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The movement of organisms and cells can be governed by occasional long distance runs, according to an approximate L\'evy walk. For T cells migrating through chronically-infected brain tissue, runs are further interrupted by long pauses, and…
Cells perform directed motion in response to external stimuli that they detect by sensing the environment with their membrane protrusions. In particular, several biochemical and biophysical cues give rise to tactic migration in the…
Despite numerous advances in the field of tissue engineering and regenerative medicine, monitoring the formation of tissue regeneration and its metabolic variations during culture is still a challenge and mostly limited to bulk volumetric…
Generative models have the potential to transform the way we emulate Earth's changing climate. Previous generative approaches rely on weather-scale autoregression for climate emulation, but this is inherently slow for long climate horizons…
Strong semantic representations improve the convergence and generation quality of diffusion and flow models. Existing approaches largely rely on external models, which require separate training, operate on misaligned objectives, and exhibit…
Diffusion models have achieved remarkable success across various domains. However, their slow generation speed remains a critical challenge. Existing acceleration methods, while aiming to reduce steps, often compromise sample quality,…
This study presents a neural network-enhanced approach to modeling disease spread dynamics over time and space. Neural networks are used to estimate time-varying parameters, with two calibration methods explored: Approximate Bayesian…
Urban wind flow modeling and simulation play an important role in air quality assessment and sustainable city planning. A key challenge for modeling and simulation is handling the complex geometries of the urban landscape. Low order models…
Spatial transcriptomics (ST) bridges gene expression and tissue morphology but faces clinical adoption barriers due to technical complexity and prohibitive costs. While computational methods predict gene expression from H&E-stained…
Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent…
Celcomen leverages a mathematical causality framework to disentangle intra- and inter- cellular gene regulation programs in spatial transcriptomics and single-cell data through a generative graph neural network. It can learn gene-gene…
A stochastic model is used to assess the effect of external parameters on the development of submerged biofilms on smooth and rough surfaces. The model includes basic cellular mechanisms, such as division and spreading, together with an…
Diffusion models have been widely used in time series and spatio-temporal data, enhancing generative, inferential, and downstream capabilities. These models are applied across diverse fields such as healthcare, recommendation, climate,…
The dynamics of urban systems can be understood from an evolutionary perspective, in some sense extending biological and cultural evolution. Models for systems of cities implementing elementary evolutionary processes remain however to be…
Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…
Collective cell migration plays a central role in tissue development, morphogenesis, wound repair and cancer progression. With the growing realization that physical forces mediate cell motility in development and physiology, a key…
Diffusion models and flow-matching models have enabled generating diverse and realistic images by learning to transfer noise to data. However, sampling from these models involves iterative denoising over many neural network passes, making…
We develop a continuous mathematical model of population dynamics that describes the sequential emergence of new genotypes under limited resources. The framework models genotype density as a nonlinear flow in mutation space, combining…
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,…
Cell-cell adhesion is one the most fundamental mechanisms regulating collective cell migration during tissue development, homeostasis and repair, allowing cell populations to self-organize and eventually form and maintain complex tissue…