A COMPARISON OF COMPUTATIONAL EFFICIENCIES OF STOCHASTIC ALGORITHMS IN TERMS OF TWO INFECTION MODELS

作者：Banks H Thomas^*; Hu Shuhua; Joyner Michele; Broido Anna; Canter Brandi; Gayvert Kaitlyn; Link Kathryn

来源：Mathematical Biosciences and Engineering, 2012, 9(3): 487-526.

DOI：10.3934/mbe.2012.9.487

• Dynamical models
• continuous time Markov chain models
• stochastic simulation algorithms
• Gillespie
• tau-leaping
• bacterial and viral infection models

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.

• 出版日期2012-7