Related papers: Reconstructing Metric Trees from Order Information…
I consider the problem of learning an optimal path graphical model from data and show the problem to be NP-hard for the maximum likelihood and minimum description length approaches and a Bayesian approach. This hardness result holds despite…
The rooted tree is an important data structure, and the subtree size, height, and depth are naturally defined attributes of every node. We consider the problem of the existence of a k-ary tree given a list of attribute sequences. We give…
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…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
The overlap graphs of subtrees in a tree (SOGs) generalise many other graphs classes with set representation characterisations. The complexity of recognising SOGs in open. The complexities of recognising many subclasses of SOGs are known.…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
The analysis of objects living on ultrametric trees, in particular the block-diagonalization of 4-replica matrices $M^{\alpha \beta ; \gamma \delta}$, is shown to be dramatically simplified through the introduction of properly chosen…
We consider the polyhedral properties of two spanning tree problems with additional constraints. In the first problem, it is required to find a tree with a minimum sum of edge weights among all spanning trees with the number of leaves less…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
Computing a minimum-area planar straight-line drawing of a graph is known to be NP-hard for planar graphs, even when restricted to outerplanar graphs. However, the complexity question is open for trees. Only a few hardness results are known…
The Metric Dimension problem asks for a minimum-sized resolving set in a given (unweighted, undirected) graph $G$. Here, a set $S \subseteq V(G)$ is resolving if no two distinct vertices of $G$ have the same distance vector to $S$. The…
Generalized trees, we call them O-trees, are defined as hierarchical partial orders, i.e., such that the elements larger than any one are linearly ordered. Quasi-trees are, roughly speaking, undirected O-trees. For O-trees and quasi-trees,…
We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
In this paper, we investigate the computational complexity of subgraph reconfiguration problems in directed graphs. More specifically, we focus on the problem of reconfiguring arborescences in a digraph, where an arborescence is a directed…
We answer, in the affirmative, the following question proposed by Mike Steel as a $100 challenge: "Is the following problem NP-hard? Given a ternary phylogenetic X-tree T and a collection Q of quartet subtrees on X, is T the only tree that…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…