Single Cell Foundation Models

Papers and Tools

• A large-scale foundation model for bulk transcriptomes (2025)

  • https://www.biorxiv.org/content/10.1101/2025.06.11.659222v1

• CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells (2025)

  • https://www.nature.com/articles/s41467-025-59926-5

• Beyond Annotation: Leveraging Raw RNA-seq Reads via Foundation Models for Multi-Cancer Early Detection (2025)

  • https://www.medrxiv.org/content/10.64898/2025.12.17.25342371v1.full.pdf

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility (2025)

  • https://pmc.ncbi.nlm.nih.gov/articles/PMC11964219/
  • https://docs.nvidia.com/bionemo-framework/1.10/models/geneformer.html

• Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions (2022)

  • https://arxiv.org/abs/2204.00300
  • https://github.com/ml4bio/RNA-FM?tab=readme-ov-file

• Large-scale foundation model on single-cell transcriptomics (2024, scFoundation)

  • https://www.nature.com/articles/s41592-024-02305-7
  • https://www.biorxiv.org/content/10.1101/2023.05.29.542705v3
  • https://github.com/biomap-research/scFoundation
  • https://huggingface.co/genbio-ai/scFoundation

• scGPT: toward building a foundation model for single-cell multi-omics using generative AI (2024)

  • https://www.nature.com/articles/s41592-024-02201-0
  • https://github.com/bowang-lab/scGPT
  • https://scgpt.readthedocs.io/en/latest/index.html

• A cell atlas foundation model for scalable search of similar human cells

  • https://www.nature.com/articles/s41586-024-08411-y
  • https://github.com/Genentech/scimilarity
  • https://genentech.github.io/scimilarity/

• scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data (2022)

  • https://www.nature.com/articles/s42256-022-00534-z
  • https://www.biorxiv.org/content/10.1101/2021.12.05.471261v1.full
  • https://github.com/TencentAILabHealthcare/scBERT

• EpiAgent: foundation model for single-cell epigenomics (2025)

  • https://www.biorxiv.org/content/10.1101/2024.12.19.629312v1
  • https://github.com/xy-chen16/EpiAgent