Related papers: Solving Tree Containment Problem for Reticulation-…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
We study Clustered Planarity with Linear Saturators, which is the problem of augmenting an $n$-vertex planar graph whose vertices are partitioned into independent sets (called clusters) with paths - one for each cluster - that connect all…
The cable-trench problem is defined as a linear combination of the shortest path and the minimum spanning tree problem. In particular, the goal is to find a spanning tree that simultaneously minimizes its total length and the total path…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
In this paper we consider the problem of connected edge searching of weighted trees. It is shown that there exists a polynomial-time algorithm for finding optimal connected search strategy for bounded degree trees with arbitrary weights on…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
The last in-tree recognition problem asks whether a given spanning tree can be derived by connecting each vertex with its rightmost left neighbor of some search ordering. In this study, we demonstrate that the last-in-tree recognition…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network.…
We consider the problem of finding weights and biases for a two-layer fully connected neural network to fit a given set of data points as well as possible, also known as EmpiricalRiskMinimization. Our main result is that the associated…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
The Steiner tree problem can be stated in terms of finding a connected set of minimal length containing a given set of finitely many points. We show how to formulate it as a mass-minimization problem for $1$-dimensional currents with…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for {\it bicombining tree-child networks}…
In a supercritical branching particle system, the trimmed tree consists of those particles which have descendants at all times. We develop this concept in the superprocess setting. For a class of continuous superprocesses with Feller…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
We study the problem of sampling a uniformly random directed rooted spanning tree, also known as an arborescence, from a possibly weighted directed graph. Classically, this problem has long been known to be polynomial-time solvable; the…
We show that the spanning tree congestion problem is NP-complete even for proper interval graphs of linear clique-width at most 4.