Fastest mixing Markov chain on graphs with symmetries

We show how to exploit symmetries of a graph to efficiently compute the fastest mixing Markov chain on the graph (i.e., find the transition probabilities on the edges to minimize the second-largest eigenvalue modulus of the transition probability matrix). Exploiting symmetry can lead to significant reduction in both the number of variables and the size of matrices in the corresponding semidefinite program, thus enable numerical solution of large-scale instances that are otherwise computationally infeasible. We obtain analytic or semi-analytic results for particular classes of graphs, such as edge-transitive and distance-transitive graphs. We describe two general approaches for symmetry exploitation, based on orbit theory and block-diagonalization, respectively. We also establish the connection between these two approaches.Comment: 39 pages, 15 figure

Generating and Sampling Orbits for Lifted Probabilistic Inference

A key goal in the design of probabilistic inference algorithms is identifying and exploiting properties of the distribution that make inference tractable. Lifted inference algorithms identify symmetry as a property that enables efficient inference and seek to scale with the degree of symmetry of a probability model. A limitation of existing exact lifted inference techniques is that they do not apply to non-relational representations like factor graphs. In this work we provide the first example of an exact lifted inference algorithm for arbitrary discrete factor graphs. In addition we describe a lifted Markov-Chain Monte-Carlo algorithm that provably mixes rapidly in the degree of symmetry of the distribution

Lie Markov models with purine/pyrimidine symmetry

Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, there are usually extra constraints on the rates, depending on the situation. If a model is formulated in this way, it is possible to generalise it and allow for an inhomogeneous process, with time-dependent rates satisfying the same constraints. It is then useful to require that there exists a homogeneous average of this inhomogeneous process within the same model. This leads to the definition of "Lie Markov models", which are precisely the class of models where such an average exists. These models form Lie algebras and hence concepts from Lie group theory are central to their derivation. In this paper, we concentrate on applications to phylogenetics and nucleotide evolution, and derive the complete hierarchy of Lie Markov models that respect the grouping of nucleotides into purines and pyrimidines -- that is, models with purine/pyrimidine symmetry. We also discuss how to handle the subtleties of applying Lie group methods, most naturally defined over the complex field, to the stochastic case of a Markov process, where parameter values are restricted to be real and positive. In particular, we explore the geometric embedding of the cone of stochastic rate matrices within the ambient space of the associated complex Lie algebra. The whole list of Lie Markov models with purine/pyrimidine symmetry is available at http://www.pagines.ma1.upc.edu/~jfernandez/LMNR.pdf.Comment: 32 page

The mathematical research of William Parry FRS

In this article we survey the mathematical research of the late William (Bill) Parry, FRS

K-theory for Cuntz-Krieger algebras arising from real quadratic maps

We compute the $K$-groups for the Cuntz-Krieger algebras $\mathcal{O}_{A_{\mathcal{K}(f_{\mu})}}$, where $A_{\mathcal{K}(f_{\mu})}$ is the Markov transition matrix arising from the \textit{kneading sequence }$\mathcal{K} (f_{\mu})$ of the one-parameter family of real quadratic maps $f_{\mu}$.Comment: 8 page