TY - GEN

T1 - Semi-dynamic compact index for short patterns and succinct van Emde Boas tree

AU - Matsuoka, Yoshiaki

AU - I, Tomohiro

AU - Inenaga, Shunsuke

AU - Bannai, Hideo

AU - Takeda, Masayuki

N1 - Publisher Copyright:
© Springer International Publishing Switzerland 2015.

PY - 2015

Y1 - 2015

N2 - We present a compact semi-dynamic text index which allows us to find short patterns efficiently. For parameters k ≤ q ≤ logσ n − logσ logσ n and alphabet size σ = O(polylog(n)), all occ occurrences of a pattern of length at most q−k+1 can be obtained in O(k×occ +logσ n) time, where n is the length of the text. Adding characters to the end of the text is supported in amortized constant time. Our index requires (n/k) log(n/k) + n log σ + o(n) bits of space, which is compact (i.e., O(n log σ)) when k = Θ(logσ n). As a byproduct, we present a succinct van Emde Boas tree which supports insertion, deletion, predecessor, and successor on a dynamic set of integers over the universe [0,m − 1] in O(log logm) time and requires only m + o(m) bits of space.

AB - We present a compact semi-dynamic text index which allows us to find short patterns efficiently. For parameters k ≤ q ≤ logσ n − logσ logσ n and alphabet size σ = O(polylog(n)), all occ occurrences of a pattern of length at most q−k+1 can be obtained in O(k×occ +logσ n) time, where n is the length of the text. Adding characters to the end of the text is supported in amortized constant time. Our index requires (n/k) log(n/k) + n log σ + o(n) bits of space, which is compact (i.e., O(n log σ)) when k = Θ(logσ n). As a byproduct, we present a succinct van Emde Boas tree which supports insertion, deletion, predecessor, and successor on a dynamic set of integers over the universe [0,m − 1] in O(log logm) time and requires only m + o(m) bits of space.

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U2 - 10.1007/978-3-319-19929-0_30

DO - 10.1007/978-3-319-19929-0_30

M3 - Conference contribution

AN - SCOPUS:84948993636

SN - 9783319199283

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 355

EP - 366

BT - Combinatorial Pattern Matching - 26th Annual Symposium, CPM 2015, Proceedings

A2 - Vaccaro, Ugo

A2 - Porat, Ely

A2 - Cicalese, Ferdinando

PB - Springer Verlag

T2 - 26th Annual Symposium on Combinatorial Pattern Matching, CPM 2015

Y2 - 29 June 2015 through 1 July 2015

ER -