SVC-Probe: A Framework for Evaluating Perturbation Generalization in Spatial Foundation-Model Embeddings
This work examines perturbation generalization in spatial foundation-model embeddings derived from fluorescence microscopy images. Although these models can discriminate drug conditions accurately, it remains unclear whether the learned representations reflect patterns consistent with expected perturbation axes that transfer across drugs. We introduce SVC-Probe, a perturbation-aware framework that combines Subcellular Embedding Atlas Stability, Mondrian Neighborhood Graphs, and a Foundation Model Perturbation Probe to assess embedding stability, neighborhood rewiring, and centroid prediction under drug treatment. Applied to the CM4AI MDA-MB-468 chemical-perturbation atlas comprising 462 a...
| Authors | Jake Y. Chen, Huu Phong Nguyen, Fuad Al Abir et al. |
|---|---|
| Primary category | q-bio.QM |
| Published | 26 June 2026 |
| Last updated at source | 26 June 2026 |
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