title: An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.
abstract: In robust biological systems, wide deviations from highly controlled normal behavior may be rare, yet they may result in catastrophic complications. While in silico analysis has gained an appreciation as a tool to offer insights into system-level properties of biological systems, analysis of such rare events provides a particularly challenging computational problem. This paper proposes an efficient stochastic simulation method to analyze rare events in biochemical systems. Our new approach can substantially increase the frequency of the rare events of interest by appropriately manipulating the underlying probability measure of the system, allowing high-precision results to be obtained with substantially fewer simulation runs than the conventional direct Monte Carlo simulation. Here, we show the algorithm of our new approach, and we apply it to the analysis of rare deviant transitions of two systems, resulting in several orders of magnitude speedup in generating high-precision estimates compared with the conventional Monte Carlo simulation.
authors.affiliation: The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Trento 38100, Italy. kuwahara@cosbi.eu
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kuwahara
authors.forename: Ivan
authors.initials: I
authors.lastname: Mura
mesh_terms: D000465:Algorithms; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D016013:Likelihood Functions; D008954:Models, Biological; D008956:Models, Chemical; D009010:Monte Carlo Method; D013269:Stochastic Processes
chemical_list: D004798:Enzymes