Related papers: Maximizing Phylogenetic Diversity under Ecological…
In a large-scale network, we want to choose some influential nodes to make a profit by paying some cost within a limited budget so that we do not have to spend more budget on some nodes adjacent to the chosen nodes; our problem is the…
Modeling of real-world systems with Petri nets allows to benefit from their generic concepts of parallelism, synchronisation and conflict, and obtain a concise yet expressive system representation. Algorithms for synthesis of a net from a…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
Let G = (V, E) be a directed and weighted graph with vertex set V of size n and edge set E of size m, such that each edge (u, v) \in E has a real-valued weight w(u, c). An arborescence in G is a subgraph T = (V, E') such that for a vertex u…
Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food…
We consider a the minimum k-way cut problem for unweighted graphs with a size bound s on the number of cut edges allowed. Thus we seek to remove as few edges as possible so as to split a graph into k components, or report that this requires…
We consider a natural variant of the well-known Feedback Vertex Set problem, namely the problem of deleting a small subset of vertices or edges to a full binary tree. This version of the problem is motivated by real-world scenarios that are…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
In $d$-Scattered Set we are given an (edge-weighted) graph and are asked to select at least $k$ vertices, so that the distance between any pair is at least $d$, thus generalizing Independent Set. We provide upper and lower bounds on the…
The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
We revisit two well-studied problems, Bounded Degree Vertex Deletion and Defective Coloring, where the input is a graph $G$ and a target degree $\Delta$ and we are asked either to edit or partition the graph so that the maximum degree…
Given a set of obstacles and two points, is there a path between the two points that does not cross more than $k$ different obstacles? This is a fundamental problem that has undergone a tremendous amount of work. It is known to be NP-hard,…
In this paper, we initiate a systematic study of the parametrised complexity in the field of Dependence Logics which finds its origin in the Dependence Logic of V\"a\"an\"anen from 2007. We study a propositional variant of this logic (PDL)…
Steiner Tree Packing (STP) is a notoriously hard problem in classical complexity theory, which is of practical relevance to VLSI circuit design. Previous research has approached this problem by providing heuristic or approximate algorithms.…
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…
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,…
We consider structural parameterizations of the fundamental Dominating Set problem and its variants in the parameter ecology program. We give improved FPT algorithms and lower bounds under well-known conjectures for dominating set in graphs…
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…