Related papers: Ordered Leaf Attachment (OLA) Vectors can Identify…
An L(2,1)-labeling of a graph $G$ is an assignment $f$ from the vertex set $V(G)$ to the set of nonnegative integers such that $|f(x)-f(y)|\ge 2$ if $x$ and $y$ are adjacent and $|f(x)-f(y)|\ge 1$ if $x$ and $y$ are at distance 2, for all…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…
We present an MPI-parallel algorithm for the in-situ visualization of computational data that is built around a distributed linear forest-of-octrees data structure. Such octrees are frequently used in element-based numerical simulations;…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
Ordered leaf attachment, Phylo2Vec, and HOP are three recently introduced vector representations for rooted phylogenetic trees where the representation is determined by an ordering of the underlying leaf set X. Comparing the vectors of two…
We consider the problem of augmenting an $n$-vertex tree with one shortcut in order to minimize the diameter of the resulting graph. The tree is embedded in an unknown space and we have access to an oracle that, when queried on a pair of…
Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene…
In this paper, we propose the Ordered Median Tree Location Problem (OMT). The OMT is a single-allocation facility location problem where p facilities must be placed on a network connected by a non-directed tree. The objective is to minimize…
The aim of rendezvous in a graph is meeting of two mobile agents at some node of an unknown anonymous connected graph. In this paper, we focus on rendezvous in trees, and, analogously to the efforts that have been made for solving the…
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 consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Labeling schemes seek to assign a short label to each node in a network, so that a function on two nodes can be computed by examining their labels alone. For the particular case of trees, optimal bounds (up to low order terms) were recently…
We present a novel factor analysis method that can be applied to the discovery of common factors shared among trajectories in multivariate time series data. These factors satisfy a precedence-ordering property: certain factors are recruited…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
The Rooted Maximum Leaf Outbranching problem consists in finding a spanning directed tree rooted at some prescribed vertex of a digraph with the maximum number of leaves. Its parameterized version asks if there exists such a tree with at…
This work studies the task of device coordination in wireless networks for over-the-air federated learning (OTA-FL). For conventional metrics of aggregation error, the task is shown to describe the zero-forcing (ZF) and minimum mean squared…
We examine the problem of learning sequential tasks from a single visual demonstration. A key challenge arises when demonstrations are temporally misaligned due to variations in timing, differences in embodiment, or inconsistencies in…
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels…