Related papers: Enumeration of Tree-like Multigraphs with a Given …
The enumeration of chemical graphs is an important topic in cheminformatics and bioinformatics, particularly in the discovery of novel drugs. These graphs are typically either tree-like multigraphs or composed of tree-like multigraphs…
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 aim of this chapter is to provide an adequate graph theoretic framework for the description of periodic bifurcations which have recently been discovered in descendant trees of finite p-groups. The graph theoretic concepts of rooted…
We consider a problem of enumerating chemical graphs from given constraints concerning their structures, which has an important application to a novel method for the inverse QSAR/QSPR recently proposed. In this paper, the structure of a…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
We present a general framework to generate trees every vertex of which has a non-negative weight and a color. The colors are used to impose certain restrictions on the weight and colors of other vertices. We first extend the enumeration…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
Recently designed biomolecular approaches to build single chain polypeptide polyhedra as molecular origami nanostructures have risen high interest in various double traces of the underlying graphs of these polyhedra. Double traces are walks…
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…
We study the joint distribution of the number of occurrences of members of a collection of nonoverlapping motifs in digital data. We deal with finite and countably infinite collections. For infinite collections, the setting requires that we…
This paper presents the novel `uniqueness tree' algorithm, as one possible method for determining whether two finite, undirected graphs are isomorphic. We prove that the algorithm has polynomial time complexity in the worst case, and that…
We give new general formulas for the asymptotics of the number of spanning trees of a large graph. A special case answers a question of McKay (1983) for regular graphs. The general answer involves a quantity for infinite graphs that we call…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Graph polynomials encode fundamental combinatorial invariants of graphs. Their computation is investigated using tree and path decomposition frameworks, with formal definitions of treewidth, k-trees, and pathwidth establishing the…
Regular tree grammars and regular path expressions constitute core constructs widely used in programming languages and type systems. Nevertheless, there has been little research so far on frameworks for reasoning about path expressions…
Graphs and various graph-like combinatorial structures, such as preorders and hypergraphs, are ubiquitous in programming. This paper focuses on representing graphs in a purely functional programming language like Haskell. There are several…
Dynamic programming is a powerful technique that is, unfortunately, often inherently sequential. That is, there exists no unified method to parallelize algorithms that use dynamic programming. In this paper, we attempt to address this issue…
Working with generating functions, the combinatorics of a recurrence relation can be expressed in a way that allows for more efficient calculation of the quantity. This is true of the Catalan numbers for an ordered binary tree…
In this paper, we introduce two families of planar and self-similar graphs which have small-world properties. The constructed models are based on an iterative process where each step of a certain formulation of modules results in a final…