Related papers: Additive Approximation for Near-Perfect Phylogeny …
We present a technique that allows for improving on some relative greedy procedures by well-chosen (non-oblivious) local search algorithms. Relative greedy procedures are a particular type of greedy algorithm that start with a simple,…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
In \cite{siebert2019linear} the authors present a set of integer programs (IPs) for the Steiner tree problem, which can be used for both, the directed and the undirected setting of the problem. Each IP finds an optimal Steiner tree with a…
This paper concerns proving almost tight (super-polynomial) running times, for achieving desired approximation ratios for various problems. To illustrate, the question we study, let us consider the Set-Cover problem with n elements and m…
In this paper, we present new efficiently solvable cases of the Minimum Uncovering Branching problem, an optimization problem with applications in cancer genomics introduced by Hujdurovi\'c, Husi\'c, Milani\v{c}, Rizzi, and Tomescu in 2018.…
We propose a simple and natural approximation algorithm for the problem of finding a 2-edge-connected spanning subgraph of minimum total edge cost in a graph. The algorithm maintains a spanning forest starting with an empty edge set. In…
Given a set $P$ of $n$ points in $\mathbb{R}^2$ and an input line $\gamma$ in $\mathbb{R}^2$, we present an algorithm that runs in optimal $\Theta(n\log n)$ time and $\Theta(n)$ space to solve a restricted version of the $1$-Steiner tree…
In this paper, we consider the Uniform Cost-Distance Steiner Tree Problem in metric spaces, a generalization of the well-known Steiner tree problem. Cost-distance Steiner trees minimize the sum of the total length and the weighted path…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
Label tree-based algorithms are widely used to tackle multi-class and multi-label problems with a large number of labels. We focus on a particular subclass of these algorithms that use probabilistic classifiers in the tree nodes. Examples…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…
We study the NP-hard problem of approximating a Minimum Routing Cost Spanning Tree in the message passing model with limited bandwidth (CONGEST model). In this problem one tries to find a spanning tree of a graph $G$ over $n$ nodes that…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Inferring a decision tree from a given dataset is one of the classic problems in machine learning. This problem consists of buildings, from a labelled dataset, a tree such that each node corresponds to a class and a path between the tree…
In 1996, Bodlaender showed the celebrated result that an optimal tree decomposition of a graph of bounded treewidth can be found in linear time. The algorithm is based on an algorithm of Bodlaender and Kloks that computes an optimal tree…
We study the complexity of finding communication trees with the lowest possible completion time for rooted, irregular gather and scatter collective communication operations in fully connected, $k$-ported communication networks under a…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…