arXiv subjects

Alexander Ly

Publications and source records attributed to Alexander Ly.

14 recordsLinked to original sources

arXiv2025

An exploration of sequential Bayesian variable selection -- A comment on Garc\'{i}a-Donato et al. (2025). "Model uncertainty and missing data: An objective Bayesian perspective"

Our comment on Garc\'ia-Donato et al. (2025). "Model uncertainty and missing data: An objective Bayesian perspective" explores a further extension of the proposed methodology. Specifically, we consider the sequential setting where (potentially missing) data accumulate over time, with the goal of continuously monitoring statistical evidence, as opposed to assessing it only once data collection terminates. We explore a new variable selection method based on sequential model confidence sets, as proposed by Arnold et al. (2024), and show that it can help stabilise the inference of Garc\'ia-Donato et al. (2025). To be published as "Invited discussion" in Bayesian Analysis.

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arXiv2023

Empirical prior distributions for Bayesian meta-analyses of binary and time to event outcomes

Bayesian model-averaged meta-analysis allows quantification of evidence for both treatment effectiveness $\mu$ and across-study heterogeneity $\tau$. We use the Cochrane Database of Systematic Reviews to develop discipline-wide empirical prior distributions for $\mu$ and $\tau$ for meta-analyses of binary and time-to-event clinical trial outcomes. First, we use 50% of the database to estimate parameters of different required parametric families. Second, we use the remaining 50% of the database to select the best-performing parametric families and explore essential assumptions about the presence or absence of the treatment effectiveness and across-study heterogeneity in real data. We find that most meta-analyses of binary outcomes are more consistent with the absence of the meta-analytic effect or heterogeneity while meta-analyses of time-to-event outcomes are more consistent with the presence of the meta-analytic effect or heterogeneity. Finally, we use the complete database - with close to half a million trial outcomes - to propose specific empirical prior distributions, both for the field in general and for specific medical subdisciplines. An example from acute respiratory infections demonstrates how the proposed prior distributions can be used to conduct a Bayesian model-averaged meta-analysis in the open-source software R and JASP.

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arXiv2022

Evidential Calibration of Confidence Intervals

We present a novel and easy-to-use method for calibrating error-rate based confidence intervals to evidence-based support intervals. Support intervals are obtained from inverting Bayes factors based on a parameter estimate and its standard error. A $k$ support interval can be interpreted as "the observed data are at least $k$ times more likely under the included parameter values than under a specified alternative". Support intervals depend on the specification of prior distributions for the parameter under the alternative, and we present several types that allow different forms of external knowledge to be encoded. We also show how prior specification can to some extent be avoided by considering a class of prior distributions and then computing so-called minimum support intervals which, for a given class of priors, have a one-to-one mapping with confidence intervals. We also illustrate how the sample size of a future study can be determined based on the concept of support. Finally, we show how the bound for the type I error rate of Bayes factors leads to a bound for the coverage of support intervals. An application to data from a clinical trial illustrates how support intervals can lead to inferences that are both intuitive and informative.

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arXiv2021

History and Nature of the Jeffreys-Lindley Paradox

The Jeffreys-Lindley paradox exposes a rift between Bayesian and frequentist hypothesis testing that strikes at the heart of statistical inference. Contrary to what most current literature suggests, the paradox was central to the Bayesian testing methodology developed by Sir Harold Jeffreys in the late 1930s. Jeffreys showed that the evidence against a point-null hypothesis $\mathcal{H}_0$ scales with $\sqrt{n}$ and repeatedly argued that it would therefore be mistaken to set a threshold for rejecting $\mathcal{H}_0$ at a constant multiple of the standard error. Here we summarize Jeffreys's early work on the paradox and clarify his reasons for including the $\sqrt{n}$ term. The prior distribution is seen to play a crucial role; by implicitly correcting for selection, small parameter values are identified as relatively surprising under $\mathcal{H}_1$. We highlight the general nature of the paradox by presenting both a fully frequentist and a fully Bayesian version. We also demonstrate that the paradox does not depend on assigning prior mass to a point hypothesis, as is commonly believed.

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arXiv2021

Bayesian Model-Averaged Meta-Analysis in Medicine

We outline a Bayesian model-averaged meta-analysis for standardized mean differences in order to quantify evidence for both treatment effectiveness $\delta$ and across-study heterogeneity $\tau$. 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 $\delta$ and $\tau$. The relative predictive performance of the competing models and rival prior distributions was assessed using the remaining 50\% of the Cochrane Database. On average, $\mathcal{H}_1^r$ -- 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 $\mathcal{H}_1^r$, 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 Bayesian model-averaged meta-analysis in the open-source software R and JASP. The preregistered analysis plan is available at https://osf.io/zs3df/.

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arXiv2021

Generic E-Variables for Exact Sequential k-Sample Tests that allow for Optional Stopping

We develop E-variables for testing whether two or more data streams come from the same source or not, and more generally, whether the difference between the sources is larger than some minimal effect size. These E-variables lead to exact, nonasymptotic tests that remain safe, i.e. keep their type-I error guarantees, under flexible sampling scenarios such as optional stopping and continuation. In special cases our E-variables also have an optimal 'growth' property under the alternative. While the construction is generic, we illustrate it through the special case of k x 2 contingency tables, where we also allow for the incorporation of different restrictions on a composite alternative. Comparison to p-value analysis in simulations and a real-world example show that E-variables, through their flexibility, often allow for early stopping of data collection, thereby retaining similar power as classical methods, while also retaining the option of extending or combining data afterwards.

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arXiv2021

Bayes Factors for Peri-Null Hypotheses

A perennial objection against Bayes factor point-null hypothesis tests is that the point-null hypothesis is known to be false from the outset. We examine the consequences of approximating the sharp point-null hypothesis by a hazy `peri-null' hypothesis instantiated as a narrow prior distribution centered on the point of interest. The peri-null Bayes factor then equals the point-null Bayes factor multiplied by a correction term which is itself a Bayes factor. For moderate sample sizes, the correction term is relatively inconsequential; however, for large sample sizes the correction term becomes influential and causes the peri-null Bayes factor to be inconsistent and approach a limit that depends on the ratio of prior ordinates evaluated at the maximum likelihood estimate. We characterize the asymptotic behavior of the peri-null Bayes factor and briefly discuss suggestions on how to construct peri-null Bayes factor hypothesis tests that are also consistent.

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arXiv2020

Default Bayes Factors for Testing the (In)equality of Several Population Variances

Testing the (in)equality of variances is an important problem in many statistical applications. We develop default Bayes factor tests to assess the (in)equality of two or more population variances, as well as a test for whether the population variances equal a specific value. The resulting test can be used to check assumptions for commonly used procedures such as the $t$-test or ANOVA, or test substantive hypotheses concerning variances directly. We show that our Bayes factor fulfills a number of desiderata. Researchers may have directed hypotheses such as $\sigma_{1}^{2} > \sigma_{2}^{2}$, they may want to extend $\mathcal{H}_{0}$ to have a null-region, or wish to combine hypotheses about equality with hypotheses about inequality, for example $\sigma_{1}^{2} = \sigma_{2}^{2} > (\sigma_{3}^{2}, \sigma_{4}^{2})$. We extend our Bayes factor test to allow for these deviations from our proposed default and illustrate it on a number of practical examples. Our procedure is implemented in the R package $bfvartest$.

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arXiv2017

Bayesian Rank-Based Hypothesis Testing for the Rank Sum Test, the Signed Rank Test, and Spearman's $\rho$

Bayesian inference for rank-order problems is frustrated by the absence of an explicit likelihood function. This hurdle can be overcome by assuming a latent normal representation that is consistent with the ordinal information in the data: the observed ranks are conceptualized as an impoverished reflection of an underlying continuous scale, and inference concerns the parameters that govern the latent representation. We apply this generic data-augmentation method to obtain Bayes factors for three popular rank-based tests: the rank sum test, the signed rank test, and Spearman's $\rho_s$.

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arXiv2017

A Tutorial on Fisher Information

In many statistical applications that concern mathematical psychologists, the concept of Fisher information plays an important role. In this tutorial we clarify the concept of Fisher information as it manifests itself across three different statistical paradigms. First, in the frequentist paradigm, Fisher information is used to construct hypothesis tests and confidence intervals using maximum likelihood estimators; second, in the Bayesian paradigm, Fisher information is used to define a default prior; lastly, in the minimum description length paradigm, Fisher information is used to measure model complexity.

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arXiv2017

Informed Bayesian T-Tests

Across the empirical sciences, few statistical procedures rival the popularity of the frequentist t-test. In contrast, the Bayesian versions of the t-test have languished in obscurity. In recent years, however, the theoretical and practical advantages of the Bayesian t-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.

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arXiv2017

A Tutorial on Bridge Sampling

The marginal likelihood plays an important role in many areas of Bayesian statistics such as parameter estimation, model comparison, and model averaging. In most applications, however, the marginal likelihood is not analytically tractable and must be approximated using numerical methods. Here we provide a tutorial on bridge sampling (Bennett, 1976; Meng & Wong, 1996), a reliable and relatively straightforward sampling method that allows researchers to obtain the marginal likelihood for models of varying complexity. First, we introduce bridge sampling and three related sampling methods using the beta-binomial model as a running example. We then apply bridge sampling to estimate the marginal likelihood for the Expectancy Valence (EV) model---a popular model for reinforcement learning. Our results indicate that bridge sampling provides accurate estimates for both a single participant and a hierarchical version of the EV model. We conclude that bridge sampling is an attractive method for mathematical psychologists who typically aim to approximate the marginal likelihood for a limited set of possibly high-dimensional models.

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arXiv2017

Bayesian Estimation of Kendall's tau Using a Latent Normal Approach

The rank-based association between two variables can be modeled by introducing a latent normal level to ordinal data. We demonstrate how this approach yields Bayesian inference for Kendall's rank correlation coefficient, improving on a recent Bayesian solution from asymptotic properties of the test statistic.

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arXiv2015

Analytic Posteriors for Pearson's Correlation Coefficient

Pearson's correlation is one of the most common measures of linear dependence. Recently, Bernardo (2015) introduced a flexible class of priors to study this measure in a Bayesian setting. For this large class of priors we show that the (marginal) posterior for Pearson's correlation coefficient and all of the posterior moments are analytic. Our results are available in the open-source software package JASP.

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