GPU accelerated analysis of treg-teff cross regulation in relapsing-remitting multiple sclerosis

Marco Beccuti, Paolo Cazzaniga, Marzio Pennisi, Daniela Besozzi, Marco S. Nobile, Simone Pernice, Giulia Russo, Andrea Tangherloni, Francesco Pappalardo

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

5 Citations (Scopus)

Abstract

The computational analysis of complex biological systems can be hindered by two main factors. First, modeling the system so that it can be easily understood and analyzed by non-expert users is not always possible, especially when dealing with systems of Ordinary Differential Equations. Second, when the system is composed of hundreds or thousands of reactions and chemical species, the classic CPU-based simulators could not be appropriate to efficiently derive the behavior of the system. To overcome these limitations, in this paper we propose a novel approach that combines the descriptive power of Stochastic Symmetric Nets–a Petri Net formalism that allows modeler to describe the system in a parametric and compact manner–with LASSIE, a GPU-powered deterministic simulator that offloads onto the GPU the calculations required to execute many simulations by following both fine-grained and coarse-grained parallelization strategies. This pipeline has been applied to carry out a parameter sweep analysis of a relapsing-remitting multiple sclerosis model, aimed at understanding the role of possible malfunctions in the cross-balancing mechanisms that regulate peripheral tolerance of self-reactive T lymphocytes. From our experiments, LASSIE achieves around 97× speed-up with respect to the sequential execution of the same number of simulations.

Original languageEnglish
Title of host publicationEuro-Par 2018: Parallel Processing Workshops
Subtitle of host publicationEuro-Par 2018 International Workshops, Turin, Italy, August 27-28, 2018, Revised Selected Papers
EditorsGabriele Mencagli, Dora B. Heras
Place of PublicationCham
PublisherSpringer
Pages626-637
Number of pages12
ISBN (Electronic)978-3-030-10549-5
ISBN (Print)978-3-030-10548-8
DOIs
Publication statusPublished - 2019
Externally publishedYes
Event24th International Conference on Parallel and Distributed Computing, Euro-Par 2018 - Turin, Italy
Duration: 27 Aug 201828 Aug 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume11339 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference24th International Conference on Parallel and Distributed Computing, Euro-Par 2018
CountryItaly
CityTurin
Period27/08/1828/08/18

Keywords

  • GPGPU computing
  • Multiple sclerosis
  • Parameter sweep analysis
  • Petri nets

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