# scGPT

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

## TL;DR

A GPT-style model for single-cell data that predicts cell types, perturbation responses, and gene networks.

## Summary

scGPT is a generative transformer for single-cell data that tokenises genes and bins expression values, borrowing the GPT recipe from language modelling. The Nature Methods 2024 paper pretrained it on 33M cells and showed fine-tuning for cell-type annotation, batch integration, perturbation response prediction and gene regulatory network inference. It is used by computational biologists as a general-purpose starting point that can be adapted to a new dataset with limited labels, including tumour microenvironment atlases. The main caveat is that its perturbation prediction is only modestly above simple baselines, a finding echoed across single-cell foundation models, so its strengths are in annotation and integration rather than in forecasting drug effects. For a newcomer: scGPT is a GPT-style model for cells that is good at naming cell types and merging datasets.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-09-08
- Tags: foundation-model; virtual-cell
- Principle: scGPT is a generative transformer over gene tokens and expression bins.
- Since: 2024
- Strengths: General-purpose fine-tuning
- Limitations: Perturbation prediction only modestly above baselines

## Sources

- Nature Methods 2024: https://doi.org/10.1038/s41592-024-02201-0

## Connected records

- roadmaps: [AI in oncology roadmap: pattern readers → foundation models → agents in the workflow](https://onco.cc/roadmaps/ai-oncology-roadmap/), [Drug discovery roadmap: screening in mice → maps of dependency → designing in silico](https://onco.cc/roadmaps/drug-discovery-roadmap/), [Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell](https://onco.cc/roadmaps/virtual-cell/)
- fronts: [AI & Computation](https://onco.cc/fronts/ai-computation/), [Drug Discovery Platforms](https://onco.cc/fronts/drug-discovery/)
- technologies: [Single-cell & spatial profiling](https://onco.cc/technologies/single-cell-spatial/)
- key papers: [scGPT: toward building a foundation model for single-cell multi-omics using generative AI](https://onco.cc/key-papers/paper-cui-nat-methods/)

---
JSON: https://onco.cc/api/v1/entities/scgpt.json