Combining biophysical modeling, simulations and AI to understand how cells self-organize into embryos and tissues @cbitoulouse.bsky.social.
Team headed by @herveturlier.bsky.social
Turlier lab
The abstract deadline for the CSHL Cell Modeling in Space and Time is this Friday 10 April. Don’t miss out!
Very glad to see this great transatlantic collaborative work published 🎉!
Congratulations to all authors: @henrydebelly.bsky.social, @andreu Fernandez Gallén, @ericneiva.bsky.social, and @oweinerlab.bsky.social
Funding from MSCA @ec.europa.eu & @cnrsbiologie.bsky.social
The @sfb1348.bsky.social Meeting “Mechanochemical Signals at Cellular Interfaces” is just around the corner! We are excited to welcome an outstanding lineup of international speakers to #Münster for three days of inspiring scientific exchange and discussion. @uni-muenster.de
Beyond synthetic benchmarks, we show applications to mechanical parameter inference from microscopy images and to inverse design problems in epithelial tissues. 4/5
A real computational tour de force by @ericneiva.bsky.social, carried out as Marie Skłodowska-Curie postdoctoral fellow in the team, now published in the Journal of Computational Physics: urlr.me/AuzK86
Congratulations, Eric!
@cnrsbiologie.bsky.social
Grateful to @ec.europa.eu for funding support
We benchmark three strategies for bilevel optimization in vertex models: automatic differentiation, implicit differentiation, and equilibrium propagation.
This gives a practical comparison of their accuracy, speed, and memory trade-offs. 3/5
VertAX unifies forward modeling and inverse modeling in the same framework.
It lets users define custom energy functions and cost functions in pure Python, while leveraging JAX and bilevel optimization for differentiation, JIT compilation, and GPU acceleration. 2/5
How can we learn tissue mechanics directly from cell patterns and images?
In our new preprint, we introduce VertAX, a differentiable vertex-model framework in JAX for simulating epithelia, inferring parameters, and designing target tissue behaviors.
shorturl.at/PUzT0
1/5
We hope VertAX can help make inverse problems & differential programming more accessible in tissue mechanics.
Thanks to @apasqui.bsky.social, Maxence Ernoult, Italian colleagues, and other members of the team for this collaboration.
Comments very welcome.
Code: github.com/VirtualEmbry... 5/5
