On Almost Monge All Scores Matrices
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The all scores matrix of a grid graph is a matrix containing the optimal scores of paths from every vertex on the first row of the graph to every vertex on its last row. This matrix is commonly used to solve diverse string comparison problems. All scores matrices have the Monge property, and this was exploited by previous works that used all scores matrices for solving various problems. In this paper, we study an extension of grid graphs that contain an additional set of edges, called bridges. Our main result is to show several properties of the all scores matrices of such graphs. We also apply these properties to obtain an \(O(r(nm+n^2))\) time algorithm for constructing the all scores matrix of an \(m\times n\) grid graph with r bridges and bounded integer weights.
KeywordsSequence alignment Longest common subsequences DIST matrices Monge matrices All path score computations Multiple-source shortest-paths
We thank the anonymous reviewers, that helped us improve the readability of the paper through their many helpful suggestions. The research of A.C and D.T was partially supported by ISF Grant No. 981/11. The research of A.C and M.Z-U was partially supported by ISF Grant 179/14.
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