相关论文: VertAX: a differentiable vertex model for learning…
Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles, and predict the…
The vertex model is widely used to describe the dynamics of epithelial tissues, because of its simplicity and versatility and the direct inclusion of biophysical parameters. Here, it is shown that quite generally, when cells modify their…
We introduce an Active Vertex Model (AVM) for cell-resolution studies of the mechanics of confluent epithelial tissues consisting of tens of thousands of cells, with a level of detail inaccessible to similar methods. The AVM combines the…
Modern deep learning methods have achieved impressive results across tasks from disease classification, estimating continuous biomarkers, to generating realistic medical images. Most of these approaches are trained to model conditional…
Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed…
Modal methods for simulating vibrations of strings, membranes, and plates are widely used in acoustics and physically informed audio synthesis. However, traditional implementations, particularly for non-linear models like the von K\'arm\'an…
A continuum model of epithelial tissue mechanics was formulated using cellular-level mechanical ingredients and cell morphogenetic processes, including cellular shape changes and cellular rearrangements. This model can include finite…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
The rapid rise of scientific machine learning (SciML) has expanded the role of differentiable modeling, surrogate modeling, and data-driven constitutive laws in large-scale simulation. The JAX framework provides an attractive environment…
The deep learning revolution has greatly been accelerated by the 'hardware lottery': Recent advances in modern hardware accelerators and compilers paved the way for large-scale batch gradient optimization. Evolutionary optimization, on the…
Many morphogenetic processes involve mechanical rearrangement of epithelial tissues that is driven by precisely regulated cytoskeletal forces and cell adhesion. The mechanical state of the cell and intercellular adhesion are not only the…
Materials science inherently spans disciplines: experimentalists use advanced microscopy to uncover micro- and nanoscale structure, while theorists and computational scientists develop models that link processing, structure, and properties.…
Optical multilayer thin-films are fundamental components that enable the precise control of reflectance, transmittance, and phase shift in the design of photonic systems. Rapid and accessible simulation of these structures holds critical…
Epithelial tissues act as barriers and, therefore, must repair themselves, respond to environmental changes and grow without compromising their integrity. Consequently, they exhibit complex viscoelastic rheological behavior where…
In order to describe two-dimensionally packed cells in epithelial tissues both mathematically and physically, there have been developed several sorts of geometrical models, such as the vertex model, the finite element model, the…
We present an implementation of interval analysis and mixed monotone interval reachability analysis as function transforms in Python, fully composable with the computational framework JAX. The resulting toolbox inherits several key features…
This paper introduces JAX-FEM, an open-source differentiable finite element method (FEM) library. Constructed on top of Google JAX, a rising machine learning library focusing on high-performance numerical computing, JAX-FEM is implemented…
Soft materials such as rubbers, hydrogels, and biological tissues undergo damage in the form of stiffness degradation without apparent changes in their stress-free geometry. Accurate simulation of this behavior is critical in applications…
Shape reconstruction from imaging volumes is a recurring need in medical image analysis. Common workflows start with a segmentation step, followed by careful post-processing and,finally, ad hoc meshing algorithms. As this sequence can be…
We introduce Atomistic learned potentials in JAX (apax), a flexible and efficient open source software package for training and inference of machine-learned interatomic potentials. Built on the JAX framework, apax supports GPU acceleration…