Transcriptome Foundation Models Confounded by Co-expression
BoWang87 · x · 2026-07-10
This post discusses a study on transcriptome foundation models: when trained under generative pre-training or masked language modeling objectives, these models are confounded by gene co-expression networks.
The author notes that while they perform well on tasks like cell type and disease classification, they often fail or face limited performance in downstream applications.
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