Efficient parallel algorithms for string editing and related problems
SIAM Journal on Computing
Perspectives of Monge properties in optimization
Discrete Applied Mathematics
SIAM Journal on Computing
High-order entropy-compressed text indexes
SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices
SIAM Journal on Computing
An all-substrings common subsequence algorithm
Discrete Applied Mathematics
Semi-local longest common subsequences in subquadratic time
Journal of Discrete Algorithms
Fast distance multiplication of unit-Monge matrices
SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
Space-Efficient and fast algorithms for multidimensional dominance reporting and counting
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
Fully incremental LCS computation
FCT'05 Proceedings of the 15th international conference on Fundamentals of Computation Theory
Monge properties of sequence alignment
Theoretical Computer Science
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In this paper we study algorithms for the max-plus product of Monge matrices. These algorithms use the underlying regularities of the matrices to be faster than the general multiplication algorithm, hence saving time. A nonnaive solution is to iterate the SMAWK algorithm. For specific classes there are more efficient algorithms. We present a new multiplication algorithm (MMT), that is efficient for general Monge matrices and also for specific classes. The theoretical and empirical analysis shows that MMT operates in near optimal space and time. Hence we give further insight into an open problem proposed by Landau. The resulting algorithms are relevant for bio-informatics, namely because Monge matrices occur in string alignment problems.