Related papers: Maximizing Phylogenetic Diversity under Ecological…
Treewidth is a useful tool in designing graph algorithms. Although many NP-hard graph problems can be solved in linear time when the input graphs have small treewidth, there are problems which remain hard on graphs of bounded treewidth. In…
A resolving set $S$ of a graph $G$ is a subset of its vertices such that no two vertices of $G$ have the same distance vector to $S$. The Metric Dimension problem asks for a resolving set of minimum size, and in its decision form, a…
We consider the Shallow-Light Steiner Network problem from a fixed-parameter perspective. Given a graph $G$, a distance bound $L$, and $p$ pairs of vertices $(s_1,t_1),\cdots,(s_p,t_p)$, the objective is to find a minimum-cost subgraph $G'$…
We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge appears in the network with its associated…
Given a directed graph $G$ and a list $(s_1,t_1),\dots,(s_d,t_d)$ of terminal pairs, the Directed Steiner Network problem asks for a minimum-cost subgraph of $G$ that contains a directed $s_i\to t_i$ path for every $1\le i \le k$. The…
A set $D$ of vertices of a graph is a \emph{defensive alliance} if, for each element of $D$, the majority of its neighbours are in $D$. We consider the notion of local minimality in this paper. We are interested in finding a locally minimal…
We continue and extend previous work on the parameterized complexity analysis of the NP-hard Stable Roommates with Ties and Incomplete Lists problem, thereby strengthening earlier results both on the side of parameterized hardness as well…
We study the NP-hard Shortest Path Most Vital Edges problem arising in the context of analyzing network robustness. For an undirected graph with positive integer edge lengths and two designated vertices $s$ and $t$, the goal is to delete as…
In this paper we study a maximization version of the classical Edge Dominating Set (EDS) problem, namely, the Upper EDS problem, in the realm of Parameterized Complexity. In this problem, given an undirected graph $G$, a positive integer…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
A graph is $d$-orientable if its edges can be oriented so that the maximum in-degree of the resulting digraph is at most $d$. $d$-orientability is a well-studied concept with close connections to fundamental graph-theoretic notions and…
The Minimum Branch Vertices Spanning Tree problem aims to find a spanning tree $T$ in a given graph $G$ with the fewest branch vertices, defined as vertices with a degree three or more in $T$. This problem, known to be NP-hard, has…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
A secure set $S$ in a graph is defined as a set of vertices such that for any $X\subseteq S$ the majority of vertices in the neighborhood of $X$ belongs to $S$. It is known that deciding whether a set $S$ is secure in a graph is…
Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…
Real food web data available in the literature presents us with the relations between various species, sizes of these species, metabolic types of the species and other useful information, which allows us to define parameters for the…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…
Graph Burning asks, given a graph $G = (V,E)$ and an integer $k$, whether there exists $(b_{0},\dots,b_{k-1}) \in V^{k}$ such that every vertex in $G$ has distance at most $i$ from some $b_{i}$. This problem is known to be NP-complete even…