Related papers: Reconstructing semi-directed level-1 networks usin…
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Motivated by questions in social networks, distributed computing and probabilistic combinatorics, the last few years have seen increasing interest in network evolution models where new vertices entering the system need to make decisions…
Motivated by the increasing need to understand the algorithmic foundations of distributed large-scale graph computations, we study a number of fundamental graph problems in a message-passing model for distributed computing where $k \geq 2$…
We study the problem of computing the minimum cut in a weighted distributed message-passing networks (the CONGEST model). Let $\lambda$ be the minimum cut, $n$ be the number of nodes in the network, and $D$ be the network diameter. Our…
This paper introduces the tensor representation of a network, here tensors are the primitive structures of the network. In view of tensor chains, two binary operations on tensor sets are defined: chain addition and reducing. Based on the…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
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…
In this paper, we investigate the computational complexity of subgraph reconfiguration problems in directed graphs. More specifically, we focus on the problem of reconfiguring arborescences in a digraph, where an arborescence is a directed…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
We present an algorithm that, with high probability, generates a random spanning tree from an edge-weighted undirected graph in $\tilde{O}(n^{4/3}m^{1/2}+n^{2})$ time (The $\tilde{O}(\cdot)$ notation hides $\operatorname{polylog}(n)$…
We present randomized algorithms that compute $(1+\epsilon)$-approximate minimum global edge and vertex cuts in weighted directed graphs in $O(\log^4(n) / \epsilon)$ and $O(\log^5(n)/\epsilon)$ single-commodity flows, respectively. With the…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
In this paper we study a family of algorithms, introduced by Chan [SODA 1999] and called LR-algorithms, for drawing ordered rooted binary trees. In particular, we are interested in constructing LR-drawings (that are drawings obtained via…
In this paper we present the first algorithm in the streaming model to characterize completely the biconnectivity properties of undirected networks: articulation points, bridges, and connected and biconnected components. The motivation of…
In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithms, new evidence in absorbed in time…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we obtain two combinatorial results on the number…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
In this work, we introduce an algorithmic approach to generate microvascular networks starting from larger vessels that can be reconstructed without noticeable segmentation errors. Contrary to larger vessels, the reconstruction of…