Article

Regulatory Logic in Larger Single-Cell Foundation Models: A Sparse Autoencoder Comparison of scFoundation and Geneformer

2026-05-18

Abstract excerpt

The emergence of large-scale single-cell foundation models (scFMs) such as scFoundation and Geneformer offers unprecedented potential to decode the regulatory logic of gene expression. However, the internal representations these models learn—particularly whether they disentangle interpretable regulatory programs—remain largely unexamined. Here, we systematically compare the regulatory logic encoded by scFoundation...

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Literature Corpus work: dc2e6875-357e-500f-a859-0e5af7b53b84
DOI: 10.14293/pr2199.003544.v2

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