Related papers: Maximizing Phylogenetic Diversity under Ecological…
Minimum $k$-Section denotes the NP-hard problem to partition the vertex set of a graph into $k$ sets of sizes as equal as possible while minimizing the cut width, which is the number of edges between these sets. When $k$ is an input…
Computing bounded depth decompositions is a bottleneck in many applications of the treedepth parameter. The fastest known algorithm, which is due to Reidl, Rossmanith, S\'{a}nchez Villaamil, and Sikdar [ICALP 2014], runs in…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
A detailed analysis of three species-rich ecosystem food webs has shown that they display scale-free distributions of connections. Such graphs of interaction are in fact shared by a number of biological and technological networks, which…
We investigate the computation of minimum-cost spanning trees satisfying prescribed vertex degree constraints: Given a graph $G$ and a constraint function $D$, we ask for a (minimum-cost) spanning tree $T$ such that for each vertex $v$, $T$…
We show that some natural problems that are XNLP-hard (which implies W[t]-hardness for all t) when parameterized by pathwidth or treewidth, become FPT when parameterized by stable gonality, a novel graph parameter based on optimal maps from…
The structure of ecological networks, in particular food webs, determines their ability to evolve further, i.e. evolvability. The knowledge about how food web evolvability is determined by the structures of diverse ecological networks can…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…
Characterization of joint probability distribution for large networks of random variables remains a challenging task in data science. Probabilistic graph approximation with simple topologies has practically been resorted to; typically the…
The Survivable Network Design problem (SNDP) is a well-studied problem, motivated by the design of networks that are robust to faults under the assumption that any subset of edges up to a specific number can fail. We consider non-uniform…
We study two variants of \textsc{Maximum Cut}, which we call \textsc{Connected Maximum Cut} and \textsc{Maximum Minimal Cut}, in this paper. In these problems, given an unweighted graph, the goal is to compute a maximum cut satisfying some…
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…
Given a graph $G$ and a digraph $D$ whose vertices are the edges of $G$, we investigate the problem of finding a spanning tree of $G$ that satisfies the constraints imposed by $D$. The restrictions to add an edge in the tree depend on its…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Vertex integrity is a graph parameter that measures the connectivity of a graph. Informally, its meaning is that a graph has small vertex integrity if it has a small separator whose removal disconnects the graph into connected components…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
A stable or locally-optimal cut of a graph is a cut whose weight cannot be increased by changing the side of a single vertex. In this paper we study Minimum Stable Cut, the problem of finding a stable cut of minimum weight. Since this…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…