Introduction to algorithms
Sparse dynamic programming I: linear cost functions
Journal of the ACM (JACM)
An improved algorithm for computing the edit distance of run-length coded strings
Information Processing Letters
Matching for run-length encoded strings
Journal of Complexity
Algorithms for the Longest Common Subsequence Problem
Journal of the ACM (JACM)
Introduction to data compression (2nd ed.)
Introduction to data compression (2nd ed.)
A fast algorithm for computing longest common subsequences
Communications of the ACM
A fast and practical bit-vector algorithm for the longest common subsequence problem
Information Processing Letters
A sub-quadratic sequence alignment algorithm for unrestricted cost matrices
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Edit distance of run-length encoded strings
Information Processing Letters
The SBC-tree: an index for run-length compressed sequences
EDBT '08 Proceedings of the 11th international conference on Extending database technology: Advances in database technology
A parallel LCS algorithm for biosequences alignment
Proceedings of the 2nd international conference on Scalable information systems
Information Processing Letters
Efficient algorithms for the block edit problems
Information and Computation
A faster algorithm for the computation of string convolutions using LZ78 parsing
Information Processing Letters
Fast sequence similarity computing with LCS on LARPBS
ISPA'05 Proceedings of the 2005 international conference on Parallel and Distributed Processing and Applications
Fast scalable algorithm on LARPBS for sequence alignment
ISPA'05 Proceedings of the 2005 international conference on Parallel and Distributed Processing and Applications
Fast parallel algorithms for the longest common subsequence problem using an optical bus
ICCSA'05 Proceedings of the 2005 international conference on Computational Science and Its Applications - Volume Part III
Fast algorithms for computing the constrained LCS of run-length encoded strings
Theoretical Computer Science
Hardness of longest common subsequence for sequences with bounded run-lengths
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
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Data compression can be used to simultaneously reduce memory, communication and computation requirements of string comparison. In this paper we address the problem of computing the length of the longest common subsequence (LCS) between run-length-encoded (RLE) strings. We exploit RLE both to reduce the complexity of LCS computation from O(M × N) to O(mN + Mn - mn), where M and N are the lengths of the original strings and m and n the number of runs in their RLE representation, and to improve the inherent parallelism of the proposed algorithm, so that it may execute in O(m + n) steps on a systolic array of M + N units.We also discuss the application of the proposed algorithm to the related problem of edit distance (ED) computation.