Köster, Till and Giabbanelli, Philippe J. and Uhrmacher, Adelinde M. (2020) Performance and Soundness of Simulation: A Case Study based on a Cellular Automaton for In-Body Spread of HIV. In: Winter Simulation Conference (WSC 2020), 13-16 Dec 2020, Orlando, Florida, USA. Proceedings, published by IEEE Computer Society, pp. 2281-2292.
Full text not available from this repository.Abstract
Cellular automata are often used for spatial dynamics in cell biology such as the spread of infections within a cell biological population. Due to the number of cells in a model, efficient simulation algorithms have received increasing attention over the last decade. Many cellular automata models are executed synchronously. In this paper, we focus on improving the efficiency of a cellular automaton model known as the 'dos Santos' model for the Human Immunodeficiency Virus (HIV). The synchronous updates in this model are driven by mostly deterministic transitions and a few highly probabilistic transitions. This design can be exploited to create an efficient simulation algorithm. We propose such an algorithm using an advanced scheme to generate random numbers (to efficiently perform robabilistic transitions) that efficiently leverages CPU vectorization. The benchmarks show a significant performance increase by a factor of 2.4x in comparison to a quality baseline implementation. We note several limitations in the model behavior and simulation outputs, which apply not only to the dos Santos design but also to the many synchronous HIV models inheriting its design. Several mitigation schemes are discussed to address some of these limitations.
| Item Type: | Conference or Workshop Item (Paper) |
|---|---|
| Projects: | ESCeMMo |
