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NoC-Based Hardware Accelerator for Breakpoint Phylogeny
June 2012 (vol. 61 no. 6)
pp. 857-869
Turbo Majumder, Washington State University, Pullman
Souradip Sarkar, Washington State University, Pullman
Partha Pratim Pande, Washington State University, Pullman
Ananth Kalyanaraman, Washington State University, Pullman
Maximum Parsimony phylogenetic tree reconstruction is based on finding the breakpoint median, given a set of species, and is represented by a bounded edge-weight graph model. This reduces the breakpoint median problem to one of solving multiple instances of the Traveling Salesman Problem (TSP), which is a classical NP-complete problem in graph theory. Exponential time algorithms that apply efficient runtime heuristics, such as branch-and-bound, to dynamically prune the search space are used to solve TSP. In this paper, we present the design and performance evaluation of a network-on-chip (NoC)-based implementation for solving TSP under the bounded edge-weight model, as used in the computation of breakpoint phylogeny. Our approach takes advantage of fine-grain parallelism from the multiple processing elements (PEs) and uses efficient NoC architecture for inter-PE communication. To accelerate the application on hardware, our PE design optimizes a particular lower bound calculation operation which typically tends to be the serial bottleneck in computation of a TSP solution. We also explore two representative NoC architectures—mesh and quad-tree—and show that the latter is more energy-efficient for this application domain. Experimental results show that this new implementation is able to achieve speedups of up to three orders of magnitude over state-of-the-art multithreaded software implementations.

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Index Terms:
Phylogenetics, breakpoint-median problem, maximum parsimony, traveling salesman problem.
Turbo Majumder, Souradip Sarkar, Partha Pratim Pande, Ananth Kalyanaraman, "NoC-Based Hardware Accelerator for Breakpoint Phylogeny," IEEE Transactions on Computers, vol. 61, no. 6, pp. 857-869, June 2012, doi:10.1109/TC.2011.100
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