Related papers: Tree decomposition of Reeb graphs, parametrized co…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
We obtain structure theorems for graphs excluding a fan (a path with a universal vertex) or a dipole ($K_{2,k}$) as a topological minor. The corresponding decompositions can be computed in FPT linear time. This is motivated by the study of…
The Tree Decomposition Conjecture by Bar\'at and Thomassen states that for every tree $T$ there exists a natural number $k(T)$ such that the following holds: If $G$ is a $k(T)$-edge-connected simple graph with size divisible by the size of…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
We obtain first order linear partial differential equations which are satisfied by exponential generating functions of two variables for the number of connected bipartite graphs with given Betti number. By solving these equations…
We study the homology of an explicit finite-index subgroup of the automorphism group of a partially commutative group, in the case when its defining graph is a tree. More concretely, we give a lower bound on the first Betti number of this…
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,…
We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…
Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic…
Let $X$ be a simplicial complex with a piecewise linear function $f:X\to\mathbb{R}$. The Reeb graph $Reeb(f,X)$ is the quotient of $X$, where we collapse each connected component of $f^{-1}(t)$ to a single point. Let the nodes of…
We show an algorithm that, given an $n$-vertex graph $G$ and a parameter $k$, in time $2^{O(k \log k)} n^{O(1)}$ finds a tree decomposition of $G$ with the following properties: * every adhesion of the tree decomposition is of size at most…
We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
Treewidth is arguably the most important structural graph parameter leading to algorithmically beneficial graph decompositions. Triggered by a strongly growing interest in temporal networks (graphs where edge sets change over time), we…
The Reeb graph is a construction which originated in Morse theory to study a real valued function defined on a topological space. More recently, it has been used in various applications to study noisy data which creates a desire to define a…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
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…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
We generalize the structure theorem of Robertson and Seymour for graphs excluding a fixed graph $H$ as a minor to graphs excluding $H$ as a topological subgraph. We prove that for a fixed $H$, every graph excluding $H$ as a topological…
We study a well known noisy model of the graph isomorphism problem. In this model, the goal is to perfectly recover the vertex correspondence between two edge-correlated Erd\H{o}s-R\'{e}nyi random graphs, with an initial seed set of…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…