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A Fast and Exact Algorithm for the Median of Three Problem—A Graph Decomposition Approach

  • Andrew Wei Xu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)

Abstract

In a previous paper, we have shown that adequate subgraphs can be used to decompose multiple breakpoint graphs, achieving a dramatic speedup in solving the median problem. In this paper, focusing on the median of three problem, we prove more important properties about adequate subgraphs with rank 3 and discuss the algorithms inventorying simple adequate subgraphs. After finding simple adequate subgraphs of small sizes, we incorporate them into ASMedian, an algorithm to solve the median of three problem. Results on simulated data show dramatic speedup so that many instances can be solved very quickly, even ones containing hundreds or thousands of genes.

Keywords

Exact Algorithm Breakpoint Graph Proper Subgraph Leaf Vertex Optimistic Search Schema 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Andrew Wei Xu
    • 1
  1. 1.Department of Mathematics and StatisticsUniversity of OttawaCanada

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