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In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
In this paper, we study the problem of finding a minimum weight spanning tree that contains each vertex in a given subset $V_{\rm NT}$ of vertices as an internal vertex. This problem, called Minimum Weight Non-Terminal Spanning Tree,…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
We develop a framework for applying treewidth-based dynamic programming on graphs with "hybrid structure", i.e., with parts that may not have small treewidth but instead possess other structural properties. Informally, this is achieved by…
We study the robustness verification problem for tree-based models, including decision trees, random forests (RFs) and gradient boosted decision trees (GBDTs). Formal robustness verification of decision tree ensembles involves finding the…
We introduce the graph theoretical parameter of edge treewidth. This parameter occurs in a natural way as the tree-like analogue of cutwidth or, alternatively, as an edge-analogue of treewidth. We study the combinatorial properties of…
Phylogenetic networks are useful in representing the evolutionary history of taxa. In certain scenarios, one requires a way to compare different networks. In practice, this can be rather difficult, except within specific classes of…
In many systems consisting of interacting subsystems, the complex interactions between elements can be represented using multilayer networks. However percolation, key to understanding connectivity and robustness, is not trivially…
We introduce the problem of finding a spanning tree along with a partition of the tree edges into fewest number of feasible sets, where constraints on the edges define feasibility. The motivation comes from wireless networking, where we…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…
The strong thin tree conjecture states that every $k$-edge-connected graph $G$ contains an $O(1/k)$-thin spanning tree, meaning a spanning tree which contains at most an $O(1/k)$ fraction of the edges across each cut in $G$. This conjecture…
Given a collection $\tau$ of subsets of a finite set $X$, we say that $\tau$ is {\em phylogenetically flexible} if, for any collection $R$ of rooted phylogenetic trees whose leaf sets comprise the collection $\tau$, $R$ is compatible (i.e.…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
This paper addresses a graph optimization problem, called the Witness Tree problem, which seeks a spanning tree of a graph minimizing a certain non-linear objective function. This problem is of interest because it plays a crucial role in…
Designing well-connected graphs is a fundamental problem that frequently arises in various contexts across science and engineering. The weighted number of spanning trees, as a connectivity measure, emerges in numerous problems and plays a…
This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
Rooted binary phylogenetic networks are extensions of rooted binary trees, adding reticulation nodes that are designed to represent evolutionary processes that involve hybridization events. Enumerative combinatorics studies have counted…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…