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The performance of Markov chain Monte Carlo calculations is determined by both ensemble variance of the Monte Carlo estimator and autocorrelation of the Markov process. In order to study autocorrelation, binning analysis is commonly used, where the autocorrelation is estimated from results grouped into bins of logarithmically increasing sizes. In this paper, we show that binning analysis comes with a bias that can be eliminated by combining bin sizes. We then show binning analysis can be performed on-the-fly with linear overhead in time and logarithmic overhead in memory with respect to the sample size. We then show that binning analysis contains information not only about the integrated effect of autocorrelation, but can be used to estimate the spectrum of autocorrelation lengths, yielding the height of phase space barriers in the system. Finally, we revisit the Ising model and apply the proposed method to recover its autocorrelation spectra.
In this paper, we propose efficient probabilistic algorithms for several problems regarding the autocorrelation spectrum. First, we present a quantum algorithm that samples from the Walsh spectrum of any derivative of $f()$. Informally, the autocorre
By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show that, due to c
Clusters form the basis of a number of research study designs including survey and experimental studies. Cluster-based designs can be less costly but also less efficient than individual-based designs due to correlation between individuals within the
In this paper, we study the prediction of a circularly symmetric zero-mean stationary Gaussian process from a window of observations consisting of finitely many samples. This is a prevalent problem in a wide range of applications in communication the
The efficient calculation of rare-event kinetics in complex dynamical systems, such as the rate and pathways of ligand dissociation from a protein, is a generally unsolved problem. Markov state models can systematically integrate ensembles of short s