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Archive of posts filed under the Statistical computing category.

Bayesian nonparametric weighted sampling inference

Yajuan Si, Natesh Pillai, and I write: It has historically been a challenge to perform Bayesian inference in a design-based survey context. The present paper develops a Bayesian model for sampling inference using inverse-probability weights. We use a hierarchical approach in which we model the distribution of the weights of the nonsampled units in the […]

WAIC and cross-validation in Stan!

Aki and I write: The Watanabe-Akaike information criterion (WAIC) and cross-validation are methods for estimating pointwise out-of-sample prediction accuracy from a fitted Bayesian model. WAIC is based on the series expansion of leave-one-out cross-validation (LOO), and asymptotically they are equal. With finite data, WAIC and cross-validation address different predictive questions and thus it is useful […]

An interesting mosaic of a data programming course

Rajit Dasgupta writes: I have been working on a website, SlideRule that in its present state, is a catalog of online courses aggregated from over 35 providers. One of the products we are building on top of this is something called Learning Paths, which are essentially a sequence of Online Courses designed to help learners […]

Thermodynamic Monte Carlo: Michael Betancourt’s new method for simulating from difficult distributions and evaluating normalizing constants

I hate to keep bumping our scheduled posts but this is just too important and too exciting to wait. So it’s time to jump the queue. The news is a paper from Michael Betancourt that presents a super-cool new way to compute normalizing constants: A common strategy for inference in complex models is the relaxation […]

“The results (not shown) . . .”

Pro tip: Don’t believe any claims about results not shown in a paper. Even if the paper has been published. Even if it’s been cited hundreds of times. If the results aren’t shown, they haven’t been checked. I learned this the hard way after receiving this note from Bin Liu, who wrote: Today I saw […]

Once more on nonparametric measures of mutual information

Ben Murell writes: Our reply to Kinney and Atwal has come out ( along with their response ( I feel like they somewhat missed the point. If you’re still interested in this line of discussion, feel free to post, and maybe the Murrells and Kinney can bash it out in your comments! Background: Too many […]

Stan (& JAGS) Tutorial on Linear Mixed Models

Shravan Vasishth sent me an earlier draft of this tutorial he co-authored with Tanner Sorensen. I liked it, asked if I could blog about it, and in response, they’ve put together a convenient web page with links to the tutorial PDF, JAGS and Stan programs, and data: Fitting linear mixed models using JAGS and Stan: […]

Discovering general multidimensional associations

Continuing our discussion of general measures of correlations, Ben Murrell sends along this paper (with corresponding R package), which begins: When two variables are related by a known function, the coefficient of determination (denoted R-squared) measures the proportion of the total variance in the observations that is explained by that function. This quantifies the strength […]

Heller, Heller, and Gorfine on univariate and multivariate information measures

Malka Gorfine writes: We noticed that the important topic of association measures and tests came up again in your blog, and we have few comments in this regard. It is useful to distinguish between the univariate and multivariate methods. A consistent multivariate method can recognise dependence between two vectors of random variables, while a univariate […]

Bayesian Uncertainty Quantification for Differential Equations!

Mark Girolami points us to this paper and software (with Oksana Chkrebtii, David Campbell, and Ben Calderhead). They write: We develop a general methodology for the probabilistic integration of differential equations via model based updating of a joint prior measure on the space of functions and their temporal and spatial derivatives. This results in a […]