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In the length-constrained minimum spanning tree (MST) problem, we are given an $n$-node edge-weighted graph $G$ and a length constraint $h \geq 1$. Our goal is to find a spanning tree of $G$ whose diameter is at most $h$ with minimum…
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…
Stagnation detection has been proposed as a mechanism for randomized search heuristics to escape from local optima by automatically increasing the size of the neighborhood to find the so-called gap size, i.e., the distance to the next…
Tree rearrangements such as Nearest Neighbor Interchange (NNI) and Subtree Prune and Regraft (SPR) are commonly used to explore phylogenetic treespace. Computing distances based on them, however, is often intractable, so the efficiently…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
The global structure of the minimal spanning tree (MST) is expected to be universal for a large class of underlying random discrete structures. However, very little is known about the intrinsic geometry of MSTs of most standard models, and…
The minimum spanning tree (MST) construction is a classical problem in Distributed Computing for creating a globally minimized structure distributedly. Self-stabilization is versatile technique for forward recovery that permits to handle…
In this paper we define a novel edit distance for merge trees, which we argue to be suitable for a good range of applications. Relying also on some technical results contained in other works, we investigate its stability properties, which…
In this paper, we present a novel heuristic algorithm for the stable but NP-complete deformation-based edit distance on merge trees. Our key contribution is the introduction of a user-controlled look-ahead parameter that allows to trade off…
We consider the problem of planning collision-free trajectories on distance fields. Our key observation is that querying a distance field at one configuration reveals a region of safe space whose radius is given by the distance value,…
Stochastic approximation algorithm is a useful technique which has been exploited successfully in probability theory and statistics for a long time. The step sizes used in stochastic approximation are generally taken to be deterministic and…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
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,…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
A recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…
Merge trees are a common topological descriptor for data with a hierarchical component, such as terrains and scalar fields. The interleaving distance, in turn, is a common distance for comparing merge trees. However, the interleaving…
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…
Sparse residual tree (SRT) is an adaptive exploration method for multivariate scattered data approximation. It leads to sparse and stable approximations in areas where the data is sufficient or redundant, and points out the possible local…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…