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A class of graph languages is definable in Monadic Second-Order logic (MSO) if and only if it consists of sets of models of MSO formul{\ae}. If, moreover, there is a computable bound on the tree-widths of the graphs in each such set, the…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…
The Gromov-Hausdorff (GH) distance is a natural way to measure distance between two metric spaces. We prove that it is $\mathrm{NP}$-hard to approximate the Gromov-Hausdorff distance better than a factor of $3$ for geodesic metrics on a…
Phylogenetic trees constitute an interesting class of objects for stochastic processes due to the non-standard nature of the space they inhabit. In particular, many statistical applications require the construction of Markov processes on…
We prove decidability of the boundedness problem for monadic least fixed-point recursion based on positive monadic second-order (MSO) formulae over trees. Given an MSO-formula phi(X,x) that is positive in X, it is decidable whether the…
Let $G$ be a connected graph with vertex set $V(G)$, and denote by $d_G(u,v)$ the distance from $u$ to $v$ in $G$, for any $u,v \in V(G)$. The average distance of an $n$-vertex connected graph $G$, denoted by $\mu(G)$, is defined to be the…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees.…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004)…
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
The (axis-parallel) stabbing number of a given set of line segments is the maximum number of segments that can be intersected by any one (axis-parallel) line. This paper deals with finding perfect matchings, spanning trees, or…
The tree metric theorem provides a combinatorial four point condition that characterizes dissimilarity maps derived from pairwise compatible split systems. A similar (but weaker) four point condition characterizes dissimilarity maps derived…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
This paper provides an optimized cable path planning solution for a tree-topology network in an irregular 2D manifold in a 3D Euclidean space, with an application to the planning of submarine cable networks. Our solution method is based on…
The fractal dimension of minimal spanning trees on percolation clusters is estimated for dimensions $d$ up to $d=5$. A robust analysis technique is developed for correlated data, as seen in such trees. This should be a robust method…