# scFoundation (BioMap)

Source: https://onco.cc/technologies/scfoundation/  
OnCo record `scfoundation` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

scFoundation is a 100-million-parameter model trained on 50 million cells, from China's BioMap.

## Summary

scFoundation is a single-cell foundation model from China's BioMap that uses masked expression modelling over the full vocabulary of about 19k human genes, with an asymmetric encoder-decoder so the expensive encoder sees only expressed genes. The Nature Methods 2024 paper describes a 100-million-parameter model trained on 50 million cells and applies it to read-depth enhancement, drug response prediction and perturbation prediction. It is aimed at computational groups who want whole-transcriptome modelling rather than a truncated gene list, including for cancer cell line drug response. The design is compute-heavy, which limits who can fine-tune or run it at scale, and like its peers its perturbation predictions await independent benchmarking. For a newcomer: scFoundation models every gene in a cell at once and tries to predict how cells will respond to drugs.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-09-08
- Tags: foundation-model; virtual-cell
- Principle: scFoundation uses masked expression modelling with a full gene vocabulary.
- Since: 2024
- Strengths: Full-gene modelling
- Limitations: Compute-heavy

## Sources

- Nature Methods 2024: https://doi.org/10.1038/s41592-024-02305-7

## Connected records

- fronts: [AI & Computation](https://onco.cc/fronts/ai-computation/)
- terms: [Cell line](https://onco.cc/terms/cell-line/), [Gene expression](https://onco.cc/terms/gene-expression/), [Single-cell and transcriptome foundation models: UCE, GeneCompass, BulkFormer, BulkRNABert](https://onco.cc/terms/single-cell-foundation-models/)
- key papers: [Large-scale foundation model on single-cell transcriptomics](https://onco.cc/key-papers/paper-hao-nat-methods/)
- technologies: [CellFM](https://onco.cc/technologies/cellfm/)
- roadmaps: [Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell](https://onco.cc/roadmaps/virtual-cell/)

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JSON: https://onco.cc/api/v1/entities/scfoundation.json