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

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 rooted phylogenetic trees with the same leaf set and whose edge lengths are constrained by either their total sum or their maximum value

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

Computing the hybridization number is fixed-parameter tractable

Reticulation processes in evolution mean that the ancestral history of certain groups of present-day species is non-tree-like. These processes include hybridization, lateral gene transfer, and recombination. Despite the existence of reticulation, such events are relatively rare and so a fundamental problem for biologists is the following: given a collection of rooted binary phylogenetic trees on sets of species that correctly represent the tree-like evolution of different parts of their genomes, what is the smallest number of "reticulation" vertices in any network that explains the evolution of the species under consideration. It has been previously shown that this problem is NP-hard even when the collection consists of only two rooted binary phylogenetic trees; however, in this paper, we show that it is fixed-parameter tractable