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.

What should be considered if you decide to build your own mathematical model for predicting the development of bacterial resistance? Recommendations based on a systematic review of the literature

“…We reviewed only models where AB consumption was introduced as an independent parameter, because we consider the process of developing resistance as a function of time and antibiotic consumption. That is why some papers were excluded at the stage of full text analysis (Bergstrom et al, 2004 ; Miller et al, 2004 ; Boni and Feldman, 2005 ; Huovinen, 2005 ; Mera, 2005 ; Reluga, 2005 ; Webb et al, 2005 ; Levin and Rozen, 2006 ; Schinazi, 2006 ; D'Agata et al, 2007 ; Zalounina et al, 2007 ; Drovandi and Pettitt, 2008 ; Pienaar et al, 2009 ; Artalejo et al, 2010 ; Haber et al, 2010 ; Kardas-Sloma et al, 2011 ; Kouyos et al, 2011 ; Opatowski et al, 2011 ; Wang et al, 2011 ; Banks et al, 2012 ; Chamchod and Ruan, 2012a , b ; Deng et al, 2012 ; Hurford et al, 2012 ; Joyner et al, 2012 ; Sotto and Lavigne, 2012 ; Yahdi et al, 2012 ; Horsburgh et al, 2013 ; Lee et al, 2013a , b ; Worby et al, 2013 ). The seven remaining models were classified according to the type of link between resistance and AB consumption.…”