From Simulated Fluids to Living Tissue: Zero-Shot Foundation Model Transfer to Perturbed Embryos

Louisa Cornelis; Haewon Jeong; Irina Espejo; Payel Mukhopadhyay

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arXiv · 2610.16236

From Simulated Fluids to Living Tissue: Zero-Shot Foundation Model Transfer to Perturbed Embryos

Louisa Cornelis·Haewon Jeong·Irina Espejo·Payel Mukhopadhyay

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Abstract

Morphogenesis is driven by the interplay of genetic regulation and tissue mechanics. In vivo video data is limited, particularly under genetic mutations and environmental perturbations, making generalization beyond the most representative conditions in the dataset challenging. However, at tissue scales, the dynamics of Drosophila can be described as a continuum flow, motivating the usage of representations learned across other physical systems as priors for developmental dynamics. We investigate finetuning Walrus, a Continuum Dynamics Foundation Model pretrained across a broad set of simulated continuous systems, on tissue velocity fields from only 12 wild-type Drosophila blastoderm videos. We evaluate autoregressive prediction both in-distribution and zero-shot under unseen temperature and genetic perturbations. Zero-shot refers to evaluation on perturbation conditions never seen during wild-type finetuning, without any additional training. In-distribution, a Fourier Neural Operator model trained from scratch achieves best performance on VRMSE. However, Walrus (CRPS) is the strongest model under the most severe distribution shift of unseen samples of mutated embryos and temperature conditions. Interestingly, predictions capture the shape of the mean surface tissue velocity trajectory and its separation between 17°C and 27°C, including the timing of the peak at Germ Band Extension onset, a biologically meaningful milestone of embryo development. Our results provide preliminary support that representations learned from different dynamical systems can transfer to experimental morphogenesis in developmental regimes, provided they admit a continuum description. More broadly, our results motivate further study of physics foundation models as a new complementary tool for the simulation of morphogenesis in low-data regimes.

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Louisa Cornelis, Haewon Jeong, Irina Espejo, Payel Mukhopadhyay. 2026-10-12. From Simulated Fluids to Living Tissue: Zero-Shot Foundation Model Transfer to Perturbed Embryos. https://arxiv.org/abs/2610.16236

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