Deep Abstractions of Chemical Reaction Networks

Multi-scale modeling of biological systems, for instance of tissues composed of millions of cells, are extremely demanding to simulate, even resorting to High Performance Computing (HPC) facilities, particularly when each cell is described by a detailed model of some intra-cellular pathways and cells are coupled and interacting at the tissue level. Model abstraction can play a crucial role in this setting, by providing simpler models of intra-cellular dynamics that are much faster to simulate so to scale better the analysis at the tissue level. Abstractions themselves can be very challenging to build ab-initio. A more viable strategy is to learn them from single cell simulation data. In this paper, we explore this direction, constructing abstract models of chemical reaction networks in terms of Discrete Time Markov Chains on a continuous space, learning transition kernels using deep neural networks. This allows us to obtain accurate simulations, greatly reducing the computational burden