D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano., "Sparse dynamic programming," 1st ACM-SIAM Symp. Discrete Algorithms, San Francisco, 513-522, 1990  Home/Search Document Not in Database Summary Related Articles Check |
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Efficient Algorithms for Approximate String Matching with Swaps - Kim, Lee (1999) (1 citation) (Correct)
....A and B. Most common edit operations are the following. i) change: replace one character of A by another single character of B. ii) deletion: delete one character from A. iii) insertion: insert one character into B. These three edit operations are the ones commonly used in applications [EGGI92, SK83,WF74, WM92], though only insertions and deletions are considered in some work [My86] A discrepancy between A and B that is corrected by an edit operation is called a difference. The problem of string matching with k differences (or the k differences problem) is defined as follows: Given a pattern A of ....
Eppstein, D., Galil, Z., Giancarlo, R., and Italiano, G. (1992), Sparse dynamic programming. I. Linear cost functions, J. Assoc. Comput. Mach. 39, 519#545.
String Editing and Longest Common Subsequences - Apostolico (1996) (1 citation) (Correct)
.... effort, it is possible to set up simpler ad hoc variants of finger trees supporting the same performance (Apostolico and Guerra [1987] A bound O(m log n d log(2mn=d) was also claimed by Hsu and Du [1984] for one of their constructions, but the claim turned out to be flawed (Apostolico [1987] Eppstein et al. 1990] observed that using Johnson s [1982] variant of the flat trees of van Emde Boas [1975] would reduce the log factor to log log. Before leaving this section, it is useful to mention also some other approaches to the LCS problem. One notable line of research concentrated on cases where the length ....
Eppstein, D., Z. Galil, R. Giancarlo, and G. Italiano [1990]. "Sparse dynamic programming," Proc. Symp. on Discrete Algorithms, San Francisco CA, 513-522.
The CGAT Proposal - Plans, Promises, and Year One - Wood (1995) (Correct)
....(for example, in the construction of consensus sequences [32] the number of spaces is limited. We are interested in algorithms whose running time is sensitive to either the number of spaces or the number of gaps required in the alignment. The newly developed sparse dynamic programming technique [6] may also be relevant here. More General Pairwise Sequence Alignments Most pairwise DNA sequence alignment algorithms are concerned with operations that correspond to local mutations such as insertion, deletion, and replacement of nucleotides. Higher level operations such as duplication, ....
D. Eppstein, Z. Galil, R. Giancarlo, and G. Italiano, Sparse dynamic programming, Journal of the ACM 39-3, 519--567, 1992.
An overview of the Italian National Project on "Algorithms.. - Ausiello, d'Amore (Correct)
.... Several efficient sequential and parallel algorithms have been obtained for the construction of such data structures [277, 279, 280, 278, 282, 281] New algorithmic techniques for dynamic programming problems, with applications to sequence alignments in molecular biology, have been described in [208, 210, 209, 214, 215, 276]. Parallel algorithms for many of the above problems have been developed in [35, 36, 33, 28, 25, 42, 32, 38, 37, 40, 27, 34, 30, 31, 26, 41, 29] 3.3 Traces Traces theory studies the subsets of free partially commutative monoids (trace languages) This theory has been introduced in order to ....
D. Eppstein, Z. Galil, R. Giancarlo, and G. F. Italiano. Sparse dynamic programming. In Proc. 1st ACM-SIAM Sympos. Discrete Algorithms, pages 513--522, 1990.
Serial Computations of Levenshtein Distances - Hirschberg (1997) (3 citations) (Correct)
....[1977] Apostolico [1986] improves its worst case performance. The notion of flat trees is from van Emde Boas [1975] they are improved in Johnson [1982] Modifications to the Hunt Szymanski algorithm are discussed in Hsu and Du [1984a] but see Apostolico [1987] Apostolico and Guerra [1987] and Eppstein, Galil, Giancarlo, and Italiano [1990]. Other algorithms are discussed in Chin and Poon [1990] and Rick [1995] The O(nD) time algorithm is due to Nakatsu, Kambayashi, and Yajima [1982] The code in Figure 4.7 is from their paper, with changes in the variable names. The linear space version of Nakatsu s algorithm is shown in Kumar and ....
Eppstein, D., Z. Galil, R. Giancarlo, and G. Italiano [1990]. "Sparse dynamic programming," Proc. Symp. on Discrete Algorithms, San Francisco CA, 513-522.
Finding the k Smallest Spanning Trees - Eppstein (1992) Self-citation (Eppstein) (Correct)
....O(log log m) each. A deletion can be charged to its corresponding insertion, so processing each point requires a constant amortized number of data structure operations. Therefore the whole operation takes time O(n log log m) # This algorithm is essentially identical to one used by Eppstein et al. [11] to compute RNA secondary structure predictions; they also used a more complicated version of the algorithm as part of a method of computing optimal sequence alignments. Our algorithm should also be compared with that of Chew and Fortune [9] which computes the orthogonal Voronoi diagram of a set ....
D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano, Sparse Dynamic Programming, 1st ACM-SIAM Symp. Discrete Algorithms, San Francisco, 1990, 513--522.
Global Pairwise Sequence Alignments With Multiple Scoring - Matrices Changjin Hong (Correct)
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D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano., "Sparse dynamic programming," 1st ACM-SIAM Symp. Discrete Algorithms, San Francisco, 513-522, 1990
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