Related papers: Diffusion vs. direct transport in the precision of…
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
Deep learning models have emerged as a powerful tool for various medical applications. However, their success depends on large, high-quality datasets that are challenging to obtain due to privacy concerns and costly annotation. Generative…
Models of ordering dynamics allow to understand natural systems in which an initially disordered population homogenizes some traits via local interactions. The simplest of these models, with wide applications ranging from evolutionary to…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
We analyze a one dimensional version of a model of morphogen transport, a biological process governing cell differentiation. The model was proposed by Hufnagel et al. to describe the forming of morphogen gradient in the wing imaginal disc…
Diffusion models have demonstrated impressive capabilities in synthesizing diverse content. However, despite their high-quality outputs, these models often perpetuate social biases, including those related to gender and race. These biases…
Continuous diffusion models are commonly acknowledged to display a deterministic probability flow, whereas discrete diffusion models do not. In this paper, we aim to establish the fundamental theory for the probability flow of discrete…
The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction partners. Moreover, given the rapid turnover in many intracellular…
Morphogen gradients play an essential role in the spatial regulation of cell patterning during early development. The classical mechanism of morphogen gradient formation involves the diffusion of morphogens away from a localized source…
Modeling the spontaneous evolution of morphology in natural systems and its preservation by proportionate growth remains a major scientific challenge. Yet, it is conceivable that if the basic mechanisms of growth and the coupled kinetic…
Diffusion models are a class of generative models that serve to establish a stochastic transport map between an empirically observed, yet unknown, target distribution and a known prior. Despite their remarkable success in real-world…
In order to characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine learning method to characterize…
Diffusion models have become the go-to method for many generative tasks, particularly for image-to-image generation tasks such as super-resolution and inpainting. Current diffusion-based methods do not provide statistical guarantees…
The widespread use of GPS devices has driven advances in spatiotemporal data mining, enabling machine learning models to simulate human decision making and generate realistic trajectories, addressing both data collection costs and privacy…
Diffusion models have emerged as state-of-the-art generative methods for image synthesis, yet their potential as general-purpose feature encoders remains underexplored. Trained for denoising and generation without labels, they can be…
A high fidelity model for the propagation of pathogens via aerosols in the presence of moving pedestrians is proposed. The key idea is the tight coupling of computational fluid dynamics and computational crowd dynamics in order to capture…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…