Decomposition algorithms for the tree edit distance problem

AbstractWe study the behavior of dynamic programming methods for the tree edit distance problem, such as [P. Klein, Computing the edit-distance between unrooted ordered trees, in: Proceedings of 6th European Symposium on Algorithms, 1998, p. 91–102; K. Zhang, D. Shasha, SIAM J. Comput. 18 (6) (1989) 1245–1262]. We show that those two algorithms may be described as decomposition strategies. We introduce the general framework of cover strategies, and we provide an exact characterization of the complexity of cover strategies. This analysis allows us to define a new tree edit distance algorithm, that is optimal for cover strategies

Edit Distance for Pushdown Automata

The edit distance between two words $w_1, w_2$ is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform $w_1$ to $w_2$. The edit distance generalizes to languages $\mathcal{L}_1, \mathcal{L}_2$, where the edit distance from $\mathcal{L}_1$ to $\mathcal{L}_2$ is the minimal number $k$ such that for every word from $\mathcal{L}_1$ there exists a word in $\mathcal{L}_2$ with edit distance at most $k$. We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1)~deciding whether, for a given threshold $k$, the edit distance from a pushdown automaton to a finite automaton is at most $k$, and (2)~deciding whether the edit distance from a pushdown automaton to a finite automaton is finite.Comment: An extended version of a paper accepted to ICALP 2015 with the same title. The paper has been accepted to the LMCS journa

Interactive visualisation and exploration of biological data

International audienceno abstrac

Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots

We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of structures and gives rises to a general parameterized algorithm, where the exponential part of the complexity depends on the family of structures. For each of the previously studied families, our algorithm has the same complexity as the specific algorithm that had been given before.Comment: (2012