Related papers: Maximizing Phylogenetic Diversity under Ecological…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
We study the problem of maximizing the number of spanning trees in a connected graph by adding at most $k$ edges from a given candidate edge set. We give both algorithmic and hardness results for this problem: - We give a greedy algorithm…
Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
In the Euclidean Bottleneck Steiner Tree problem, the input consists of a set of $n$ points in $\mathbb{R}^2$ called terminals and a parameter $k$, and the goal is to compute a Steiner tree that spans all the terminals and contains at most…
The Minimum Size Tree Decomposition (MSTD) and Minimum Size Path Decomposition (MSPD) problems ask for a given n-vertex graph G and integer k, what is the minimum number of bags of a tree decomposition (respectively, path decomposition) of…
Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of species), it is possible to determine in polynomial time whether there exists a level-1…
We study the parameterized complexity of separating a small set of vertices from a graph by a small vertex-separator. That is, given a graph $G$ and integers $k$, $t$, the task is to find a vertex set $X$ with $|X| \le k$ and $|N(X)| \le…
We study the Steiner Tree problem on the intersection graph of most natural families of geometric objects, e.g., disks, squares, polygons, etc. Given a set of $n$ objects in the plane and a subset $T$ of $t$ terminal objects, the task is to…
We report the results of carrying out a large number of simulations on a coevolutionary model of multispecies communities. A wide range of parameter values were investigated which allowed a rather complete picture of the change in behaviour…
The problem of $\tau$-synthesis consists in deciding whether a given directed labeled graph $A$ is isomorphic to the reachability graph of a Boolean Petri net $N$ of type $\tau$. In case of a positive decision, $N$ should be constructed.…
In the Dominated Cluster Deletion problem, we are given an undirected graph $G$ and integers $k$ and $d$ and the question is to decide whether there exists a set of at most $k$ vertices whose removal results in a graph in which each…
The performance of distributed and data-centric applications often critically depends on the interconnecting network. Applications are hence modeled as virtual networks, also accounting for resource demands on links. At the heart of…
The stability of ecosystems as well as the relation between topology and dynamics on multilayer networks are important questions that are usually discussed in separate communities. Here, we combine these two topics by investigating the…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
We present the first fixed-parameter tractable (FPT) algorithms for exact computation of generalized hypertree width (ghw) and fractional hypertree width (fhw). Our algorithms are parameterized by the target width, the rank, and the maximum…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
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…
We consider the k-outconnected directed Steiner tree problem (k-DST). Given a directed edge-weighted graph $G=(V,E,w)$, where $V=\{r\}\cup S \cup T$, and an integer $k$, the goal is to find a minimum cost subgraph of $G$ in which there are…
For a given set $\mathcal{L}$ of species and a set $\mathcal{T}$ of triplets on $\mathcal{L}$, one wants to construct a phylogenetic network which is consistent with $\mathcal{T}$, i.e which represents all triplets of $\mathcal{T}$. The…