Related papers: A 2-approximation algorithm for the softwired pars…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…
Decision-theoretic troubleshooting is one of the areas to which Bayesian networks can be applied. Given a probabilistic model of a malfunctioning man-made device, the task is to construct a repair strategy with minimal expected cost. The…
Given two sets of points in the plane, $P$ of $n$ terminals and $S$ of $m$ Steiner points, a Steiner tree of $P$ is a tree spanning all points of $P$ and some (or none or all) points of $S$. A Steiner tree with length of longest edge…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…
Many combinatorial optimization problems can be formulated as the search for a subgraph that satisfies certain properties and minimizes the total weight. We assume here that the vertices correspond to points in a metric space and can take…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
This work studies the combinatorial optimization problem of finding an optimal core tensor shape, also called multilinear rank, for a size-constrained Tucker decomposition. We give an algorithm with provable approximation guarantees for its…
Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods.…
There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the…
Finding schedules for pairwise meetings between the members of a complex social group without creating interpersonal conflict is challenging, especially when different relationships have different needs. We formally define and study the…
We study the following problem that is motivated by demand-aware network design: Given a tree~$G$, the task is to find a binary tree~$H$ on the same vertex set. The objective is to minimize the sum of distances in~$H$ between vertex pairs…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
Graph connectivity and network design problems are among the most fundamental problems in combinatorial optimization. The minimum spanning tree problem, the two edge-connected spanning subgraph problem (2-ECSS) and the tree augmentation…
We study a general class of bicriteria network design problems. A generic problem in this class is as follows: Given an undirected graph and two minimization objectives (under different cost functions), with a budget specified on the first,…
This paper focuses on finding a spanning tree of a graph to maximize the number of its internal vertices. We present an approximation algorithm for this problem which can achieve a performance ratio $\frac{4}{3}$ on undirected simple…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…