Learning noisy tissue dynamics across time scales
This work addresses the challenge of modeling noisy tissue dynamics for bioengineering and clinical applications, representing an incremental advance with a novel hybrid method.
The authors tackled the problem of predicting noisy multicellular tissue dynamics by introducing a biomimetic machine learning framework that infers these dynamics from experimental movies, demonstrating accurate generation of developmental and signaling processes like the fly wing and stochastic ERK waves.
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.