Scholars Critique scFM Review: Definitions Too Loose, Mixes General and Specialized Models
jmuiuc · x · 2026-08-20
- Background: In response to a comprehensive review on single-cell foundation models (scFMs), the author offers a critical perspective.
- Key Points:
- Argues that the definition of scFM has become too loose. For instance, the actual model unit of GET is celltype pseudobulk aggregated from scATAC-seq, hence not a single cell model.
- Notes that TissueNarrator, highlighted in the review, is not considered a bona fide scFM but a specialized spatial transcriptomics model built leveraging an existing foundation LLM (Qwen).
- Conclusion: Figure 1 in the review seems to mix FMs, specialized models built on FMs, and task-specific models into one big family tree, lacking clear distinctions.
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