Math Bio Seminar: A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation

January 20, 2023, 3:30-4:00pm | Zoom

Speaker: Albin Salazar, Ecole Normale Superieure, Paris



A generic framework to coarse-grain stochastic reaction networks by Abstract InterpretationIn the last decades, logical or discrete models have emerged as a successful paradigm for capturing and predicting the behaviors of systems of molecular interactions. Intuitively, they consist in sampling the abundance of each kind of biochemical entity within finite sets of intervals and deriving transitions accordingly. On one hand, formally-proven sound derivation from more precise descriptions (such as from reaction networks) may include many fictitious behaviors. On the other hand, direct modeling usually favors dominant interactions with no guarantee on the behaviors that are neglected. In this paper, we formalize a sound coarse-graining approach for stochastic reaction networks. Its originality relies on two main ingredients. Firstly, we abstract values by intervals that overlap in order to introduce a minimal effort for the system to go back to the previous interval, hence limiting fictitious oscillations in the coarse-grained models. Secondly, we compute for pairs of transitions (in the coarse-grained model) bounds on the probabilities on which one will occur first. We illustrate our ideas on two case studies and demonstrate how techniques from Abstract Interpretation can be used to design more precise discretization methods, while providing a framework to further investigate the underlying structure of logical and discrete models.