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Reading Mechanism off Biological Foundation Models: An Empirical Analysis of Genomic Neighborhood Structure in scGPT Gene Embeddings

2026-07-27

Abstract excerpt

<title>Abstract</title> <p>Biological foundation models are often said to organize genes according to biological function. Such claims are difficult to interpret when the tested property is also present in the model’s training data. We examine a property that scGPT never receives explicitly: a gene’s coordinate in the human genome. We extracted the 512-dimensional input embeddings from the public wholehuman scGPT...

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Literature Corpus work: da41f330-f15d-5f33-87c1-94b2dba808ae
DOI: 10.21203/rs.3.rs-10462221/v1

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