Skip to content

Single-Cell Foundation Model

Definition
AI-generated

A single-cell foundation model is a large machine-learning model pretrained on massive single-cell transcriptomic (or multi-omic) corpora—often with self-supervised objectives—so that embeddings or heads transfer to tasks such as cell-type annotation, batch correction, gene regulatory prediction, or perturbation response forecasting.

Topics
Single-cell analysis
Related
Deep Generative Model Foundation Model Gene Regulatory Network Inference

Why it matters in GWAS

These models increasingly mediate how atlases are queried and how in silico interventions are proposed for GWAS genes; claims require scrutiny against simple baselines and independent benchmarks, as in broader foundation model debates.

Example usage

"The discussion compared a single-cell foundation model’s zero-shot cell annotation to marker-based labels in the eQTL panel."

Deep Generative Model Foundation Model Gene Regulatory Network Inference In Silico Perturbation Prediction Large Language Model (LLM) Single-Cell GWAS Integration Single-Cell Sequencing
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Cui H, et al. (2024). scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nat Methods.
  • Hao M, et al. (2024). Large-scale foundation model on single-cell transcriptomics. Nat Methods.
  • Dimitrov D, Schrod S, Rohbeck M, et al. (2026). Interpretation, extrapolation and perturbation of single cells. Nat Rev Genet. https://doi.org/10.1038/s41576-025-00920-4
← Single-Cell Expression Quantitative Trait Locus (sc-eQTL) Single-Cell GWAS Integration →

Last updated (UTC · Git history)