1,209 research outputs found
Compressed Subsequence Matching and Packed Tree Coloring
We present a new algorithm for subsequence matching in grammar compressed
strings. Given a grammar of size compressing a string of size and a
pattern string of size over an alphabet of size , our algorithm
uses space and or time. Here
is the word size and is the number of occurrences of the pattern. Our
algorithm uses less space than previous algorithms and is also faster for
occurrences. The algorithm uses a new data structure
that allows us to efficiently find the next occurrence of a given character
after a given position in a compressed string. This data structure in turn is
based on a new data structure for the tree color problem, where the node colors
are packed in bit strings.Comment: To appear at CPM '1
Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package
Dynamic time warping is a popular technique for comparing time series, providing both a distance measure that is insensitive to local compression and stretches and the warping which optimally deforms one of the two input series onto the other. A variety of algorithms and constraints have been discussed in the literature. The dtw package provides an unification of them; it allows R users to compute time series alignments mixing freely a variety of continuity constraints, restriction windows, endpoints, local distance definitions, and so on. The package also provides functions for visualizing alignments and constraints using several classic diagram types.
Multiple serial episode matching
12In a previous paper we generalized the Knuth-Morris-Pratt (KMP) pattern matching algorithm and defined a non-conventional kind of RAM, the MP--RAMs (RAMS equipped with extra operations), and designed an on-line algorithm for solving the serial episode matching problem on MP--RAMs when there is only one single episode. We here give two extensions of this algorithm to the case when we search for several patterns simultaneously and compare them. More preciseley, given strings (a text of length and patterns ) and a natural number , the {\em multiple serial episode matching problem} consists in finding the number of size windows of text which contain patterns as subsequences, i.e. for each , if , the letters occur in the window, in the same order as in , but not necessarily consecutively (they may be interleaved with other letters).} The main contribution is an algorithm solving this problem on-line in time
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