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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…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
In this paper, some special distance spectral properties of graphs are considered. Concretely, we recursively construct an infinite family of trees with distance eigenvalue $-1$, and determine all $\{C_3,C_4\}$-free connected graphs with…
A communication network can be modeled as a directed connected graph with edge weights that characterize performance metrics such as loss and delay. Network tomography aims to infer these edge weights from their pathwise versions measured…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
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…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
The $\textit{$m$-deck}$ of an $n$-vertex graph is the multiset of unlabeled induced subgraphs with $m$ vertices. Caterpillars are trees in which all nonleaf vertices lie on a single path. We prove for $n\ge48$ that any $n$-vertex…
Tree-decompositions of graphs are of fundamental importance in structural and algorithmic graph theory. The main property of tree-decompositions is the width (the maximum size of a bag minus 1). We show that every graph has a…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
We study the representations of a class of non-commutative polynomial algebras truncated at degree 3, with one additional relation. We determine the irreducible components of their varieties of representations. We do this by showing that…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
The graph reconstruction conjecture asserts that every simple graph on at least three vertices is uniquely determined by its deck of vertex-deleted subgraphs. In this expository article we survey the conjecture and present an…
We address the problem of computing a single linkage dendrogram. A possible approach is to: (i) Form an edge weighted graph $G$ over the data, with edge weights reflecting dissimilarities. (ii) Calculate the MST $T$ of $G$. (iii) Break the…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
We study the problem of learning tree-structured Markov random fields (MRF) on discrete random variables with common support when the observations are corrupted by a $k$-ary symmetric noise channel with unknown probability of error. For…
A three-path-configuration is a graph consisting of three pairwise internally-disjoint paths the union of every two of which is an induced cycle of length at least four. A graph is 3PC-free if no induced subgraph of it is a…
A method for creating a forest of model trees to fit samples of a function defined on images is described in several steps: down-sampling the images, determining a tree's hyperplanes, applying convolutions to the hyperplanes to handle small…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…