Single-Cell Model Hub

A curated collection of foundation models, virtual cells, and AI systems for single-cell biology — papers, code, and resources.

All Models Foundation Model Geneformer-like Virtual Cell Multi-modal Spatial Perturbation Generative Other
#Cell Atlas #Cross-species #Foundation Model #GPT #Gene Expression #Geneformer #Generative #Masked Modeling #Multi-omics #Perturbation #Spatial #Transformer #Virtual Cell #scBERT #scFoundation #scGPT #scRNA-seq

#Gene Expression

7
Foundation Model

scFoundation

Large-scale pre-trained model for single-cell transcriptomics with 100M parameters, trained on 50M+ cells.

2024 · 06 100M params Paper → GitHub →
Foundation Model Gene Expression scFoundation
Foundation Model

scGPT

Generative pre-trained transformer for single-cell biology. Pre-trained on 33M+ cells from CELLxGENE.

2024 · 02 ~300M params Paper → GitHub →
Foundation Model Gene Expression Transformer scGPT
Foundation Model

UCE

Universal Cell Embedding — species-agnostic cell representation model for cross-species analysis.

2023 · 11 Paper → GitHub →
Cross-species Foundation Model Gene Expression scRNA-seq
Foundation Model

SATURN

Cross-species single-cell foundation model using protein language models.

2023 · 11 Paper → GitHub →
Cross-species Foundation Model Gene Expression
Foundation Model

CELLxGENE Census Models

Foundation models from CZI, trained on CELLxGENE Census data (50M+ cells).

2023 · 07 Paper → GitHub →
Cell Atlas Foundation Model Gene Expression scRNA-seq
Geneformer-like

Geneformer

Context-aware foundation model for gene network predictions. Transfer learning from 30M single-cell transcriptomes.

2023 · 05 ~100M params Paper → GitHub →
Foundation Model Gene Expression Geneformer Masked Modeling
Foundation Model

scBERT

BERT-based pre-trained model for single-cell transcriptomics with gene-level tokenization.

2022 · 09 ~100M params Paper → GitHub →
Gene Expression Masked Modeling scBERT