Reversible Markov chain estimation using convex-concave programming

We present a convex-concave reformulation of the reversible Markov chain estimation problem and outline an efficient numerical scheme for the solution of the resulting problem based on a primal-dual interior point method for monotone variational inequalities. Extensions to situations in which information about the stationary vector is available can also be solved via the convex- concave reformulation. The method can be generalized and applied to the discrete transition matrix reweighting analysis method to perform inference from independent chains with specified couplings between the stationary probabilities. The proposed approach offers a significant speed-up compared to a fixed-point iteration for a number of relevant applications.Comment: 17pages, 2 figure

Information Geometry of Reversible Markov Chains

We analyze the information geometric structure of time reversibility for parametric families of irreducible transition kernels of Markov chains. We define and characterize reversible exponential families of Markov kernels, and show that irreducible and reversible Markov kernels form both a mixture family and, perhaps surprisingly, an exponential family in the set of all stochastic kernels. We propose a parametrization of the entire manifold of reversible kernels, and inspect reversible geodesics. We define information projections onto the reversible manifold, and derive closed-form expressions for the e-projection and m-projection, along with Pythagorean identities with respect to information divergence, leading to some new notion of reversiblization of Markov kernels. We show the family of edge measures pertaining to irreducible and reversible kernels also forms an exponential family among distributions over pairs. We further explore geometric properties of the reversible family, by comparing them with other remarkable families of stochastic matrices. Finally, we show that reversible kernels are, in a sense we define, the minimal exponential family generated by the m-family of symmetric kernels, and the smallest mixture family that comprises the e-family of memoryless kernels

Event-chain Monte Carlo: foundations, applications, and prospects

This review treats the mathematical and algorithmic foundations of non-reversible Markov chains in the context of event-chain Monte Carlo (ECMC), a continuous-time lifted Markov chain that employs the factorized Metropolis algorithm. It analyzes a number of model applications, and then reviews the formulation as well as the performance of ECMC in key models in statistical physics. Finally, the review reports on an ongoing initiative to apply the method to the sampling problem in molecular simulation, that is, to real-world models of peptides, proteins, and polymers in aqueous solution.Comment: 35 pages, no figure