Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals
We report the discovery and extraction of a compact hematopoietic algorithm from the single-cell foundation model scGPT, to our knowledge the first biologically useful, competitive algorithm extracted from a foundation model via mechanistic interpretability. We show that scGPT internally encodes a compact hematopoietic manifold with significant developmental branch structure, validated on a strict non-overlap Tabula Sapiens external panel and confirmed via frozen-head zero-shot transfer to an independent multi-donor immune panel. To isolate this geometry, we introduce a general three-stage extraction method consisting of direct operator export from frozen attention weights, a lightweight ...
| Authors | Ihor Kendiukhov |
|---|---|
| Primary category | cs.LG |
| Published | 10 March 2026 |
| Last updated at source | 10 March 2026 |
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