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Andrew Gelman

Publications and source records attributed to Andrew Gelman.

At least 73 records · Page 4Linked to original sources

Expectation propagation as a way of life: A framework for Bayesian inference on partitioned data

A common divide-and-conquer approach for Bayesian computation with big data is to partition the data, perform local inference for each piece separately, and combine the results to obtain a global posterior approximation. While being conceptually and computationally appealing, this method involves the problematic need to also split the prior for the local inferences; these weakened priors may not provide enough regularization for each separate computation, thus eliminating one of the key advantages of Bayesian methods. To resolve this dilemma while still retaining the generalizability of the underlying local inference method, we apply the idea of expectation propagation (EP) as a framework for distributed Bayesian inference. The central idea is to iteratively update approximations to the local likelihoods given the state of the other approximations and the prior. The present paper has two roles: we review the steps that are needed to keep EP algorithms numerically stable, and we suggest a general approach, inspired by EP, for approaching data partitioning problems in a way that achieves the computational benefits of parallelism while allowing each local update to make use of relevant information from the other sites. In addition, we demonstrate how the method can be applied in a hierarchical context to make use of partitioning of both data and parameters. The paper describes a general algorithmic framework, rather than a specific algorithm, and presents an example implementation for it.

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The experiment is just as important as the likelihood in understanding the prior: A cautionary note on robust cognitive modelling

Cognitive modelling shares many features with statistical modelling, making it seem trivial to borrow from the practices of robust Bayesian statistics to protect the practice of robust cognitive modelling. We take one aspect of statistical workflow-prior predictive checks-and explore how they might be applied to a cognitive modelling task. We find that it is not only the likelihood that is needed to interpret the priors, we also need to incorporate experiment information as well. This suggests that while cognitive modelling might borrow from statistical practices, especially workflow, care must be made to make the adaptions necessary.

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The Political Significance of Social Penumbras

To explain the political clout of different social groups, traditional accounts typically focus on the group's size, resources, or commonality and intensity of its members' interests. We contend that a group's "penumbra"-the set of individuals who are personally familiar with people in that group--is another important explanatory factor that merits systematic analysis. To this end, we designed a panel study that allows us to learn about the characteristics of the penumbras of politically relevant groups such as gay people, the unemployed or recent immigrants. Our study reveals major and systematic differences in the penumbras of various social groups, even ones of similar size. Moreover, we find evidence that entering a group's penumbra is associated with a change in attitude on related political questions. Taken together, our findings suggest that penumbras help account for variation in the political standing of different groups in society.

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Many perspectives on Deborah Mayo's "Statistical Inference as Severe Testing: How to Get Beyond the Statistics Wars"

The new book by philosopher Deborah Mayo is relevant to data science for topical reasons, as she takes various controversial positions regarding hypothesis testing and statistical practice, and also as an entry point to thinking about the philosophy of statistics. The present article is a slightly expanded version of a series of informal reviews and comments on Mayo's book. We hope this discussion will introduce people to Mayo's ideas along with other perspectives on the topics she addresses.

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Abandon Statistical Significance

We discuss problems the null hypothesis significance testing (NHST) paradigm poses for replication and more broadly in the biomedical and social sciences as well as how these problems remain unresolved by proposals involving modified p-value thresholds, confidence intervals, and Bayes factors. We then discuss our own proposal, which is to abandon statistical significance. We recommend dropping the NHST paradigm--and the p-value thresholds intrinsic to it--as the default statistical paradigm for research, publication, and discovery in the biomedical and social sciences. Specifically, we propose that the p-value be demoted from its threshold screening role and instead, treated continuously, be considered along with currently subordinate factors (e.g., related prior evidence, plausibility of mechanism, study design and data quality, real world costs and benefits, novelty of finding, and other factors that vary by research domain) as just one among many pieces of evidence. We have no desire to "ban" p-values or other purely statistical measures. Rather, we believe that such measures should not be thresholded and that, thresholded or not, they should not take priority over the currently subordinate factors. We also argue that it seldom makes sense to calibrate evidence as a function of p-values or other purely statistical measures. We offer recommendations for how our proposal can be implemented in the scientific publication process as well as in statistical decision making more broadly.

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Yes, but Did It Work?: Evaluating Variational Inference

While it's always possible to compute a variational approximation to a posterior distribution, it can be difficult to discover problems with this approximation. We propose two diagnostic algorithms to alleviate this problem. The Pareto-smoothed importance sampling (PSIS) diagnostic gives a goodness of fit measurement for joint distributions, while simultaneously improving the error in the estimate. The variational simulation-based calibration (VSBC) assesses the average performance of point estimates.

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Large Scale Replication Projects in Contemporary Psychological Research

Replication is complicated in psychological research because studies of a given psychological phenomenon can never be direct or exact replications of one another, and thus effect sizes vary from one study of the phenomenon to the next--an issue of clear importance for replication. Current large scale replication projects represent an important step forward for assessing replicability, but provide only limited information because they have thus far been designed in a manner such that heterogeneity either cannot be assessed or is intended to be eliminated. Consequently, the non-trivial degree of heterogeneity found in these projects represents a lower bound on heterogeneity. We recommend enriching large scale replication projects going forward by em- bracing heterogeneity. We argue this is key for assessing replicability: if effect sizes are sufficiently heterogeneous--even if the sign of the effect is consistent--the phenomenon in question does not seem particularly replicable and the theory underlying it seems poorly constructed and in need of enrichment. Uncovering why and revising theory in light of it will lead to improved theory that explains heterogeneity and in- creases replicability. Given this, large scale replication projects can play an important role not only in assessing replicability but also in advancing theory.

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Visualization in Bayesian workflow

Bayesian data analysis is about more than just computing a posterior distribution, and Bayesian visualization is about more than trace plots of Markov chains. Practical Bayesian data analysis, like all data analysis, is an iterative process of model building, inference, model checking and evaluation, and model expansion. Visualization is helpful in each of these stages of the Bayesian workflow and it is indispensable when drawing inferences from the types of modern, high-dimensional models that are used by applied researchers.

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Bayesian Inference under Cluster Sampling with Probability Proportional to Size

Cluster sampling is common in survey practice, and the corresponding inference has been predominantly design-based. We develop a Bayesian framework for cluster sampling and account for the design effect in the outcome modeling. We consider a two-stage cluster sampling design where the clusters are first selected with probability proportional to cluster size, and then units are randomly sampled inside selected clusters. Challenges arise when the sizes of nonsampled cluster are unknown. We propose nonparametric and parametric Bayesian approaches for predicting the unknown cluster sizes, with this inference performed simultaneously with the model for survey outcome. Simulation studies show that the integrated Bayesian approach outperforms classical methods with efficiency gains. We use Stan for computing and apply the proposal to the Fragile Families and Child Wellbeing study as an illustration of complex survey inference in health surveys.

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Using stacking to average Bayesian predictive distributions

The widely recommended procedure of Bayesian model averaging is flawed in the M-open setting in which the true data-generating process is not one of the candidate models being fit. We take the idea of stacking from the point estimation literature and generalize to the combination of predictive distributions, extending the utility function to any proper scoring rule, using Pareto smoothed importance sampling to efficiently compute the required leave-one-out posterior distributions and regularization to get more stability. We compare stacking of predictive distributions to several alternatives: stacking of means, Bayesian model averaging (BMA), pseudo-BMA using AIC-type weighting, and a variant of pseudo-BMA that is stabilized using the Bayesian bootstrap. Based on simulations and real-data applications, we recommend stacking of predictive distributions, with BB-pseudo-BMA as an approximate alternative when computation cost is an issue.

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The prior can generally only be understood in the context of the likelihood

A key sticking point of Bayesian analysis is the choice of prior distribution, and there is a vast literature on potential defaults including uniform priors, Jeffreys' priors, reference priors, maximum entropy priors, and weakly informative priors. These methods, however, often manifest a key conceptual tension in prior modeling: a model encoding true prior information should be chosen without reference to the model of the measurement process, but almost all common prior modeling techniques are implicitly motivated by a reference likelihood. In this paper we resolve this apparent paradox by placing the choice of prior into the context of the entire Bayesian analysis, from inference to prediction to model evaluation.

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The statistical significance filter leads to overconfident expectations of replicability

We show that publishing results using the statistical significance filter---publishing only when the p-value is less than 0.05---leads to a vicious cycle of overoptimistic expectation of the replicability of results. First, we show analytically that when true statistical power is relatively low, computing power based on statistically significant results will lead to overestimates of power. Then, we present a case study using 10 experimental comparisons drawn from a recently published meta-analysis in psycholinguistics (Jäger et al., 2017). We show that the statistically significant results yield an illusion of replicability. This illusion holds even if the researcher doesn't conduct any formal power analysis but just uses statistical significance to informally assess robustness (i.e., replicability) of results.

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Fitting Bayesian item response models in Stata and Stan

Stata users have access to two easy-to-use implementations of Bayesian inference: Stata's native {\tt bayesmh} function and StataStan, which calls the general Bayesian engine Stan. We compare these on two models that are important for education research: the Rasch model and the hierarchical Rasch model. Stan (as called from Stata) fits a more general range of models than can be fit by {\tt bayesmh} and is also more scalable, in that it could easily fit models with at least ten times more parameters than could be fit using Stata's native Bayesian implementation. In addition, Stan runs between two and ten times faster than {\tt bayesmh} as measured in effective sample size per second: that is, compared to Stan, it takes Stata's built-in Bayesian engine twice to ten times as long to get inferences with equivalent precision. We attribute Stan's advantage in flexibility to its general modeling language, and its advantages in scalability and speed to an efficient sampling algorithm: Hamiltonian Monte Carlo using the no-U-turn sampler. In order to further investigate scalability, we also compared to the package Jags, which performed better than Stata's native Bayesian engine but not as well as StataStan. Given its advantages in speed, generality, and scalability, and that Stan is open-source and can be run directly from Stata using StataStan, we recommend that Stata users adopt Stan as their Bayesian inference engine of choice.

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Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC

Leave-one-out cross-validation (LOO) and the widely applicable information criterion (WAIC) are methods for estimating pointwise out-of-sample prediction accuracy from a fitted Bayesian model using the log-likelihood evaluated at the posterior simulations of the parameter values. LOO and WAIC have various advantages over simpler estimates of predictive error such as AIC and DIC but are less used in practice because they involve additional computational steps. Here we lay out fast and stable computations for LOO and WAIC that can be performed using existing simulation draws. We introduce an efficient computation of LOO using Pareto-smoothed importance sampling (PSIS), a new procedure for regularizing importance weights. Although WAIC is asymptotically equal to LOO, we demonstrate that PSIS-LOO is more robust in the finite case with weak priors or influential observations. As a byproduct of our calculations, we also obtain approximate standard errors for estimated predictive errors and for comparing of predictive errors between two models. We implement the computations in an R package called 'loo' and demonstrate using models fit with the Bayesian inference package Stan.

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The 2008 election: A preregistered replication analysis

We present an increasingly stringent set of replications of Ghitza & Gelman (2013), a multilevel regression and poststratification analysis of polls from the 2008 U.S. presidential election campaign, focusing on a set of plots showing the estimated Republican vote share for whites and for all voters, as a function of income level in each of the states. We start with a nearly-exact duplication that uses the posted code and changes only the model-fitting algorithm; we then replicate using already-analyzed data from 2004; and finally we set up preregistered replications using two surveys from 2008 that we had not previously looked at. We have already learned from our preliminary, non-preregistered replication, which has revealed a potential problem with the published analysis of Ghitza & Gelman (2013); it appears that our model may not sufficiently account for nonsampling error, and that some of the patterns presented in that earlier paper may simply reflect noise. In addition to the substantive interest in validating earlier findings about demographics, geography, and voting, the present project serves as a demonstration of preregistration in a setting where the subject matter is historical (and thus the replication data exist before the preregistration plan is written) and where the analysis is exploratory (and thus a replication cannot be simply deemed successful or unsuccessful based on the statistical significance of some particular comparison).

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Automatic Differentiation Variational Inference

Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist only provides a probabilistic model and a dataset, nothing else. ADVI automatically derives an efficient variational inference algorithm, freeing the scientist to refine and explore many models. ADVI supports a broad class of models-no conjugacy assumptions are required. We study ADVI across ten different models and apply it to a dataset with millions of observations. ADVI is integrated into Stan, a probabilistic programming system; it is available for immediate use.

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