Isomorph-free generation of 2-connected graphs with applications

Many interesting graph families contain only 2-connected graphs, which have ear decompositions. We develop a technique to generate families of unlabeled 2-connected graphs using ear augmentations and apply this technique to two problems. In the first application, we search for uniquely K_r-saturated graphs and find the list of uniquely K_4-saturated graphs on at most 12 vertices, supporting current conjectures for this problem. In the second application, we verifying the Edge Reconstruction Conjecture for all 2-connected graphs on at most 12 vertices. This technique can be easily extended to more problems concerning 2-connected graphs.Comment: 15 pages, 3 figures, 4 table

Computing Unique Maximum Matchings in O(m) time for Konig-Egervary Graphs and Unicyclic Graphs

Let alpha(G) denote the maximum size of an independent set of vertices and mu(G) be the cardinality of a maximum matching in a graph G. A matching saturating all the vertices is perfect. If alpha(G) + mu(G) equals the number of vertices of G, then it is called a Konig-Egervary graph. A graph is unicyclic if it has a unique cycle. In 2010, Bartha conjectured that a unique perfect matching, if it exists, can be found in O(m) time, where m is the number of edges. In this paper we validate this conjecture for Konig-Egervary graphs and unicylic graphs. We propose a variation of Karp-Sipser leaf-removal algorithm (Karp and Spiser, 1981), which ends with an empty graph if and only if the original graph is a Konig-Egervary graph with a unique perfect matching obtained as an output as well. We also show that a unicyclic non-bipartite graph G may have at most one perfect matching, and this is the case where G is a Konig-Egervary graph.Comment: 10 pages, 5 figure

Realising fusion systems

We show that every fusion system on a p-group S is equal to the fusion system associated to a discrete group G with the property that every p-subgroup of G is conjugate to a subgroup of S

Circumstances in which parsimony but not compatibility will be provably misleading

Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting phylogenetic information from aligned sequence data when each site (character) is subject to a common process. However, for other types of data (e.g. morphological data), characters can be too ambiguous, homoplastic or saturated to develop models that are effective at capturing the underlying process of change. To address this, we examine the properties of a classic but neglected method for inferring splits in an underlying tree, namely, maximum compatibility. By adopting a simple and extreme model in which each character either fits perfectly on some tree, or is entirely random (but it is not known which class any character belongs to) we are able to derive exact and explicit formulae regarding the performance of maximum compatibility. We show that this method is able to identify a set of non-trivial homoplasy-free characters, when the number $n$ of taxa is large, even when the number of random characters is large. By contrast, we show that a method that makes more uniform use of all the data --- maximum parsimony --- can provably estimate trees in which {\em none} of the original homoplasy-free characters support splits.Comment: 37 pages, 2 figure

On the extremal properties of the average eccentricity

The eccentricity of a vertex is the maximum distance from it to another vertex and the average eccentricity $ecc (G)$ of a graph $G$ is the mean value of eccentricities of all vertices of $G$. The average eccentricity is deeply connected with a topological descriptor called the eccentric connectivity index, defined as a sum of products of vertex degrees and eccentricities. In this paper we analyze extremal properties of the average eccentricity, introducing two graph transformations that increase or decrease $ecc (G)$. Furthermore, we resolve four conjectures, obtained by the system AutoGraphiX, about the average eccentricity and other graph parameters (the clique number, the Randi\' c index and the independence number), refute one AutoGraphiX conjecture about the average eccentricity and the minimum vertex degree and correct one AutoGraphiX conjecture about the domination number.Comment: 15 pages, 3 figure

Realising fusion systems

We show that every fusion system (saturated or not) on a p-group S is equal to the fusion system associated to a discrete group G containing S as a subgroup and such that every finite subgroup of G is conjugate to a subgroup of S

Discovery of statistical equivalence classes using computer algebra

Discrete statistical models supported on labelled event trees can be specified using so-called interpolating polynomials which are generalizations of generating functions. These admit a nested representation. A new algorithm exploits the primary decomposition of monomial ideals associated with an interpolating polynomial to quickly compute all nested representations of that polynomial. It hereby determines an important subclass of all trees representing the same statistical model. To illustrate this method we analyze the full polynomial equivalence class of a staged tree representing the best fitting model inferred from a real-world dataset.Comment: 26 pages, 9 figure