Author

Yong-Qi Huang

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Open access Oct 2026

The recoverable resolution of cellular perturbation-response prediction

Virtual cell models aim to predict how cells respond to perturbations, yet accurate prediction of post-perturbation gene expression can conceal failures to recover context-specific responses. Here we identify context geometry compression (CGC), in which models preserve cellular identity and shared perturbation effects...

Yong-Qi Huang, Han-Zhi Wang, Chen-Yu Li et al. · bioRxiv · 0 citations

Open access Aug 2026

Virtual-cell models compress unseen intervention geometry through a target-specific generalization bottleneck

Predictive models of cellular perturbation are often judged by how closely they reconstruct molecular states after unseen interventions. We show that high state-level similarity can coexist with loss of the relationships that distinguish perturbations, a failure we term Intervention Geometry Compression (IGC). Across e...

Yong-Qi Huang, Hanzhi Wang, Parker C. Wilson · bioRxiv · 0 citations