tumor Diseases DresdenFebruary 2, 2026flow_matchinggene_expressiongenerative+5

    A pan-cancer generative model that predicts spatial gene expression from H&E histology using conditional flow matching with a mixture-of-experts velocity field.

    PathologySpatial omics
    9Openness
  • SAGE-FM

    Stanford UniversityJanuary 21, 2026cell_type_annotationfoundation_modelgene_expression+4

    A lightweight graph-convolutional foundation model for spatial transcriptomics that learns spatially coherent, interpretable spot embeddings via masked central-spot prediction.

    Spatial omicsSingle-cell
    10Openness
  • OmniCell

    BGI ResearchDecember 29, 2025cell_type_annotationfoundation_modelgene_expression+6

    A foundation model jointly pretrained on 67M single-cell and spatial transcriptomic profiles to model intra-cellular expression and inter-cellular spatial dependencies.

    Single-cellSpatial omics
    9Openness
  • Baylor College of MedicineDecember 25, 2025cancerfoundation_modelligand_target_inference+7

    A pair of spatially aware transcriptomic foundation models (50um-Local and 250um-Extended) for multi-scale analysis of spot-resolution cancer spatial transcriptomes.

    Spatial omics
    12Openness
  • FOCUS

    University of CambridgeDecember 23, 2025diffusionfoundation_modelgene_expression_imputation+8

    Generative foundation model that enhances spatial transcriptomics by conditioning on H&E histology, scRNA-seq references, and spatial co-expression priors.

    Spatial omicsPathologySingle-cell
    4Openness
  • scMOBA

    Chinese Academy of Sciences +1 otherDecember 2, 2025cell_biologycell_type_annotationdata_integration+6

    A conversational single-cell and spatial multi-omics brain agent pretrained on 130 million cells across species for zero-shot cell annotation and disease prediction.

    Single-cellLanguage model
    5Openness