Abstract
Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html.
Document Type
Article
Publication Date
11-11-2016
Digital Object Identifier (DOI)
https://doi.org/10.3389/fnins.2016.00513
Funding Information
DM was partially funded by a startup fund from the College of Arts and Sciences at the University of Kentucky.
Related Content
Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html.
Repository Citation
Murrugarra, David; Miller, Jacob; and Mueller, Alex N., "Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms" (2016). Mathematics Faculty Publications. 19.
https://uknowledge.uky.edu/math_facpub/19
Notes/Citation Information
Published in Frontiers in Neuroscience, v. 10, article 513, p. 1-9.
Copyright © 2016 Murrugarra, Miller and Mueller.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.