Michel Fruchart

Matthew S. Schmitt, Maciej Koch-Janusz, Michel Fruchart et al.

Model reduction is the construction of simple yet predictive descriptions of the dynamics of many-body systems in terms of a few relevant variables. A prerequisite to model reduction is the identification of these variables, a task for which no general method exists. Here, we develop an approach to identify relevant variables, defined as those most predictive of the future, using the so-called information bottleneck. We elucidate analytically the relation between these relevant variables and the eigenfunctions of the transfer operator describing the dynamics. In the limit of high compression, the relevant variables are directly determined by the slowest-decaying eigenfunctions. Our results provide a firm foundation to interpret deep learning tools that automatically identify reduced variables. Combined with equation learning methods this procedure yields the hidden dynamical rules governing the system's evolution in a data-driven manner. We illustrate how these tools work in diverse settings including model chaotic and quasiperiodic systems in which we also learn the underlying dynamical equations, uncurated satellite recordings of atmospheric fluid flows, and experimental videos of cyanobacteria colonies in which we discover an emergent synchronization order parameter.

Ming Han, John Devany, Michel Fruchart et al.

Tissue dynamics play a crucial role in biological processes ranging from inflammation to morphogenesis. However, these noisy multicellular dynamics are notoriously hard to predict. Here, we introduce a biomimetic machine learning framework capable of inferring noisy multicellular dynamics directly from experimental movies. This generative model combines graph neural networks, normalizing flows and WaveNet algorithms to represent tissues as neural stochastic differential equations where cells are edges of an evolving graph. Cell interactions are encoded in a dual signaling graph capable of handling signaling cascades. The dual graph architecture of our neural networks reflects the architecture of the underlying biological tissues, substantially reducing the amount of data needed for training, compared to convolutional or fully-connected neural networks. Taking epithelial tissue experiments as a case study, we show that our model not only captures stochastic cell motion but also predicts the evolution of cell states in their division cycle. Finally, we demonstrate that our method can accurately generate the experimental dynamics of developmental systems, such as the fly wing, and cell signaling processes mediated by stochastic ERK waves, paving the way for its use as a digital twin in bioengineering and clinical contexts.