SC is the International Conference for
High Performance Computing, Networking,
Storage and Analysis

SCHEDULE: NOV 12-18, 2011

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A Fast Solver for Modeling the Evolution of Virus Populations

SESSION: Applications


TIME: 4:30PM - 5:00PM

AUTHOR(S):Gerhard Niederbrucker, Wilfried N. Gansterer


Solving Eigen's quasispecies model for the evolution of virus populations involves the computation of the dominant eigenvector of a matrix whose size N grows exponentially with the chain length of the virus to be modeled. Most biologically interesting viruses are so far well beyond the reach of existing algorithms and hardware. We show how to exploit special properties of the problem under consideration and design a fast and accurate solver which reduces the complexity to O(N log N). Our solver is even faster than existing approximative strategies and contrary to those can also be applied to more general formulations of the quasispecies model. Substantial further improvements and high parallelism can be achieved for special fitness landscapes in the evolution model. Beyond theoretical analysis, we evaluate the performance of our new solver experimentally on a GPU with an OpenCL implementation and illustrate speedup factors of more than 10^7 over standard approaches.

Chair/Author Details:

Gerhard Niederbrucker - University of Vienna

Wilfried N. Gansterer - University of Vienna

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The full paper can be found in the ACM Digital Library

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