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The complexity of a graph is the number of its labeled spanning trees. In this work complexity is studied in settings that admit regular graphs. An exact formula is established linking complexity of the complement of a regular graph to…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
Graphs with given k vertices generate an (acyclic) simplicial complex. We describe the homology of its quotient complex, formed by all connected graphs, and demonstrate its applications to the topology of braid groups, knot theory,…
Using the ordered analogue of Farley-Sabalka's discrete gradient field on the configuration space of a graph, we unravel a levelwise behavior of the generators of the pure braid group on a tree. This allows us to generalize Farber's…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
The recently introduced A-homotopy groups for graphs are investigated. The main concern of the present article is the construction of an infinite cell complex, the homotopy groups of which are isomorphic to the A-homotopy groups of the…
This paper starts with an observation that two infinite series of simplicial complexes, which a priori do not seem to have anything to do with each other, have the same homotopy type. One series consists of the complexes of directed forests…
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…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
Matchings and coverings are central topics in graph theory. The close relationship between these two has been key to many fundamental algorithmic and polyhedral results. For mixed graphs, the notion of matching forest was proposed as a…
Let p be a fibration over a finite simplicial complex, whose fibers have the homotopy type of finite simplicial complexes. Then p is equivalent to an approximate fibration whose total space is a compact ENR. The proof uses homotopy coherent…
The topology of the matching complex for the $2\times n$ grid graph is mysterious. We describe a discrete Morse matching for a family of independence complexes $\mathrm{Ind}(\Delta_n^m)$ that include these matching complexes. Using this…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…
There are several interrelated notions of discrete curvature on graphs. Many approaches utilize the optimal transportation metric on its probability simplex or the distance matrix of the graph. In this survey article, we compute formulas…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…
We define decision trees for monotone functions on a simplicial complex. We define homology decidability of monotone functions, and show that various monotone functions related to semimatroids are homology decidable. Homology decidability…
This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…
A perfect forest is a spanning forest of a connected graph $G$, all of whose components are induced subgraphs of $G$ and such that all vertices have odd degree in the forest. A perfect forest generalised a perfect matching since, in a…
The graph matching problem aims to discover a latent correspondence between the vertex sets of two observed graphs. This problem has proven to be quite challenging, with few satisfying methods that are computationally tractable and widely…