HCLS Foundation Models Map

I track foundation models across health and life sciences and judge every one against the same rubric, but the calls are mine. Treat it as a well-kept notebook, not gospel. Last updated Nov 2026.

Jump to all 178 modelsData on GitHubSuggest a model
178foundation models tracked
12categories in 4 areas
60prominent, 34% of the list
81%have downloadable weights

Where the models are

Biology80
32
28
11
4
3
2
Chemistry7
7
Clinical86
36
33
14
3
Emerging5
5
Darker: prominentLighter: tracked

How fast the field grew

050100150200201820192020202120222023202420252026178
050100150200201820192020202120222023202420252026178
BiologyChemistryClinicalEmerging

Who builds them

Microsoft12
Stanford12
Harvard11
NVIDIA11
Tsinghua10
Google8
Shanghai Jiao Tong6
Tencent5
Arc Institute4
CUHK4
U Toronto4
MIT3

The 60 prominent models

Biology 25
Chemistry 4
Clinical 31

All 178 models

Area

Category

Prominence

Tags

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Model Category Modality Description Tags
Biology
AlphaGenome Genomics DNA DeepMind regulatory-genomics model for variant-effect prediction across modalities including expression, splicing, chromatin, and contact maps.
private
Borzoi Genomics DNA Convolution-transformer predicting RNA-seq coverage from DNA sequence.
Carbon-X Genomics DNA Open 14B language model for DNA understanding and generation, from the Hugging Face Carbon family.
generative
DNABERT-2 Genomics DNA Multispecies genome language model using byte-pair-encoding tokenization.
multispecies
DNAGPT Genomics DNA Generalized pre-trained tool for multiple DNA sequence analysis tasks.
generative
Evo 2 Genomics DNA 7B and 40B-parameter DNA model that processes up to 1M base pairs at nucleotide resolution; backbone of the Mayo Clinic EVEE variant pathogenicity work
generativeinterpretability
gLM Genomics DNA Genomic language model that predicts protein co-regulation and function from contig context.
GPN-MSA Genomics DNA Alignment-based DNA language model for genome-wide variant effect prediction.
HyenaDNA Genomics DNA Long-context DNA sequence model based on the Hyena architecture
ModernGENA Genomics DNA ModernBERT-based DNA foundation model (up to 377M) positioned as an efficient encoder baseline.
Nucleotide Transformer v3 Genomics DNA Multispecies DNA foundation model family (8M to 650M) with long-context pretraining, post-trained and generative variants.
multispecies
3UTRBERT Transcriptomics RNA Language model over mRNA 3' UTR sequences for post-transcriptional regulation tasks.
ATOM-1 Transcriptomics RNA RNA foundation model trained on chemical mapping data for structure and function.
private
CellPLM Transcriptomics scRNA Cell language model pre-trained beyond single cells, using spatially resolved transcriptomics.
CodonBERT Transcriptomics RNA Language model over codon sequences for mRNA property prediction.
ERNIE-RNA Transcriptomics RNA RNA language model with structure-enhanced representations.
GeneCompass Transcriptomics scRNA Knowledge-informed cross-species single-cell foundation model for gene regulation.
multispecies
Geneformer Transcriptomics RNA Transformer pre-trained on about 104M single-cell human transcriptomes (V2); widely used for drug-target and cell-state inference.
GenePT Transcriptomics scRNA Single-cell and gene embeddings derived from gene-description text via an LLM.
multimodal
GenerRNA Transcriptomics RNA Generative pre-trained language model for de novo RNA design.
generative
Orthrus Transcriptomics RNA Evolutionary and functional RNA foundation model.
RiNALMo Transcriptomics RNA General-purpose RNA language model that generalizes to structure prediction tasks.
RNA-FM Transcriptomics RNA Interpretable RNA foundation model trained on unannotated ncRNA for structure and function prediction.
RNA-MSM Transcriptomics RNA MSA-based RNA language model leveraging homologous sequences for structure signal.
RNABERT Transcriptomics RNA Informative RNA base embedding via masked LM for structural alignment and clustering.
scBERT Transcriptomics RNA BERT-style single-cell RNA-seq foundation model for cell type annotation
scFoundation Transcriptomics scRNA Large-scale foundation model on single-cell transcriptomics.
scGPT Transcriptomics RNA Single-cell foundation model encoding gene and cell relationships across large atlases
SCimilarity Transcriptomics scRNA Cell-embedding foundation model for rapid similar-cell-profile retrieval.
scMulan Transcriptomics scRNA Multitask generative pre-trained language model for single-cell analysis.
generative
scPRINT Transcriptomics scRNA Single-cell RNA FM pre-trained on 50M cells for robust gene network prediction.
SpliceBERT Transcriptomics RNA Language model pretrained on precursor-mRNA for RNA splicing prediction.
Stack Transcriptomics RNA Arc Institute virtual-cell effort focused on in-context learning over cellular conditions.
private
State Transcriptomics RNA Arc Institute virtual-cell model aimed at perturbation prediction over cellular conditions.
private
TranscriptFormer Transcriptomics RNA Cross-species generative single-cell transcriptomics model from the Chan Zuckerberg Initiative.
multispecies
UNI-RNA Transcriptomics RNA Universal pre-trained RNA representation model.
private
Universal Cell Embeddings Transcriptomics scRNA Single-cell foundation model producing universal cell representations across species.
multispecies
UTR-LM Transcriptomics mRNA -UTR 5' UTR language model for decoding untranslated regions of mRNA.
xTrimoGene Transcriptomics scRNA Efficient and scalable representation learner for single-cell RNA-seq data.
private
AlphaFold 3 Protein protein Atomic structures of proteins DNA RNA and ligand complexes
multimodalprivate
Ankh Protein protein Optimized protein language model for general-purpose modelling.
BioEmu-2 Protein protein -conformation Diffusion model (~500M) that generates all-atom conformational ensembles for proteins, complexes, ligands and nucleic acids.
generative
Boltz-2 Protein protein Open-source biomolecular co-folding model that also predicts small-molecule binding affinity.
generative
CaLM Protein codon Codon language embeddings for protein engineering.
CARP Protein protein Convolutional protein sequence model competitive with transformers.
Chai-1 Protein protein Open biomolecular structure prediction model for complexes.
generative
ESM-3 Protein protein Multimodal protein language model over sequence structure and function
multimodalgenerative
ESMFold2 Protein protein -structure Single-sequence protein structure predictor built on ESM protein language model embeddings.
EvoDiff Protein protein Sequence-based diffusion generative model for protein design.
generative
Evolla Protein protein + text Decodes molecular language of proteins for question answering and annotation.
multimodal
GearNet Protein protein -structure Geometric structure pretraining for protein representation learning.
HelixFold-Single Protein protein -structure MSA-free protein structure prediction using a protein language model.
MSA Transformer Protein protein Protein language model with axial attention over multiple-sequence alignments.
OmegaFold Protein protein Predicts high-resolution protein structure from a single sequence without MSAs.
OntoProtein Protein protein Protein pretraining with gene ontology embeddings.
OpenFold3 Protein protein Open-source effort to support reproducible biomolecular co-folding models.
PrimateAI-3D Protein protein Variant-effect prediction model integrating 3D structure
private
Profluent E1 Protein protein Retrieval-augmented protein language model family (150M to 600M) that conditions on homologous sequences.
ProGen2 Protein protein Family of autoregressive protein language models up to 6.4B parameters for design and fitness.
generative
ProteinBERT Protein protein Universal deep-learning model of protein sequence and function with GO annotation pretraining.
ProteinDT Protein protein Text-guided protein design coupling sequence and language representations.
multimodal
ProtGPT2 Protein protein Deep unsupervised generative language model for protein design.
generative
ProTrek Protein protein + structure + text Tri-modal contrastive learning across protein sequence, structure, and text.
multimodal
ProtST Protein protein + text Multi-modality learning of protein sequences and biomedical texts.
multimodal
ProtTrans Protein protein Family of protein language models (T5, BERT, Albert, XLNet, Electra) trained via self-supervision at HPC scale.
RFD4-Proteína Protein protein Flow-matching model that co-designs protein sequence and all-atom structure conditioned on targets, motifs or ligands.
generative
RoseTTAFold All-Atom Protein protein Open structure-prediction and design model from the Baker Lab, extending RoseTTAFold to broader biomolecular assemblies including proteins, nucleic acids, small molecules, and covalent modifications.
SaProt Protein protein + structure Protein language model with structure-aware vocabulary.
multimodal
Uni-Fold Protein protein Open reimplementation and training of AlphaFold-style protein structure prediction.
UniRep Protein protein Unified rational protein engineering with sequence-based deep representation learning.
xTrimoPGLM Protein protein Unified 100B-scale pre-trained transformer for protein language.
private
EpiGePT Epigenomics epigenome Pretrained transformer for epigenomics.
Pleiades Epigenomics cfDNA Epigenetic foundation model for cell-free DNA currently focused on Alzheimer's biomarker discovery
interpretabilityprivate
AbLang2 Antibody and biologics antibody -sequence Antibody-specific language model for infilling and humanization
AntiBERTa2 Antibody and biologics antibody -sequence Antibody-specific transformer language model
private
AntiBERTy Antibody and biologics antibody -sequence BERT-style antibody language model trained on the Observed Antibody Space
IgLM Antibody and biologics antibody -sequence Generative antibody language model for heavy and light chain design
generative
Cell2Sentence Multi-omics and systems scRNA + text Teaches LLMs the language of biology by rendering scRNA cells as sentences.
multimodal
KRONOS Multi-omics and systems spatial -proteomics Foundation model for spatial proteomics, learning cell and tissue representations from multiplex protein imaging.
Nicheformer Multi-omics and systems scRNA + spatial Single-cell and spatial omics foundation model for tissue context modeling.
multimodal
Chemistry
ChemBERTa-2 Small-molecule SMILES Transformer pretrained on ~77M SMILES for molecular property prediction.
ChemGPT Small-molecule SMILES Large-scale generative model for chemistry over SMILES
generative
GROVER (molecule) Small-molecule molecular -graph Self-supervised graph-transformer pretraining on large-scale molecular data.
MegaMolBART Small-molecule SMILES BART-style model for SMILES part of the BioNeMo umbrella
generativeprivate
MoleculeSTM Small-molecule SMILES Multimodal molecule-text model linking chemical structures and natural language.
multimodal
MoLFormer Small-molecule SMILES Large-scale chemical language model over SMILES originally explored with AstraZeneca
MolMIM Small-molecule SMILES Controlled molecule generation with property guidance
generativeprivate
Clinical
BiomedCLIP Medical imaging vision -language Biomedical vision-language model pretrained on 15M PubMed image-text pairs
BioViL Medical imaging vision -language Joint chest X-ray image and radiology-report representation learning.
multimodal
CheXFound Medical imaging radiograph Chest X-ray foundation model
private
CheXzero Medical imaging radiograph Self-supervised chest X-ray model for zero-shot pathology detection from reports.
multimodal
Clinical-BERT (VLM) Medical imaging vision -language Vision-language pretraining for radiograph diagnosis and report generation.
multimodal
CLIP-Driven Universal Model Medical imaging CT CLIP-guided universal model for multi-organ CT segmentation and tumor detection.
multimodal
ConVIRT Medical imaging vision -language Contrastive image-text pretraining of medical images from paired radiology reports.
multimodal
CT-CLIP Medical imaging CT Contrastive foundation model on paired 3D chest CT volumes and radiology reports.
multimodal
CXR Foundation Medical imaging radiograph Chest X-ray foundation model from Google
private
GLoRIA Medical imaging vision -language Global-local contrastive image-text pretraining for chest X-ray.
multimodal
KAD Medical imaging radiograph Knowledge-augmented chest X-ray diagnosis via image-text pretraining.
multimodal
KoBo Medical imaging vision -language Knowledge-boosted contrastive vision-language pretraining for radiology.
multimodal
LLaVA-Med Medical imaging vision -language Biomedical vision-language assistant adapted from LLaVA on PMC figure-caption data.
multimodal
LVM-Med Medical imaging medical -imaging Self-supervised large vision model pretrained on 1.3M medical images.
MAIRA-2 Medical imaging vision -language Grounded radiology report generation from chest X-rays.
multimodal
Med-Flamingo Medical imaging vision -language Few-shot multimodal medical model adapted from Flamingo.
multimodal
Med-Gemini Medical imaging multimodal Multimodal medical foundation model for radiology report generation and visual question answering
multimodalprivate
Med3D Medical imaging 3D -medical -imaging Pretrained 3D CNN backbones for volumetric medical imaging (MedicalNet).
MedCLIP Medical imaging vision -language Contrastive vision-language pretraining from decoupled medical images and reports.
multimodal
MedKLIP Medical imaging vision -language Knowledge-enhanced medical image-text pretraining for radiology.
multimodal
MedSAM2 Medical imaging medical -image -segmentation Promptable segmentation foundation model for 3D medical images and videos.
MedVersa Medical imaging vision -language Generalist learner for multifaceted medical image interpretation and reporting.
multimodal
Models Genesis Medical imaging 3D -medical -imaging Self-supervised pretrained 3D models for medical image analysis.
NV-Reason-CT Medical imaging CT -3D 3D CT vision-language model for radiology reports, question answering and multi-step reasoning on chest and abdominal CT.
multimodalclinical-reasoning
PMC-CLIP Medical imaging vision -language CLIP pretrained on PubMed Central figure-caption biomedical pairs.
multimodal
PubMedCLIP Medical imaging vision -language CLIP fine-tuned on PubMed image-text pairs for medical visual question answering.
multimodal
RAD-DINO Medical imaging radiograph Image-only DINOv2 chest X-ray encoder trained without text supervision.
RadFM Medical imaging radiology Radiology foundation model for general medical imaging tasks
private
RETFound Medical imaging retina MAE-pretrained retinal-image foundation model for ocular and systemic disease.
SAM-Med3D Medical imaging 3D -medical -imaging Fully-learnable 3D SAM-style foundation model for volumetric segmentation.
SegVol Medical imaging CT Promptable volumetric CT segmentation foundation model.
STU-Net Medical imaging CT Scalable nnU-Net pretrained on TotalSegmentator for transferable CT segmentation.
UniverSeg Medical imaging medical -image -segmentation Universal in-context medical image segmentation across unseen tasks.
USFM Medical imaging ultrasound Spatial-frequency dual-masked self-supervised ultrasound foundation model.
VisionFM Medical imaging ophthalmic -imaging Multi-task ophthalmology foundation model across eye-imaging modalities.
multimodal
VISTA3D Medical imaging CT Unified 3D CT foundation model for automatic and interactive segmentation.
CHIEF Digital pathology WSI Generalizable whole-slide pathology foundation model.
CONCH Digital pathology vision -language Vision-language pathology model from the Mahmood Lab
private
CTransPath Digital pathology WSI Self-supervised transformer backbone for histopathology (TransPath line).
H-optimus-1 Digital pathology WSI Bioptimus histology foundation model (1.1B-parameter ViT) for downstream pathology tasks.
MUSK Digital pathology vision -language Vision-language pathology foundation model for precision oncology.
multimodal
PathChat Digital pathology vision -language Multimodal conversational assistant for whole-slide pathology. Weights gated.
multimodalprivate
PLIP Digital pathology WSI Pathology vision-language CLIP trained on OpenPath social-media histopathology.
multimodal
PRISM2 Digital pathology WSI Paige's second-generation multimodal slide-level pathology model, trained with clinical dialogue.
multimodal
Prov-GigaPath Digital pathology WSI Gigapixel pathology foundation model with tile-to-slide hierarchical representations
private
QuiltNet Digital pathology vision -language Pathology CLIP trained on Quilt-1M video-derived image-text pairs.
multimodal
RudolfV Digital pathology WSI DINOv2 pathology foundation model built with pathologist guidance. Weights closed.
private
TITAN Digital pathology vision -language Multimodal whole-slide pathology foundation model, multi-site validated.
multimodal
UNI2-h Digital pathology WSI General-purpose pathology foundation model (ViT-H) from the Mahmood Lab, trained on over 200M tiles from H&E and IHC slides.
private
Virchow2 Digital pathology WSI Paige's second-generation pathology foundation model, scaled with mixed-magnification self-supervised training.
private
AMIE Clinical language and patient medical -text Google Research diagnostic-dialogue research system for medical reasoning and conversations.
clinical-reasoningprivate
BEHRT Clinical language and patient EHR Transformer over structured EHR diagnosis-code sequences to predict future diagnoses.
EHRlongitudinal
Bio_ClinicalBERT Clinical language and patient clinical -text Clinical BERT pretrained on MIMIC-III notes, initialized from BioBERT.
clinical-NLPEHR
BioBART Clinical language and patient biomedical -text BART sequence-to-sequence model pretrained on biomedical literature for generative NLP.
generativeclinical-NLP
BioBERT Clinical language and patient biomedical -text BERT pretrained on PubMed and PMC for biomedical text mining.
clinical-NLP
BioGPT Clinical language and patient biomedical -text Generative biomedical transformer pretrained on PubMed literature for text generation and mining.
generativeclinical-NLP
BioLinkBERT Clinical language and patient biomedical -text Document-link-aware biomedical language model pretrained on PubMed.
clinical-NLP
BiomedGPT Clinical language and patient vision -language Generalist biomedical transformer spanning vision, language, and multimodal tasks.
multimodal
BioMedLM Clinical language and patient biomedical -text 2.7B GPT trained on PubMed for biomedical language (also called PubMedGPT).
generative
BioMegatron Clinical language and patient biomedical -text Large Megatron-style biomedical language model pretrained on PubMed-scale corpora.
clinical-NLP
BioMistral Clinical language and patient biomedical -text Mistral-7B further pretrained on PubMed Central for biomedical domains.
ChatDoctor Clinical language and patient medical -text LLaMA finetuned on patient-doctor medical dialogue.
ClinicalBERT (Huang) Clinical language and patient EHR -text BERT modeling clinical notes for hospital-readmission prediction.
EHRclinical-NLP
ClinicalGPT Clinical language and patient clinical -text LLM fine-tuned on clinical records and medical dialogue with multi-task evaluation.
ClinicalT5 Clinical language and patient clinical -text T5 encoder-decoder pretrained on MIMIC clinical text. Weights gated.
clinical-NLPprivate
CLMBR Clinical language and patient EHR -codes Clinical Language Model Based Representations from Stanford's Shah lab
EHRlongitudinalprivate
GatorTron Clinical language and patient EHR -text Clinical LM backbone for downstream NLP at UF Health
EHRclinical-NLP
GatorTronGPT Clinical language and patient EHR -text Generative clinical LLM trained on de-identified EHR notes; generative sibling of GatorTron.
EHRclinical-NLPgenerative
HuatuoGPT-II Clinical language and patient clinical -text Baichuan-2-based Chinese medical LLM for consultation and question answering.
KeBioLM Clinical language and patient biomedical -text Knowledge-enhanced biomedical language model integrating biomedical entity knowledge.
clinical-NLP
Me-LLaMA Clinical language and patient biomedical -text LLaMA-2 medical foundation family for clinical NLP and reasoning tasks.
Med-BERT Clinical language and patient EHR BERT pretrained on structured EHR diagnosis-code sequences for clinical prediction.
EHRlongitudinal
Med-PaLM 2 Clinical language and patient medical -text PaLM-2 model tuned for medical question answering; successor to Med-PaLM. Weights closed.
clinical-reasoningprivate
MedAlpaca Clinical language and patient medical -text Open medical-QA LLM collection finetuned on LLaMA.
MedCPT Clinical language and patient biomedical -text Contrastively pretrained biomedical text encoder for PubMed retrieval.
clinical-NLP
MedGemma 1.5 Clinical language and patient vision -language Google open medical vision-language model (4B) for imaging and clinical text tasks.
multimodal
Meditron3-70B Clinical language and patient medical -text EPFL's third-generation 70B medical language model for clinical reasoning.
NYUTron Clinical language and patient EHR -text Clinical language model trained on NYU Langone clinical notes
EHRclinical-NLPprivate
PMC-LLaMA Clinical language and patient biomedical -text LLaMA further pretrained on PubMed Central papers and medical books.
PubMedBERT Clinical language and patient biomedical -text BERT pretrained from scratch on PubMed abstracts and full text (aka BiomedBERT).
clinical-NLP
Radiology-Llama2 Clinical language and patient radiology -text Llama-2 model specialized for radiology report generation and understanding.
clinical-NLP
Standard Model Bio Clinical language and patient EHR -multi -omics Sits between EHR foundation models and multi-omics patient-trajectory modeling, learning unified patient representations for stratification and clinical-development use cases.
longitudinalprivate
Truveta Language Model Clinical language and patient EHR -text Trained on the largest linked EHR corpus in the United States; clinical reasoning over longitudinal records
EHRlongitudinalclinical-reasoningprivate
Endo-FM Surgical video video Endoscopy foundation model with video pre-training for downstream endoscopic tasks
SurgVISTA Surgical video video Surgical video spatio-temporal transformer for phase recognition and instrument tracking
private
SurgVLP Surgical video vision -language Surgical vision-language pre-training
private
Emerging
BioT5+ Emerging molecules + protein + text Generalized biological understanding with IUPAC integration and multi-task tuning.
multimodal
HeartBEiT Emerging ECG ECG-specific foundation model exploring transformer pretraining for cardiac waveforms.
clinical-waveformsprivate
LaBraM Emerging EEG Large-scale pretraining for EEG signals; representative early entry in the brain-waveform foundation-model space.
clinical-waveforms
METAGENE-1 Emerging DNA -metagenomic Arc Institute foundation model for metagenomic sequence, oriented toward microbiome and pathogen-surveillance applications.
TxGNN Emerging knowledge -graph Graph foundation model for zero-shot drug repurposing over a biomedical knowledge graph.
drug-target-interaction