Related papers: Parameterized Algorithms for Diversity of Networks…
This paper categorizes the parameterized complexity of the algorithmic problems Perfect Phylogeny and Triangulating Colored Graphs when parameterized by the number of genes and colors, respectively. We show that they are complete for the…
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…
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…
Parameterized analysis provides powerful mechanisms for obtaining fine-grained insights into different types of algorithms. In this work, we combine this field with evolutionary algorithms and provide parameterized complexity analysis of…
We show that the Minimal Length-Bounded L-But problem can be computed in linear time with respect to L and the tree-width of the input graph as parameters. In this problem the task is to find a set of edges of a graph such that after…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks…
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 introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
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…
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…
We study computational complexity of the class of distance-constrained graph labeling problems from the fixed parameter tractability point of view. The parameters studied are neighborhood diversity and clique width. We rephrase the distance…
We study the well-established problem of finding an optimal routing of unsplittable flows in a graph. While by now there is an extensive body of work targeting the problem on graph classes such as paths and trees, we aim at using the…
Given a simple connected undirected graph G = (V, E), a set X \subseteq V(G), and integers k and p, STEINER SUBGRAPH EXTENSION problem asks if there exists a set S \supseteq X with at most k vertices such that G[S] is p-edge-connected. This…
In the problem Fault-Tolerant Path (FTP), we are given an edge-weighted directed graph G = (V, E), a subset U \subseteq E of vulnerable edges, two vertices s, t \in V, and integers k and \ell. The task is to decide whether there exists a…
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…
The C-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired network class C. This problem arises, for example, when visualising evolutionary data, as popular methods…
The online dominating set problem is an online variant of the minimum dominating set problem, which is one of the most important NP-hard problems on graphs. This problem is defined as follows: Given an undirected graph $G = (V, E)$, in…
Ecological networks such as plant-pollinator systems and food webs vary in space and time. This variability includes fluctuations in global network properties such as total number and intensity of interactions but also in the local…