Trees, Tight-Spans and Point Configuration

Tight-spans of metrics were first introduced by Isbell in 1964 and rediscovered and studied by others, most notably by Dress, who gave them this name. Subsequently, it was found that tight-spans could be defined for more general maps, such as directed metrics and distances, and more recently for diversities. In this paper, we show that all of these tight-spans as well as some related constructions can be defined in terms of point configurations. This provides a useful way in which to study these objects in a unified and systematic way. We also show that by using point configurations we can recover results concerning one-dimensional tight-spans for all of the maps we consider, as well as extend these and other results to more general maps such as symmetric and unsymmetric maps.Comment: 21 pages, 2 figure

Hyperconvexity and Tight Span Theory for Diversities

The tight span, or injective envelope, is an elegant and useful construction that takes a metric space and returns the smallest hyperconvex space into which it can be embedded. The concept has stimulated a large body of theory and has applications to metric classification and data visualisation. Here we introduce a generalisation of metrics, called diversities, and demonstrate that the rich theory associated to metric tight spans and hyperconvexity extends to a seemingly richer theory of diversity tight spans and hyperconvexity.Comment: revised in response to referee comment

On the half-plane property and the Tutte group of a matroid

A multivariate polynomial is stable if it is non-vanishing whenever all variables have positive imaginary parts. A matroid has the weak half-plane property (WHPP) if there exists a stable polynomial with support equal to the set of bases of the matroid. If the polynomial can be chosen with all of its nonzero coefficients equal to one then the matroid has the half-plane property (HPP). We describe a systematic method that allows us to reduce the WHPP to the HPP for large families of matroids. This method makes use of the Tutte group of a matroid. We prove that no projective geometry has the WHPP and that a binary matroid has the WHPP if and only if it is regular. We also prove that T_8 and R_9 fail to have the WHPP.Comment: 8 pages. To appear in J. Combin. Theory Ser.

Computing the blocks of a quasi-median graph

Quasi-median graphs are a tool commonly used by evolutionary biologists to visualise the evolution of molecular sequences. As with any graph, a quasi-median graph can contain cut vertices, that is, vertices whose removal disconnect the graph. These vertices induce a decomposition of the graph into blocks, that is, maximal subgraphs which do not contain any cut vertices. Here we show that the special structure of quasi-median graphs can be used to compute their blocks without having to compute the whole graph. In particular we present an algorithm that, for a collection of $n$ aligned sequences of length $m$, can compute the blocks of the associated quasi-median graph together with the information required to correctly connect these blocks together in run time $\mathcal O(n^2m^2)$, independent of the size of the sequence alphabet. Our primary motivation for presenting this algorithm is the fact that the quasi-median graph associated to a sequence alignment must contain all most parsimonious trees for the alignment, and therefore precomputing the blocks of the graph has the potential to help speed up any method for computing such trees.Comment: 17 pages, 2 figure

Embedding into the rectilinear plane in optimal O*(n^2)

We present an optimal O*(n^2) time algorithm for deciding if a metric space (X,d) on n points can be isometrically embedded into the plane endowed with the l_1-metric. It improves the O*(n^2 log^2 n) time algorithm of J. Edmonds (2008). Together with some ingredients introduced by J. Edmonds, our algorithm uses the concept of tight span and the injectivity of the l_1-plane. A different O*(n^2) time algorithm was recently proposed by D. Eppstein (2009).Comment: 12 pages, 13 figure

On the relation between hyperrings and fuzzy rings

We construct a full embedding of the category of hyperfields into Dress's category of fuzzy rings and explicitly characterize the essential image --- it fails to be essentially surjective in a very minor way. This embedding provides an identification of Baker's theory of matroids over hyperfields with Dress's theory of matroids over fuzzy rings (provided one restricts to those fuzzy rings in the essential image). The embedding functor extends from hyperfields to hyperrings, and we study this extension in detail. We also analyze the relation between hyperfields and Baker's partial demifields

On Patchworks and Hierarchies

Motivated by questions in biological classification, we discuss some elementary combinatorial and computational properties of certain set systems that generalize hierarchies, namely, 'patchworks', 'weak patchworks', 'ample patchworks' and 'saturated patchworks' and also outline how these concepts relate to an apparently new 'duality theory' for cluster systems that is based on the fundamental concept of 'compatibility' of clusters.Comment: 17 pages, 2 figure

Searching for Realizations of Finite Metric Spaces in Tight Spans

An important problem that commonly arises in areas such as internet traffic-flow analysis, phylogenetics and electrical circuit design, is to find a representation of any given metric $D$ on a finite set by an edge-weighted graph, such that the total edge length of the graph is minimum over all such graphs. Such a graph is called an optimal realization and finding such realizations is known to be NP-hard. Recently Varone presented a heuristic greedy algorithm for computing optimal realizations. Here we present an alternative heuristic that exploits the relationship between realizations of the metric $D$ and its so-called tight span $T_D$. The tight span $T_D$ is a canonical polytopal complex that can be associated to $D$, and our approach explores parts of $T_D$ for realizations in a way that is similar to the classical simplex algorithm. We also provide computational results illustrating the performance of our approach for different types of metrics, including $l_1$-distances and two-decomposable metrics for which it is provably possible to find optimal realizations in their tight spans.Comment: 20 pages, 3 figure

A matroid associated with a phylogenetic tree

A (pseudo-)metric D on a finite set X is said to be a `tree metric' if there is a finite tree with leaf set X and non-negative edge weights so that, for all x,y ∈X, D(x,y) is the path distance in the tree between x and y. It is well known that not every metric is a tree metric. However, when some such tree exists, one can always find one whose interior edges have strictly positive edge weights and that has no vertices of degree 2, any such tree is 13; up to canonical isomorphism 13; uniquely determined by D, and one does not even need all of the distances in order to fully (re-)construct the tree's edge weights in this case. Thus, it seems of some interest to investigate which subsets of X, 2 suffice to determine (`lasso') these edge weights. In this paper, we use the results of a previous paper to discuss the structure of a matroid that can be associated with an (unweighted) X-tree T defined by the requirement that its bases are exactly the `tight edge-weight lassos' for T, i.e, the minimal subsets of X, 2 that lasso the edge weights of T