Related papers: Parameterized Algorithms for Diversity of Networks…
Finding a few solutions for a given problem that are diverse, as opposed to finding a single best solution to solve the problem, has recently become a notable topic in theoretical computer science. Recently, Baste, Fellows, Jaffke,…
We present a data structure that we call a Dynamic Representative Set. In its most basic form, it is given two parameters $0< k < n$ and allows us to maintain a representation of a family $\mathcal{F}$ of subsets of $\{1,\ldots,n\}$. It…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…
The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet which tries to construct an optimal rooted phylogenetic…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
The question what determines the structure of natural food webs has been listed among the nine most important unanswered questions in ecology. It arises naturally from many problems related to ecosystem stability and resilience. The…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
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…
Matroids, particularly linear ones, have been a powerful tool in parameterized complexity for algorithms and kernelization. They have sped up or replaced dynamic programming. Delta-matroids generalize matroids by encapsulating structures…
A principle of evolutionary adaptation is applied to the Lotka--Volterra models, in particular to the food webs. We present a relatively simple computational algorithm of optimization with respect to a given criterion. This algorithm boils…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Deletion problems are those where given a graph $G$ and a graph property $\pi$, the goal is to find a subset of edges such that after its removal the graph $G$ will satisfy the property $\pi$. Typically, we want to minimize the number of…
Mathematical modeling is a standard approach to solve many real-world problems and {\em diversity} of solutions is an important issue, emerging in applying solutions obtained from mathematical models to real-world problems. Many studies…
The fundamental caching problem in networks asks to find an allocation of contents to a network of caches with the aim of maximizing the cache hit rate. Despite the problem's importance to a variety of research areas -- including not only…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
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…
For a given graph $G$, a depth-first search (DFS) tree $T$ of $G$ is an $r$-rooted spanning tree such that every edge of $G$ is either an edge of $T$ or is between a \textit{descendant} and an \textit{ancestor} in $T$. A graph $G$ together…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…