RAGTIMER 1.0: Rapid Rare-Event Partial State Space Construction for Stochastic VAS (extended version)

Abstract

Transient reachability analysis of rare events in Continuous-Time Stochastic Vector Addition Systems (CTSVAS) such as Chemical Reaction Networks (CRNs) has proven a formidable challenge to cutting-edge tools. Underlying a CTSVAS is a continuous-time Markov chain (CTMC), and CTMC transient reachability analysis calls for Probabilistic Model Checking (PMC). This analysis requires the explicit representation of a model's entire state space. Rare events occur with extremely low probability, compounding the challenge of probabilistic analysis. In CRNs, it is imperative to verify the probability of rare events; even a low concentration of a species can have pathological consequences. This paper presents the RAGTIMER 1.0 tool, which efficiently builds a partial state space for a CTSVAS by enumerating traces to a rare event of interest and expanding them to exploit concurrency and cycles, providing a guaranteed lower bound on the probability of a rare event. Guaranteed lower bounds are particularly useful in synthetic biological applications because they indicate how and when a rare event can be experimentally observed. RAGTIMER is an attractive alternative to existing rare event analysis methods for CTSVAS models. It outperforms existing PMC tools and refutes multiple probability estimates from rare-event stochastic simulation on multiple challenging CRN models. RAGTIMER uses optimized data structures, a simple input format, and memory-safe Rust code to improve the scalability and accessibility of PMC for industry professionals.