Informed Bayesian t-Tests

Across the empirical sciences, few statistical procedures rival the popularity of the frequentist (Formula presented.) -test. In contrast, the Bayesian versions of the (Formula presented.) -test have languished in obscurity. In recent years, however, the theoretical and practical advantages of the Bayesian (Formula presented.) -test have become increasingly apparent and various Bayesian t-tests have been proposed, both objective ones (based on general desiderata) and subjective ones (based on expert knowledge). Here, we propose a flexible t-prior for standardized effect size that allows computation of the Bayes factor by evaluating a single numerical integral. This specification contains previous objective and subjective t-test Bayes factors as special cases. Furthermore, we propose two measures for informed prior distributions that quantify the departure from the objective Bayes factor desiderata of predictive matching and information consistency. We illustrate the use of informed prior distributions based on an expert prior elicitation effort. Supplementary materials for this article are available online

The CP violating phase γ\gamma from global fit of rare charmless hadronic B decays

We study constraints on the CP violating phase $\gamma$ in the Kobayashi-Maskawa model using available experimental data. We first follow the conventional method to up date the constraint on $\gamma$ by performing a $\chi^2$ analysis using data from $|\epsilon_K|$, $\Delta m_{B_{d,s}}$ and $|V_{ub}/V_{cb}|$. We also include the recent information on $\sin2\beta$ in the analysis. We obtain the best fit for $\gamma$ to be $66^\circ$ and the 95% C.L. allowed range to be $42^\circ \sim 87^\circ$. We then develop a method to carry out a $\chi^2$ analysis based on SU(3) symmetry using data from $B\to \pi \pi$ and $B\to K \pi$. We also discuss SU(3) breaking effects from model estimate. We find that present data on $B\to \pi\pi, K \pi$ can also give some constraint on $\gamma$ although weaker than the earlier method limited by the present experimental errors. Future improved data will provide more stringent constraint. Finally we perform a combined fit using data from $|\epsilon_K|$, $\Delta m_{B_{d,s}}$, $|V_{ub}/V_{cb}|$, $\sin2\beta$ and rare charmless hadronic B decays. The combined analysis gives $\gamma=67^\circ$ for the best fit value and $43^\circ \sim 87^\circ$ as the 95% C.L. allowed range. Several comments on other methods to determine $\gamma$ based on SU(3) symmetry are also provided.Comment: Revised verion with the new experimental data from Belle and Babar included in the analysis to obtain the global fit for the CP violating phase gamma. RevTex, 32 pages and 8 figure

On Large Final-State Phases in Heavy Meson Decays

An attempt is made to identify circumstances under which the weak decays of $D$ and $B$ mesons may display large differences between eigenphases of strong final-state interactions. There are several cases in which rescattering from other final states appears to enhance decay rates with respect to estimates based on the factorization hypothesis.Comment: 24 pages, latex, 4 figures, to be submitted to Phys. Rev.

Bayesian model-averaged meta-analysis in medicine

We outline a Bayesian model-averaged (BMA) meta-analysis for standardized mean differences in order to quantify evidence for both treatment effectiveness (Formula presented.) and across-study heterogeneity (Formula presented.). We construct four competing models by orthogonally combining two present-absent assumptions, one for the treatment effect and one for across-study heterogeneity. To inform the choice of prior distributions for the model parameters, we used 50% of the Cochrane Database of Systematic Reviews to specify rival prior distributions for (Formula presented.) and (Formula presented.). The relative predictive performance of the competing models and rival prior distributions was assessed using the remaining 50% of the Cochrane Database. On average, (Formula presented.) —the model that assumes the presence of a treatment effect as well as across-study heterogeneity—outpredicted the other models, but not by a large margin. Within (Formula presented.), predictive adequacy was relatively constant across the rival prior distributions. We propose specific empirical prior distributions, both for the field in general and for each of 46 specific medical subdisciplines. An example from oral health demonstrates how the proposed prior distributions can be used to conduct a BMA meta-analysis in the open-source software R and JASP. The preregistered analysis plan is available at https://osf.io/zs3df/

The hidden sterile neutrino and the (2+2) sum rule

We discuss oscillations of atmospheric and solar neutrinos into sterile neutrinos in the 2+2 scheme. A zeroth order sum rule requires equal probabilities for oscillation into nu_s and nu_tau in the solar+atmospheric data sample. Data does not favor this claim. Here we use scatter plots to assess corrections of the zeroth order sum rule when (i) the 4 x 4 neutrino mixing matrix assumes its full range of allowed values, and (ii) matter effects are included. We also introduce a related "product rule". We find that the sum rule is significantly relaxed, due to both the inclusion of the small mixing angles (which provide a short-baseline contribution) and to matter effects. The product rule is also dramatically altered. The observed relaxation of the sum rule weakens the case against the 2+2 model and the sterile neutrino. To invalidate the 2+2 model, a global fit to data with the small mixing angles included seems to be required.Comment: 43 pages, 11 figures (same as v2, accidental replacement

Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum

Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy generation, nutrient utilization, and biomass production using an extended methodology that accounts for dynamically changing transport patterns, including those that arise from interactions among the supplied metabolites. Moreover, we widen the scope of our analysis to include phototrophic conditions to explore the interplay between different bioenergetic modes. Surprisingly, we found that cells also degrade essential amino acids even during phototropy, when energy should already be abundant. We also found that under both conditions considerable amounts of nutrients that were taken up were neither incorporated into the biomass nor used as respiratory substrates, implying the considerable production and accumulation of several metabolites in the medium. Some of these are likely the products of forms of overflow metabolism. In addition, our results also show that arginine fermentation, contrary to what is typically assumed, occurs simultaneously with respiration and photosynthesis and can contribute energy in levels that are comparable to the primary bioenergetic modes, if not more. These findings portray a picture that the organism takes an approach toward growth that favors the here and now, even at the cost of longer-term concerns. We believe that the seemingly "greedy" behavior exhibited actually consists of adaptations by the organism to its natural environments, where nutrients are not only irregularly available but may altogether be absent for extended periods that may span several years. Such a setting probably predisposed the cells to grow as much as possible when the conditions become favorable

Model-Independent Global Constraints on New Physics

Using effective-lagrangian techniques we perform a systematic survey of the lowest-dimension effective interactions through which heavy physics might manifest itself in present experiments. We do not restrict ourselves to special classes of effective interactions (such as `oblique' corrections). We compute the effects of these operators on all currently well-measured electroweak observables, both at low energies and at the $Z$ resonance, and perform a global fit to their coefficients. Despite the fact that a great many operators arise in our survey, we find that most are quite strongly bounded by the current data. We use our survey to systematically identify those effective interactions which are {\it not} well-bounded by the data -- these could very well include large new-physics contributions. Our results may also be used to efficiently confront specific models for new physics with the data, as we illustrate with an example.Comment: plain TeX, 68 pages, 2 figures (postscript files appended), McGill-93/12, NEIPH-93-008, OCIP/C-93-6, UQAM-PHE-93/08, UdeM-LPN-TH-93-15

A tutorial on Bayesian multi-model linear regression with BAS and JASP

Linear regression analyses commonly involve two consecutive stages of statistical inquiry. In the first stage, a single ‘best’ model is defined by a specific selection of relevant predictors; in the second stage, the regression coefficients of the winning model are used for prediction and for inference concerning the importance of the predictors. However, such second-stage inference ignores the model uncertainty from the first stage, resulting in overconfident parameter estimates that generalize poorly. These drawbacks can be overcome by model averaging, a technique that retains all models for inference, weighting each model’s contribution by its posterior probability. Although conceptually straightforward, model averaging is rarely used in applied research, possibly due to the lack of easily accessible software. To bridge the gap between theory and practice, we provide a tutorial on linear regression using Bayesian model averaging in JASP, based on the BAS package in R. Firstly, we provide theoretical background on linear regression, Bayesian inference, and Bayesian model averaging. Secondly, we demonstrate the method on an example data set from the World Happiness Report. Lastly, we discuss limitations of model averaging and directions for dealing with violations of model assumptions

Model of the Quark Mixing Matrix

The structure of the Cabibbo-Kobayashi-Maskawa (CKM) matrix is analyzed from the standpoint of a composite model. A model is constructed with three families of quarks, by taking tensor products of sufficient numbers of spin-1/2 representations and imagining the dominant terms in the mass matrix to arise from spin-spin interactions. Generic results then obtained include the familiar relation $|V_{us}| = (m_d/m_s)^{1/2} - (m_u/m_c)^{1/2}$, and a less frequently seen relation $|V_{cb}| = \sqrt{2} [(m_s/m_b) - (m_c/m_t)]$. The magnitudes of $V_{ub}$ and $V_{td}$ come out naturally to be of the right order. The phase in the CKM matrix can be put in by hand, but its origin remains obscure.Comment: Presented by Mihir P. Worah at DPF 92 Meeting, Fermilab, November, 1992. 3 pages, LaTeX fil