All Competitors

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

Showing 889912 of 943 models

  • RoentGen

    88
    Stanford UniversityNovember 23, 2022chest_radiographydata_augmentationfoundation_model+5

    Text-conditioned latent diffusion model that generates synthetic chest X-rays from free-form radiology prompts by adapting Stable Diffusion.

    ImagingLanguage model
    20Openness
  • Galactica

    2.7K1.1K701
    Meta AINovember 16, 2022foundation_modellanguage_modelmultimodal

    Scientific large language model trained on 48 million papers, textbooks, and reference works to store, combine, and reason about scientific knowledge.

    Language model
    46Openness
  • Seoul National UniversityNovember 4, 2022chromatindeep_learningepigenomic_prediction+4

    Transformer predicting gene expression from histone modifications, using promoter-enhancer Hi-C interactions to capture distal regulatory effects.

    DNA & Gene
    71Openness
  • BioGPT

    4.5K1.5K98.3K
    Microsoft Research Asia +1 otherOctober 19, 2022biomedical_literaturegenerativegpt+6

    Generative transformer pretrained on PubMed abstracts for biomedical text generation and mining, including relation extraction and question answering.

    Language model
    66Openness
  • iDNA-ABF

    15
    Shandong UniversityOctober 17, 2022dna_methylationepigenomic_predictionepigenomics+4

    DNA language model for interpretable prediction of 4mC, 5hmC, and 6mA methylation sites across species, using multi-scale k-mer BERT encoders.

    DNA & Gene
    53Openness
  • GenSLM

    142142
    Argonne National LaboratoryOctober 12, 2022foundation_modelgene_expressiongenomics+4

    Genome-scale language model trained on prokaryotic genes and SARS-CoV-2 genomes to model viral evolution and flag emerging variants of concern.

    DNA & Gene
    56Openness
  • EquiFold

    12952
    Prescient Design +1 otherOctober 8, 2022graph_neural_networkprotein_designproteomics+4

    Protein structure prediction model pairing SE(3)-equivariant networks with a coarse-grained representation to fold sequences fast, without MSA inputs.

    Protein
    46Openness
  • Cellpose 2.0

    2.3K1.1K
    HHMI Janelia Research CampusOctober 3, 2022active_learningcell_biologyfluorescence_microscopy+3

    Human-in-the-loop cell segmentation framework enabling custom model training from as few as 100-200 corrected annotations.

    Imaging
    59Openness
  • MoLFormer-XL

    405143K
    IBM ResearchOctober 3, 2022drug_discoveryfoundation_modellanguage_model+4

    Large-scale chemical language model trained on 1.1 billion SMILES strings using linear attention transformers for molecular property prediction.

    Small molecule
    86Openness
  • Burstein LabSeptember 29, 2022foundation_modelgene_function_predictionmetagenomics

    Word2vec-based language model trained on 360 million microbial genes that predicts gene function from genomic context without sequence homology.

    DNA & Gene
    87Openness
  • Shenzhen Research Institute of Big Data +2 othersSeptember 15, 2022chest_x_rayfoundation_modelimage_text_retrieval+7

    Medical vision-language pretraining framework that injects structured medical knowledge into radiology image-text learning for VQA and retrieval.

    ImagingLanguage model
    29Openness
  • CheXzero

    234524
    Stanford UniversitySeptember 15, 2022chest_radiographycontrastive_learningimage_classification+7

    Self-supervised vision-language model for zero-shot detection of chest X-ray pathologies, trained on image-report pairs without explicit labels.

    ImagingPathology
    70Openness
  • ProteinMPNN

    1.8K1.9K
    Institute for Protein DesignSeptember 15, 2022graph_neural_networkinverse_foldingprotein_design+1

    Message passing neural network for fixed-backbone protein sequence design. Achieves 52.4% native sequence recovery, far surpassing Rosetta's 32.9%.

    Protein
    85Openness
  • M3AE

    134171
    Shenzhen Research Institute of Big Data +2 othersSeptember 15, 2022autoencoderimage_text_retrievalmultimodal+5

    Self-supervised medical vision-and-language pretraining via multi-modal masked autoencoders that reconstruct masked image patches and text tokens.

    PathologyLanguage model
    29Openness
  • scBERT

    3594
    Tencent AI LabSeptember 1, 2022cell_type_annotationfoundation_model

    Pretrained transformer for cell type annotation of scRNA-seq data. Trained on 1.1M cells; outperforms supervised methods on cross-dataset transfer.

    Single-cell
    46Openness
  • INTERACT

    1125
    Lieber Institute for Brain DevelopmentAugust 16, 2022deep_learningdna_methylationepigenomic_prediction+4

    Deep learning model predicting DNA methylation regulatory variants at CpG sites in the human brain, fine-mapping psychiatric disorder risk loci.

    DNA & Gene
    9Openness
  • RNA-FM

    386256
    ml4bio +3 othersAugust 6, 2022foundation_modellanguage_modelstructure_prediction

    RNA foundation model pretrained on 23.7 million non-coding RNA sequences, producing embeddings for structure prediction, annotation, and RNA design.

    RNA
    62Openness
  • MoDNA

    27
    University of Texas at ArlingtonAugust 1, 2022dnafoundation_modelgenomics+2

    Motif-oriented DNA pre-training framework that adds motif prediction to an ELECTRA generator-discriminator setup for motif-aware genomic embeddings.

    DNA & Gene
    11Openness
  • ProtGPT2

    86615.6K
    University of BayreuthJuly 27, 2022foundation_modelgenerativeprotein_design

    Autoregressive protein language model based on GPT-2 that generates de novo protein sequences sampling unexplored regions of protein space.

    Protein
    54Openness
  • ESM-2 & ESMFold

    4.2K5.1K1.4M
    Meta AIJuly 20, 2022foundation_modellanguage_modelstructure_prediction

    Meta AI's family of protein language models scaled to 15B parameters, paired with ESMFold for fast, alignment-free atomic-level structure prediction.

    Protein
    83Openness
  • Casanovo

    1944
    Noble LabJuly 17, 2022foundation_modelmass_spectrometryproteomics

    Transformer model for de novo peptide sequencing that reads amino acid sequences directly from tandem mass spectra, with no protein sequence database.

    Protein
    91Openness
  • EMDLP

    126
    China University of Mining and TechnologyJune 8, 2022ensemblemethylationsequence_analysis

    RNA methylation site predictor combining multiple sequence encodings with dilated convolution and BiLSTM layers to identify m6A and m1A sites.

    RNA
    34Openness
  • CARP

    259
    Microsoft ResearchMay 19, 2022embeddingsfoundation_modelvariant_effect_prediction

    Protein language model family built on CNNs rather than transformers, matching transformer quality while scaling linearly with sequence length.

    Protein
    81Openness
  • AntiBERTa

    65159
    AlchemabMay 18, 2022antibodyfoundation_modelimmunology+1

    BERT-based antibody language model pretrained on 57M B cell receptor sequences for paratope prediction and convergent antibody discovery.

    Protein
    60Openness