Why bayesian “evidence for H1” in one condition and bayesian “evidence for H0” in another condition does not mean good-enough bayesian evidence for a difference between the conditions

Psychologists are often interested in whether an independent variable has a different effect in condition A than in condition B. To test such a question, one needs to directly compare the effect of that variable in the two conditions (i.e., test the interaction). Yet many researchers tend to stop when they find a significant test in one condition and a nonsignificant test in the other condition, deeming this as sufficient evidence for a difference between the two conditions. In this Tutorial, we aim to raise awareness of this inferential mistake when Bayes factors are used with conventional cutoffs to draw conclusions. For instance, some researchers might falsely conclude that there must be good-enough evidence for the interaction if they find good-enough Bayesian evidence for the alternative hypothesis, H1, in condition A and good-enough Bayesian evidence for the null hypothesis, H0, in condition B. The case study we introduce highlights that ignoring the test of the interaction can lead to unjustified conclusions and demonstrates that the principle that any assertion about the existence of an interaction necessitates the direct comparison of the conditions is as true for Bayesian as it is for frequentist statistics. We provide an R script of the analyses of the case study and a Shiny app that can be used with a 2 × 2 design to develop intuitions on this issue, and we introduce a rule of thumb with which one can estimate the sample size one might need to have a well-powered design

Bayesian Analysis of Inflation II: Model Selection and Constraints on Reheating

We discuss the model selection problem for inflationary cosmology. We couple ModeCode, a publicly-available numerical solver for the primordial perturbation spectra, to the nested sampler MultiNest, in order to efficiently compute Bayesian evidence. Particular attention is paid to the specification of physically realistic priors, including the parametrization of the post-inflationary expansion and associated thermalization scale. It is confirmed that while present-day data tightly constrains the properties of the power spectrum, it cannot usefully distinguish between the members of a large class of simple inflationary models. We also compute evidence using a simulated Planck likelihood, showing that while Planck will have more power than WMAP to discriminate between inflationary models, it will not definitively address the inflationary model selection problem on its own. However, Planck will place very tight constraints on any model with more than one observationally-distinct inflationary regime -- e.g. the large- and small-field limits of the hilltop inflation model -- and put useful limits on different reheating scenarios for a given model.Comment: ModeCode package available from http://zuserver2.star.ucl.ac.uk/~hiranya/ModeCode/ModeCode (requires CosmoMC and MultiNest); to be published in PRD. Typos fixe

Attempts to detect retrotransposition and de novo deletion of Alus and other dispersed repeats at specific loci in the human genome

Dispersed repeat elements contribute to genome instability by de novo insertion and unequal recombination between repeats. To study the dynamics of these processes, we have developed single DNA molecule approaches to detect de novo insertions at a single locus and Alu-mediated deletions at two different loci in human genomic DNA. Validation experiments showed these approaches could detect insertions and deletions at frequencies below 10(-6) per cell. However, bulk analysis of germline (sperm) and somatic DNA showed no evidence for genuine mutant molecules, placing an upper limit of insertion and deletion rates of 2 x 10(-7) and 3 x 10(-7), respectively, in the individuals tested. Such re-arrangements at these loci therefore occur at a rate lower than that detectable by the most sensitive methods currently available

XAFS spectroscopy. I. Extracting the fine structure from the absorption spectra

Three independent techniques are used to separate fine structure from the absorption spectra, the background function in which is approximated by (i) smoothing spline. We propose a new reliable criterion for determination of smoothing parameter and the method for raising of stability with respect to k_min variation; (ii) interpolation spline with the varied knots; (iii) the line obtained from bayesian smoothing. This methods considers various prior information and includes a natural way to determine the errors of XAFS extraction. Particular attention has been given to the estimation of uncertainties in XAFS data. Experimental noise is shown to be essentially smaller than the errors of the background approximation, and it is the latter that determines the variances of structural parameters in subsequent fitting.Comment: 16 pages, 7 figures, for freeware XAFS analysis program, see http://www.crosswinds.net/~klmn/viper.htm

Determining the Neutrino Mass Hierarchy with Cosmology

The combination of current large scale structure and cosmic microwave background (CMB) anisotropies data can place strong constraints on the sum of the neutrino masses. Here we show that future cosmic shear experiments, in combination with CMB constraints, can provide the statistical accuracy required to answer questions about differences in the mass of individual neutrino species. Allowing for the possibility that masses are non-degenerate we combine Fisher matrix forecasts for a weak lensing survey like Euclid with those for the forthcoming Planck experiment. Under the assumption that neutrino mass splitting is described by a normal hierarchy we find that the combination Planck and Euclid will possibly reach enough sensitivity to put a constraint on the mass of a single species. Using a Bayesian evidence calculation we find that such future experiments could provide strong evidence for either a normal or an inverted neutrino hierachy. Finally we show that if a particular neutrino hierachy is assumed then this could bias cosmological parameter constraints, for example the dark energy equation of state parameter, by > 1\sigma, and the sum of masses by 2.3\sigma.Comment: 9 pages, 6 figures, 3 table

Constructing smooth potentials of mean force, radial, distribution functions and probability densities from sampled data

In this paper a method of obtaining smooth analytical estimates of probability densities, radial distribution functions and potentials of mean force from sampled data in a statistically controlled fashion is presented. The approach is general and can be applied to any density of a single random variable. The method outlined here avoids the use of histograms, which require the specification of a physical parameter (bin size) and tend to give noisy results. The technique is an extension of the Berg-Harris method [B.A. Berg and R.C. Harris, Comp. Phys. Comm. 179, 443 (2008)], which is typically inaccurate for radial distribution functions and potentials of mean force due to a non-uniform Jacobian factor. In addition, the standard method often requires a large number of Fourier modes to represent radial distribution functions, which tends to lead to oscillatory fits. It is shown that the issues of poor sampling due to a Jacobian factor can be resolved using a biased resampling scheme, while the requirement of a large number of Fourier modes is mitigated through an automated piecewise construction approach. The method is demonstrated by analyzing the radial distribution functions in an energy-discretized water model. In addition, the fitting procedure is illustrated on three more applications for which the original Berg-Harris method is not suitable, namely, a random variable with a discontinuous probability density, a density with long tails, and the distribution of the first arrival times of a diffusing particle to a sphere, which has both long tails and short-time structure. In all cases, the resampled, piecewise analytical fit outperforms the histogram and the original Berg-Harris method.Comment: 14 pages, 15 figures. To appear in J. Chem. Phy

Tests of Bayesian Model Selection Techniques for Gravitational Wave Astronomy

The analysis of gravitational wave data involves many model selection problems. The most important example is the detection problem of selecting between the data being consistent with instrument noise alone, or instrument noise and a gravitational wave signal. The analysis of data from ground based gravitational wave detectors is mostly conducted using classical statistics, and methods such as the Neyman-Pearson criteria are used for model selection. Future space based detectors, such as the \emph{Laser Interferometer Space Antenna} (LISA), are expected to produced rich data streams containing the signals from many millions of sources. Determining the number of sources that are resolvable, and the most appropriate description of each source poses a challenging model selection problem that may best be addressed in a Bayesian framework. An important class of LISA sources are the millions of low-mass binary systems within our own galaxy, tens of thousands of which will be detectable. Not only are the number of sources unknown, but so are the number of parameters required to model the waveforms. For example, a significant subset of the resolvable galactic binaries will exhibit orbital frequency evolution, while a smaller number will have measurable eccentricity. In the Bayesian approach to model selection one needs to compute the Bayes factor between competing models. Here we explore various methods for computing Bayes factors in the context of determining which galactic binaries have measurable frequency evolution. The methods explored include a Reverse Jump Markov Chain Monte Carlo (RJMCMC) algorithm, Savage-Dickie density ratios, the Schwarz-Bayes Information Criterion (BIC), and the Laplace approximation to the model evidence. We find good agreement between all of the approaches.Comment: 11 pages, 6 figure

Extended Heat-Fluctuation Theorems for a System with Deterministic and Stochastic Forces

Heat fluctuations over a time \tau in a non-equilibrium stationary state and in a transient state are studied for a simple system with deterministic and stochastic components: a Brownian particle dragged through a fluid by a harmonic potential which is moved with constant velocity. Using a Langevin equation, we find the exact Fourier transform of the distribution of these fluctuations for all \tau. By a saddle-point method we obtain analytical results for the inverse Fourier transform, which, for not too small \tau, agree very well with numerical results from a sampling method as well as from the fast Fourier transform algorithm. Due to the interaction of the deterministic part of the motion of the particle in the mechanical potential with the stochastic part of the motion caused by the fluid, the conventional heat fluctuation theorem is, for infinite and for finite \tau, replaced by an extended fluctuation theorem that differs noticeably and measurably from it. In particular, for large fluctuations, the ratio of the probability for absorption of heat (by the particle from the fluid) to the probability to supply heat (by the particle to the fluid) is much larger here than in the conventional fluctuation theorem.Comment: 23 pages, 6 figures. Figures are now in color, Eq. (67) was corrected and a footnote was added on the d-dimensional cas

Gravitational oscillations in multidimensional anisotropic model with cosmological constant and their contributions into the energy of vacuum

Were studied classical oscillations of background metric in the multidimensional anisotropic model of Kazner in the de-Sitter stage. Obtained dependence of fluctuations on dimension of space-time with infinite expansion. Stability of the model could be achieved when number of space-like dimensions equals or more then four. Were calculated contributions to the density of "vacuum energy", that are providing by proper oscillations of background metric and compared with contribution of cosmological arising of particles due to expansion. As it turned out, contribution of gravitational oscillation of metric into density of "vacuum energy" should play significant role in the de-Sitter stage