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We consider the problem of discovering overlapping communities in networks which we model as generalizations of Graph Packing problems with overlap. We seek a collection $\mathcal{S}' \subseteq \mathcal{S}$ consisting of at least $k$ sets…
The notion of $\mathcal{H}$-treewidth, where $\mathcal{H}$ is a hereditary graph class, was recently introduced as a generalization of the treewidth of an undirected graph. Roughly speaking, a graph of $\mathcal{H}$-treewidth at most $k$…
A widely studied problem in communication networks is that of finding the maximum number of communication requests that can be scheduled concurrently, subject to node and/or link capacity constraints. In this paper, we consider the problem…
A new search method for large polarization kernels is proposed. The algorithm produces a kernel with given partial distances by employing depth-first search combined with some methods which reduce the search space. Using the proposed…
For a family of graphs $\cal F$, the $\mathcal{F}$-Contraction problem takes as an input a graph $G$ and an integer $k$, and the goal is to decide if there exists $S \subseteq E(G)$ of size at most $k$ such that $G/S$ belongs to $\cal F$.…
A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…
We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the currently best algorithms for the binary case. The size of an…
In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
An $\alpha$-approximate polynomial Turing kernelization is a polynomial-time algorithm that computes an $(\alpha c)$-approximate solution for a parameterized optimization problem when given access to an oracle that can compute…
In this paper we present novel algorithmic techniques with a O(H(N)+N/H(N)) time complexity for performing several types of queries and updates on general rooted trees, binary search trees and lists of size N. For rooted trees we introduce…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
The Steiner Tree problem is a classical problem in combinatorial optimization: the goal is to connect a set $T$ of terminals in a graph $G$ by a tree of minimum size. Karpinski and Zelikovsky (1996) studied the $\delta$-dense version of…
The accuracy and complexity of machine learning algorithms based on kernel optimization are limited by the set of kernels over which they are able to optimize. An ideal set of kernels should: admit a linear parameterization (for…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
In the $k$-Leaf Out-Branching and $k$-Internal Out-Branching problems we are given a directed graph $D$ with a designated root $r$ and a nonnegative integer $k$. The question is to determine the existence of an outbranching rooted at $r$…
Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…
We give an algorithm that for an input n-vertex graph G and integer k>0, in time 2^[O(k)]n either outputs that the treewidth of G is larger than k, or gives a tree decomposition of G of width at most 5k+4. This is the first algorithm…