Paper Info
Title
GPU Accelerated Analysis of Treg-Teff Cross Regulation in Relapsing-Remitting Multiple Sclerosis.
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 coarsegrained 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 97x speed-up with respect to the sequential execution of the same number of simulations.
Year
DOI
Venue
2018
10.1007/978-3-030-10549-5_49
Lecture Notes in Computer Science
Keywords
Field
DocType
Multiple sclerosis,GPGPU computing,Petri nets,Parameter sweep analysis
Petri net,Ordinary differential equation,Computer science,Gpgpu computing,Parallel computing,Parametric statistics,Formalism (philosophy),Cross regulation,Computational analysis
Conference
Volume
ISSN
Citations 
11339
0302-9743
0
PageRank 
References 
Authors
0.34
7
9
Name
Order
Citations
PageRank
Marco Beccuti119526.04
Paolo Cazzaniga223527.16
Marzio Pennisi310923.03
Daniela Besozzi439139.10
Marco S. Nobile514323.69
Simone Pernice611.40
Giulia Russo71510.89
Andrea Tangherloni8407.88
F. Pappalardo97620.14