Keynote on "the propagation approach for computing biochemical reaction networks"

Abstract

Joint work with Maria Mateescu. Propagation models provide a framework for describing algorithms for the transient analysis of stochastic state transition systems, such as computing event probabilities, expectancies, and variances on biochemical reaction networks. We discuss the syntax, semantics, and pragmatics of propagation models. We give three use cases for propagation models: the chemical master equation, the reaction rate equation, and a hybrid method that combines these two equations. We present a propagation abstract data type (ADT) for implementing uniformization and integration algorithms on propagation models. The propagation ADT is based on an update operator, which propagates continuous mass values through a discrete state space. The update operator can be implemented using a threshold abstraction, which propagates only "significant" mass values and thus achieves a controllable compromise between efficiency and accuracy.