The quadratic assignment problem is easy for Robinsonian matrices with Toeplitz structure

We present a new polynomially solvable case of the Quadratic Assignment Problem in Koopmans-Beckman form $QAP(A,B)$, by showing that the identity permutation is optimal when $A$ and $B$ are respectively a Robinson similarity and dissimilarity matrix and one of $A$ or $B$ is a Toeplitz matrix. A Robinson (dis)similarity matrix is a symmetric matrix whose entries (increase) decrease monotonically along rows and columns when moving away from the diagonal, and such matrices arise in the classical seriation problem.Comment: 15 pages, 2 figure

The Kalmanson Complex

Let X be a finite set of cardinality n. The Kalmanson complex K_n is the simplicial complex whose vertices are non-trivial X-splits, and whose facets are maximal circular split systems over X. In this paper we examine K_n from three perspectives. In addition to the T-theoretic description, we show that K_n has a geometric realization as the Kalmanson conditions on a finite metric. A third description arises in terms of binary matrices which possess the circular ones property. We prove the equivalence of these three definitions. This leads to a simplified proof of the well-known equivalence between Kalmanson and circular decomposable metrics, as well as a partial description of the f-vector of K_n.Comment: Improved exposition. 24 pages, 2 figures, 1 tabl

Minimum Contradiction Matrices in Whole Genome Phylogenies

Minimum contradiction matrices are a useful complement to distance-based phylogenies. A minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix Yi, jn. A matrix element corresponds to the distance from a reference vertex n to the path (i, j). For an X-tree or a split network, the minimum contradiction matrix is a Robinson matrix. It therefore fulfills all the inequalities defining perfect order: Yi, jn ≥ Yi,kn, Yk jn ≥ Yk, In, i ≤ j ≤ k < n. In real phylogenetic data, some taxa may contradict the inequalities for perfect order. Contradictions to perfect order correspond to deviations from a tree or from a split network topology. Efficient algorithms that search for the best order are presented and tested on whole genome phylogenies with 184 taxa including many Bacteria, Archaea and Eukaryota. After optimization, taxa are classified in their correct domain and phyla. Several significant deviations from perfect order correspond to well-documented evolutionary events

Affine and Projective Tree Metric Theorems

The tree metric theorem provides a combinatorial four-point condition that characterizes dissimilarity maps derived from pairwise compatible split systems. A related weaker four point condition characterizes dissimilarity maps derived from circular split systems known as Kalmanson metrics. The tree metric theorem was first discovered in the context of phylogenetics and forms the basis of many tree reconstruction algorithms, whereas Kalmanson metrics were first considered by computer scientists, and are notable in that they are a non-trivial class of metrics for which the traveling salesman problem is tractable. We present a unifying framework for these theorems based on combinatorial structures that are used for graph planarity testing. These are (projective) PC-trees, and their affine analogs, PQ-trees. In the projective case, we generalize a number of concepts from clustering theory, including hierarchies, pyramids, ultrametrics, and Robinsonian matrices, and the theorems that relate them. As with tree metrics and ultrametrics, the link between PC-trees and PQ-trees is established via the Gromov product

The multi-stripe travelling salesman problem

In the classical Travelling Salesman Problem (TSP), the objective function sums the costs for travelling from one city to the next city along the tour. In the q-stripe TSP with q ≥ 1, the objective function sums the costs for travelling from one city to each of the next q cities along the tour. The resulting q-stripe TSP generalizes the TSP and forms a special case of the quadratic assignment problem. We analyze the computational complexity of the q-stripe TSP for various classes of specially structured distance matrices. We derive NP-hardness results as well as polyomially solvable cases. One of our main results generalizes a well-known theorem of Kalmanson from the classical TSP to the q-stripe TSP

Order distances and split systems

Given a pairwise distance D on the elements in a finite set X, the order distanceΔ(D) on X is defined by first associating a total preorder ≼ x on X to each x ∈X based on D, and then quantifying the pairwise disagreement between these total preorders. The order distance can be useful in relational analyses because using Δ(D) instead of D may make such analyses less sensitive to small variations in D. Relatively little is known about properties of Δ(D) for general distances D. Indeed, nearly all previous work has focused on understanding the order distance of a treelike distance, that is, a distance that arises as the shortest path distances in a tree with non-negative edge weights and X mapped into its vertex set. In this paper we study the order distance Δ(D) for distances D that can be decomposed into sums of simpler distances called split-distances. Such distances D generalize treelike distances, and have applications in areas such as classification theory and phylogenetics