Metric Construction, Stopping Times and Path Coupling

In this paper we examine the importance of the choice of metric in path coupling, and the relationship of this to \emph{stopping time analysis}. We give strong evidence that stopping time analysis is no more powerful than standard path coupling. In particular, we prove a stronger theorem for path coupling with stopping times, using a metric which allows us to restrict analysis to standard one-step path coupling. This approach provides insight for the design of non-standard metrics giving improvements in the analysis of specific problems. We give illustrative applications to hypergraph independent sets and SAT instances, hypergraph colourings and colourings of bipartite graphs.Comment: 21 pages, revised version includes statement and proof of general stopping times theorem (section 2.2), and additonal remarks in section

Path Coupling Using Stopping Times and Counting Independent Sets and Colourings in Hypergraphs

We give a new method for analysing the mixing time of a Markov chain using path coupling with stopping times. We apply this approach to two hypergraph problems. We show that the Glauber dynamics for independent sets in a hypergraph mixes rapidly as long as the maximum degree Delta of a vertex and the minimum size m of an edge satisfy m>= 2Delta+1. We also show that the Glauber dynamics for proper q-colourings of a hypergraph mixes rapidly if m>= 4 and q > Delta, and if m=3 and q>=1.65Delta. We give related results on the hardness of exact and approximate counting for both problems.Comment: Simpler proof of main theorem. Improved bound on mixing time. 19 page

Determining phylogenetic networks from inter-taxa distances

We consider the problem of determining the topological structure of a phylogenetic network given only information about the path-length distances between taxa. In particular, one of the main results of the paper shows that binary tree-child networks are essentially determined by such information

Quantifying the difference between phylogenetic diversity and diversity indices

Phylogenetic diversity is a popular measure for quantifying the biodiversity of a collection $Y$ of species, while phylogenetic diversity indices provide a way to apportion phylogenetic diversity to individual species. Typically, for some specific diversity index, the phylogenetic diversity of $Y$ is not equal to the sum of the diversity indices of the species in $Y.$ In this paper, we investigate the extent of this difference for two commonly-used indices: Fair Proportion and Equal Splits. In particular, we determine the maximum value of this difference under various instances including when the associated rooted phylogenetic tree is allowed to vary across all root phylogenetic trees with the same leaf set and whose edge lengths are constrained by either their total sum or their maximum value.Comment: 26 pages, 5 figure

On the computational complexity of the rooted subtree prune and regraft distance

The graph-theoretic operation of rooted subtree prune and regraft is increasingly being used as a tool for understanding and modelling reticulation events in evolutionary biology. In this paper, we show that computing the rooted subtree prune and regraft distance between two rooted binary phylogenetic trees on the same label set is NP-hard. This resolves a longstanding open problem. Furthermore, we show that this distance is xed parameter tractable when parameterised by the distance between the two trees

Approximating the partition function of the ferromagnetic Potts model

We provide evidence that it is computationally difficult to approximate the partition function of the ferromagnetic q-state Potts model when q>2. Specifically we show that the partition function is hard for the complexity class #RHPi_1 under approximation-preserving reducibility. Thus, it is as hard to approximate the partition function as it is to find approximate solutions to a wide range of counting problems, including that of determining the number of independent sets in a bipartite graph. Our proof exploits the first order phase transition of the "random cluster" model, which is a probability distribution on graphs that is closely related to the q-state Potts model.Comment: Minor correction