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The <i>edit distance</i> between two ordered rooted trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. In this article, we present a worst-case <i>O</i>(<i>n</i><sup>3</sup>)-time algorithm for the… (More)

We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast navigational queries directly on the compressed representation.… (More)

The Local Alignment problem is a classical problem with applications in biology. Given two input strings and a scoring function on pairs of letters, one is asked to find the substrings of the two input strings that are most similar under the scoring function. The best algorithms for Local Alignment run in time that is roughly quadratic in the string length.… (More)

We address the extension of the binary search technique from sorted arrays and totally ordered sets to trees and tree-like partially ordered sets. As in the sorted array case, the goal is to minimize the number of queries required to find a target element in the worst case. However, while the optimal strategy for searching an array is straightforward… (More)

Let <i>S</i> be a string of length <i>N</i> compressed into a context-free grammar <i>S</i> of size <i>n</i>. We present two representations of <i>S</i> achieving <i>O</i>(log <i>N</i>) random access time, and either <i>O</i>(<i>n</i> · α<sub><i>k</i></sub>(<i>n</i>)) construction time and space on the pointer machine model, or <i>O</i>(<i>n</i>)… (More)

The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic-programming solution for this problem computes the edit-distance between a pair of strings of total length O(N) in O(N 2) time. To this date, this quadratic upper-bound has never been… (More)

We present new results on Cartesian trees with applications in range minimum queries and bottleneck edge queries. We introduce a cache-oblivious Cartesian tree for solving the range minimum query problem, a Cartesian tree for the bottleneck edge query problem on trees and undirected graphs, and a proof that no Cartesian tree exists for the two-dimensional… (More)

Permutations on strings representing gene clusters on genomes have been studied earlier by Uno and Yagiura (2000), Heber and Stoye (2001), Bergeron et al. (2002), Eres et al. (2003), and Schmidt and Stoye (2004) and the idea of a maximal permutation pattern was introduced by Eres et al. (2003). In this paper, we present a new tool for representation and… (More)

We present a novel approach for computing all maximum consecutive subsums in a sequence of positive integers in near linear time. Solutions for this problem over binary sequences can be used for reporting existence (and possibly one occurrence) of Parikh vectors in a bit string. Recently, several attempts have been tried to build indexes for all Parikh… (More)

Binary jumbled pattern matching asks to preprocess a binary string $$S$$ S in order to answer queries $$(i,j)$$ ( i , j ) which ask for a substring of $$S$$ S that is of length $$i$$ i and has exactly $$j$$ j 1-bits. This problem naturally generalizes to vertex-labeled trees and graphs by replacing “substring” with “connected subgraph”. In this paper, we… (More)