Related papers: Finding agreement cherry-reduced subnetworks in le…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We consider a variant of treewidth that we call clique-partitioned treewidth in which each bag is partitioned into cliques. This is motivated by the recent development of FPT-algorithms based on similar parameters for various problems. With…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
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…
Markov Networks are widely used through out computer vision and machine learning. An important subclass are the Associative Markov Networks which are used in a wide variety of applications. For these networks a good approximate minimum cost…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
The minimum degree spanning tree (MDST) problem requires the construction of a spanning tree $T$ for graph $G=(V,E)$ with $n$ vertices, such that the maximum degree $d$ of $T$ is the smallest among all spanning trees of $G$. In this paper,…
It is a critical issue to compute the shortest paths between nodes in networks. Exact algorithms for shortest paths are usually inapplicable for large scale networks due to the high computational complexity. In this paper, we propose a…
We study the min-cost seed selection problem in online social networks, where the goal is to select a set of seed nodes with the minimum total cost such that the expected number of influenced nodes in the network exceeds a predefined…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
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…
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
We propose the first branch-&-price algorithm for the maximum agreement forest problem on unrooted binary trees: given two unrooted X-labelled binary trees we seek to partition X into a minimum number of blocks such that the induced…
We study a maximization problem for geometric network design. Given a set of $n$ compact neighborhoods in $\mathbb{R}^d$, select a point in each neighborhood, so that the longest spanning tree on these points (as vertices) has maximum…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…