Related papers: Monadic Datalog Containment on Trees
This study examines the time complexities of the unbalanced optimal transport problems from an algorithmic perspective for the first time. We reveal which problems in unbalanced optimal transport can/cannot be solved efficiently.…
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.…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…
The finite satisfiability problem of monadic second order logic is decidable only on classes of structures of bounded tree-width by the classic result of Seese (1991). We prove the following problem is decidable: Input: (i) A monadic second…
The finite satisfiability problem for the two-variable fragment of first-order logic interpreted over trees was recently shown to be ExpSpace-complete. We consider two extensions of this logic. We show that adding either additional binary…
A data tree is a finite tree whose every node carries a label from a finite alphabet and a datum from some infinite domain. We introduce a new model of automata over unranked data trees with a decidable emptiness problem. It is essentially…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
We consider the satisfiability problem for the two-variable fragment of the first-order logic extended with modulo counting quantifiers and interpreted over finite words or trees. We prove a small-model property of this logic, which gives a…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
We combine two methods for the lossless compression of unlabeled graphs - entropy compressing adjacency lists and computing canonical names for vertices - and solve an ensuing novel optimisation problem: Minimum-Entropy Tree-Extraction…
This paper deals with the facility location problems with balancing on allocation clients to servers. Two bi-objective models are considered, in which one objective is the traditional p-median or p-maxian objective and the second is to…
A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…
Interpreting three-leaf binary trees or {\em rooted triples} as constraints yields an entailment relation, whereby binary trees satisfying some rooted triples must also thus satisfy others, and thence a closure operator, which is known to…
The meander problem is a combinatorial problem which provides a toy model of the compact folding of polymer chains. In this paper we study various questions relating to the enumeration of meander diagrams, using diagrammatical methods. By…
We study the crossing-minimization problem in a layered graph drawing of planar-embedded rooted trees whose leaves have a given total order on the first layer, which adheres to the embedding of each individual tree. The task is then to…
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 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…
We prove complex contraction for zero-free regions of counting weighted set cover problem in which an element can appear in an unbounded number of sets, thus obtaining fully polynomial-time approximation schemes(FPTAS) via Barvinok's…