Related papers: Monadic Datalog Containment on Trees Using the Des…

We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…

Motivated by the problem of enumerating all tree decompositions of a graph, we consider in this article the problem of listing all the minimal chordal completions of a graph. In \cite{carmeli2020} (\textsc{Pods 2017}) Carmeli \emph{et al.}…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

In this paper, we define and study the new problem Simultaneous PQ-Ordering. Its input consists of a set of PQ-trees, which represent sets of circular orders of their leaves, together with a set of child-parent relations between these…

A tree decomposition of a graph facilitates computations by grouping vertices into bags that are interconnected in an acyclic structure, hence their importance in a plethora of problems such as query evaluation over databases and inference…

Bounded treewidth and Monadic Second Order (MSO) logic have proved to be key concepts in establishing fixed-parameter tractability results. Indeed, by Courcelle's Theorem we know: Any property of finite structures, which is expressible by…

In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…

One of Courcelle's celebrated results states that if C is a class of graphs of bounded tree-width, then model-checking for monadic second order logic is fixed-parameter tractable on C by linear time parameterised algorithms. An immediate…

The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively…

We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for…

A grammar-compressed ranked tree is represented with a linear space overhead so that a single traversal step, i.e., the move to the parent or the i-th child, can be carried out in constant time. Moreover, we extend our data structure such…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

We continue the study of graph classes in which the treewidth can only be large due to the presence of a large clique, and, more specifically, of graph classes with bounded tree-independence number. In [Dallard, Milani\v{c}, and…

We revisit tree compression with top trees (Bille et al, ICALP'13) and present several improvements to the compressor and its analysis. By significantly reducing the amount of information stored and guiding the compression step using a…

Reverse search is a convenient method for enumerating structured objects, that can be used both to address theoretical issues and to solve data mining problems. This method has already been successfully developed to handle unordered trees.…

Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

We study the guarded negation fragment of transitive closure logic (GNTC). We show that the satisfiability problem for GNTC is 2ExpTime-complete, by establishing the following reductions: (i) a polynomial-time reduction from the…

The last in-tree recognition problem asks whether a given spanning tree can be derived by connecting each vertex with its rightmost left neighbor of some search ordering. In this study, we demonstrate that the last-in-tree recognition…

The problem of determining whether a graph $G$ contains another graph $H$ as a minor, referred to as the minor containment problem, is a fundamental problem in the field of graph algorithms. While it is NP-complete when $G$ and $H$ are…