An elementary chromatic reduction for gain graphs and special hyperplane arrangements

A gain graph is a graph whose edges are labelled invertibly by "gains" from a group. "Switching" is a transformation of gain graphs that generalizes conjugation in a group. A "weak chromatic function" of gain graphs with gains in a fixed group satisfies three laws: deletion-contraction for links with neutral gain, invariance under switching, and nullity on graphs with a neutral loop. The laws lead to the "weak chromatic group" of gain graphs, which is the universal domain for weak chromatic functions. We find expressions, valid in that group, for a gain graph in terms of minors without neutral-gain edges, or with added complete neutral-gain subgraphs, that generalize the expression of an ordinary chromatic polynomial in terms of monomials or falling factorials. These expressions imply relations for chromatic functions of gain graphs. We apply our relations to some special integral gain graphs including those that correspond to the Shi, Linial, and Catalan arrangements, thereby obtaining new evaluations of and new ways to calculate the zero-free chromatic polynomial and the integral and modular chromatic functions of these gain graphs, hence the characteristic polynomials and hypercubical lattice-point counting functions of the arrangements. We also calculate the total chromatic polynomial of any gain graph and especially of the Catalan, Shi, and Linial gain graphs.Comment: 31 page

Disjoint compatibility graph of non-crossing matchings of points in convex position

Let $X_{2k}$ be a set of $2k$ labeled points in convex position in the plane. We consider geometric non-intersecting straight-line perfect matchings of $X_{2k}$. Two such matchings, $M$ and $M'$, are disjoint compatible if they do not have common edges, and no edge of $M$ crosses an edge of $M'$. Denote by $\mathrm{DCM}_k$ the graph whose vertices correspond to such matchings, and two vertices are adjacent if and only if the corresponding matchings are disjoint compatible. We show that for each $k \geq 9$, the connected components of $\mathrm{DCM}_k$ form exactly three isomorphism classes -- namely, there is a certain number of isomorphic small components, a certain number of isomorphic medium components, and one big component. The number and the structure of small and medium components is determined precisely.Comment: 46 pages, 30 figure

A tree-decomposed transfer matrix for computing exact Potts model partition functions for arbitrary graphs, with applications to planar graph colourings

Combining tree decomposition and transfer matrix techniques provides a very general algorithm for computing exact partition functions of statistical models defined on arbitrary graphs. The algorithm is particularly efficient in the case of planar graphs. We illustrate it by computing the Potts model partition functions and chromatic polynomials (the number of proper vertex colourings using Q colours) for large samples of random planar graphs with up to N=100 vertices. In the latter case, our algorithm yields a sub-exponential average running time of ~ exp(1.516 sqrt(N)), a substantial improvement over the exponential running time ~ exp(0.245 N) provided by the hitherto best known algorithm. We study the statistics of chromatic roots of random planar graphs in some detail, comparing the findings with results for finite pieces of a regular lattice.Comment: 5 pages, 3 figures. Version 2 has been substantially expanded. Version 3 shows that the worst-case running time is sub-exponential in the number of vertice

Optimal Recombination in Genetic Algorithms

This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We consider efficient reductions of the ORPs, allowing to establish polynomial solvability or NP-hardness of the ORPs, as well as direct proofs of hardness results

Simultaneous Embeddability of Two Partitions

We study the simultaneous embeddability of a pair of partitions of the same underlying set into disjoint blocks. Each element of the set is mapped to a point in the plane and each block of either of the two partitions is mapped to a region that contains exactly those points that belong to the elements in the block and that is bounded by a simple closed curve. We establish three main classes of simultaneous embeddability (weak, strong, and full embeddability) that differ by increasingly strict well-formedness conditions on how different block regions are allowed to intersect. We show that these simultaneous embeddability classes are closely related to different planarity concepts of hypergraphs. For each embeddability class we give a full characterization. We show that (i) every pair of partitions has a weak simultaneous embedding, (ii) it is NP-complete to decide the existence of a strong simultaneous embedding, and (iii) the existence of a full simultaneous embedding can be tested in linear time.Comment: 17 pages, 7 figures, extended version of a paper to appear at GD 201

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