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

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

Characterizing Block Graphs in Terms of their Vertex-Induced Partitions

Given a finite connected simple graph $G=(V,E)$ with vertex set $V$ and edge set $E\subseteq \binom{V}{2}$, we will show that $1.$ the (necessarily unique) smallest block graph with vertex set $V$ whose edge set contains $E$ is uniquely determined by the $V$-indexed family ${\bf P}_G:=\big(\pi_0(G^{(v)})\big)_{v \in V}$ of the various partitions $\pi_0(G^{(v)})$ of the set $V$ into the set of connected components of the graph $G^{(v)}:=(V,\{e\in E: v\notin e\})$, $2.$ the edge set of this block graph coincides with set of all $2$-subsets $\{u,v\}$ of $V$ for which $u$ and $v$ are, for all $w\in V-\{u,v\}$, contained in the same connected component of $G^{(w)}$, $3.$ and an arbitrary $V$-indexed family ${\bf P}p=({\bf p}_v)_{v \in V}$ of partitions $\pi_v$ of the set $V$ is of the form ${\bf P}p={\bf P}p_G$ for some connected simple graph $G=(V,E)$ with vertex set $V$ as above if and only if, for any two distinct elements $u,v\in V$, the union of the set in ${\bf p}_v$ that contains $u$ and the set in ${\bf p}_u$ that contains $v$ coincides with the set $V$, and $\{v\}\in {\bf p}_v$ holds for all $v \in V$. As well as being of inherent interest to the theory of block graphs, these facts are also useful in the analysis of compatible decompositions and block realizations of finite metric spaces

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

Operating envelope charts for the Langley 0.3-meter transonic cryogenic wind tunnel

To take full advantage of the unique Reynolds number capabilities of the 0.3-meter Transonic Cryogenic Tunnel (0.3-m TCT) at the NASA Langley Research Center, it was designed to accommodate test sections other than the original, octagonal, three-dimensional test section. A 20- by 60-cm two-dimensional test section was installed in 1976 and was extensively used, primarily for airfoil testing, through the fall of 1984. The tunnel was inactive during 1985 so that a new test section and improved high speed diffuser could be installed in the tunnel circuit. The new test section has solid adaptive top and bottom walls to reduce or eliminate wall interference for two-dimensional testing. The test section is 33- by 33-cm in cross section at the entrance and is 142 cm long. In the planning and running of past airfoil tests in the 0.3-m TCT, the use of operating envelope charts have proven very useful. These charts give the variation of total temperature and pressure with Mach number and Reynolds number. The operating total temperature range of the 0.3-m TCT is from about 78 K to 327 K with total pressures ranging from about 17.5 psia to 88 psia. This report presents the operating envelope charts for the 0.3-m TCT with the adaptive wall tes t section installed. They were all generated based on a 1-foot chord model. The Mach numbers vary from 0.1 to 0.95

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

Number of right ideals and a qq-analogue of indecomposable permutations

We prove that the number of right ideals of codimension $n$ in the algebra of noncommutative Laurent polynomials in two variables over the finite field $\mathbb F\_q$ is equal to $(q-1)^{n+1} q^{\frac{(n+1)(n-2)}{2}}\sum\_\theta q^{inv(\theta)}$, where the sum is over all indecomposable permutations in $S\_{n+1}$ and where $inv(\theta)$stands for the number of inversions of $\theta$.Comment: submitte

Computing the bounded subcomplex of an unbounded polyhedron

We study efficient combinatorial algorithms to produce the Hasse diagram of the poset of bounded faces of an unbounded polyhedron, given vertex-facet incidences. We also discuss the special case of simple polyhedra and present computational results.Comment: 16 page