title: A comparison of computational efficiencies of stochastic algorithms in terms of two infection models.
abstract: In this paper, we investigate three particular algorithms: a stochastic simulation algorithm (SSA), and explicit and implicit tau-leaping algorithms. To compare these methods, we used them to analyze two infection models: a Vancomycin-resistant enterococcus (VRE) infection model at the population level, and a Human Immunodeficiency Virus (HIV) within host infection model. While the first has a low species count and few transitions, the second is more complex with a comparable number of species involved. The relative efficiency of each algorithm is determined based on computational time and degree of precision required. The numerical results suggest that all three algorithms have the similar computational efficiency for the simpler VRE model, and the SSA is the best choice due to its simplicity and accuracy. In addition, we have found that with the larger and more complex HIV model, implementation and modification of tau-Leaping methods are preferred.
authors.affiliation: Center for Research in Scientic Computation, North Carolina State University, Raleigh, NC 27695-8212, United States. htbanks@ncsu.edu
authors.forename: H Thomas
authors.initials: HT
authors.lastname: Banks
authors.forename: Shuhua
authors.initials: S
authors.lastname: Hu
authors.forename: Michele
authors.initials: M
authors.lastname: Joyner
authors.forename: Anna
authors.initials: A
authors.lastname: Broido
authors.forename: Brandi
authors.initials: B
authors.lastname: Canter
authors.forename: Kaitlyn
authors.initials: K
authors.lastname: Gayvert
authors.forename: Kathryn
authors.initials: K
authors.lastname: Link
mesh_terms: D000465:Algorithms; D003198:Computer Simulation / Q000706:statistics & numerical data; D016983:Enterococcus / Q000187:drug effects; D016908:Gram-Positive Bacterial Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000635:transmission*; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission*; D006801:Humans; D015233:Models, Statistical; D011157:Population Dynamics; D020713:Vancomycin Resistance