Nonlinear shrinkage estimation of large-dimensional covariance matrices

Many statistical applications require an estimate of a covariance matrix and/or its inverse. When the matrix dimension is large compared to the sample size, which happens frequently, the sample covariance matrix is known to perform poorly and may suffer from ill-conditioning. There already exists an extensive literature concerning improved estimators in such situations. In the absence of further knowledge about the structure of the true covariance matrix, the most successful approach so far, arguably, has been shrinkage estimation. Shrinking the sample covariance matrix to a multiple of the identity, by taking a weighted average of the two, turns out to be equivalent to linearly shrinking the sample eigenvalues to their grand mean, while retaining the sample eigenvectors. Our paper extends this approach by considering nonlinear transformations of the sample eigenvalues. We show how to construct an estimator that is asymptotically equivalent to an oracle estimator suggested in previous work. As demonstrated in extensive Monte Carlo simulations, the resulting bona fide estimator can result in sizeable improvements over the sample covariance matrix and also over linear shrinkage.Comment: Published in at http://dx.doi.org/10.1214/12-AOS989 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

On the efficient numerical solution of lattice systems with low-order couplings

We apply the Quasi Monte Carlo (QMC) and recursive numerical integration methods to evaluate the Euclidean, discretized time path-integral for the quantum mechanical anharmonic oscillator and a topological quantum mechanical rotor model. For the anharmonic oscillator both methods outperform standard Markov Chain Monte Carlo methods and show a significantly improved error scaling. For the quantum mechanical rotor we could, however, not find a successful way employing QMC. On the other hand, the recursive numerical integration method works extremely well for this model and shows an at least exponentially fast error scaling

Efficient Monte Carlo Integration Using Boosted Decision Trees and Generative Deep Neural Networks

New machine learning based algorithms have been developed and tested for Monte Carlo integration based on generative Boosted Decision Trees and Deep Neural Networks. Both of these algorithms exhibit substantial improvements compared to existing algorithms for non-factorizable integrands in terms of the achievable integration precision for a given number of target function evaluations. Large scale Monte Carlo generation of complex collider physics processes with improved efficiency can be achieved by implementing these algorithms into commonly used matrix element Monte Carlo generators once their robustness is demonstrated and performance validated for the relevant classes of matrix elements

An alternative marginal likelihood estimator for phylogenetic models

Bayesian phylogenetic methods are generating noticeable enthusiasm in the field of molecular systematics. Many phylogenetic models are often at stake and different approaches are used to compare them within a Bayesian framework. The Bayes factor, defined as the ratio of the marginal likelihoods of two competing models, plays a key role in Bayesian model selection. We focus on an alternative estimator of the marginal likelihood whose computation is still a challenging problem. Several computational solutions have been proposed none of which can be considered outperforming the others simultaneously in terms of simplicity of implementation, computational burden and precision of the estimates. Practitioners and researchers, often led by available software, have privileged so far the simplicity of the harmonic mean estimator (HM) and the arithmetic mean estimator (AM). However it is known that the resulting estimates of the Bayesian evidence in favor of one model are biased and often inaccurate up to having an infinite variance so that the reliability of the corresponding conclusions is doubtful. Our new implementation of the generalized harmonic mean (GHM) idea recycles MCMC simulations from the posterior, shares the computational simplicity of the original HM estimator, but, unlike it, overcomes the infinite variance issue. The alternative estimator is applied to simulated phylogenetic data and produces fully satisfactory results outperforming those simple estimators currently provided by most of the publicly available software

Connecting the Dots: Towards Continuous Time Hamiltonian Monte Carlo

Continuous time Hamiltonian Monte Carlo is introduced, as a powerful alternative to Markov chain Monte Carlo methods for continuous target distributions. The method is constructed in two steps: First Hamiltonian dynamics are chosen as the deterministic dynamics in a continuous time piecewise deterministic Markov process. Under very mild restrictions, such a process will have the desired target distribution as an invariant distribution. Secondly, the numerical implementation of such processes, based on adaptive numerical integration of second order ordinary differential equations is considered. The numerical implementation yields an approximate, yet highly robust algorithm that, unlike conventional Hamiltonian Monte Carlo, enables the exploitation of the complete Hamiltonian trajectories (hence the title). The proposed algorithm may yield large speedups and improvements in stability relative to relevant benchmarks, while incurring numerical errors that are negligible relative to the overall Monte Carlo errors