Archive for Data augmentation

congrats [IMS related]

Posted in Statistics with tags , , , , , , , , , , , on July 21, 2021 by xi'an

When I read through the June-July issue of the IMS Bulletin, I saw many causes for celebration and congratulations!, from Richard Samworth’s award of an Advanced ERC grant, to the new IMS fellows, including my friends, Ismael Castillo, Steve Mc Eachern, and Natesh Pillai, as well as my current or former associate editors, Johan Segers (JRSS B) and Changbao Wu (Biometrika). To my friends Alicia Carriquiry, David Dunson, and Tamara Broderick receiving 2021 COPSS awards, along others, including Wing Hung Wong (of the precursor Tanner & Wong, 1987 fame!). Natesh also figures among the “Quadfecta 23”, the exclusive club of authors having published at least one paper in each of the four Annals published by the IMS!

Roberto Casarin’s talk at CREST tomorrow

Posted in Statistics with tags , , , , , , , , , , , on March 13, 2019 by xi'an

My former student and friend Roberto Casarin (University Ca’Foscari, Venice) will talk tomorrow at the CREST Financial Econometrics seminar on

“Bayesian Markov Switching Tensor Regression for Time-varying Networks”

Time: 10:30
Date: 14 March 2019
Place: Room 3001, ENSAE, Université Paris-Saclay

Abstract : We propose a new Bayesian Markov switching regression model for multi-dimensional arrays (tensors) of binary time series. We assume a zero-inflated logit dynamics with time-varying parameters and apply it to multi-layer temporal networks. The original contribution is threefold. First, in order to avoid over-fitting we propose a parsimonious parameterisation of the model, based on a low-rank decomposition of the tensor of regression coefficients. Second, the parameters of the tensor model are driven by a hidden Markov chain, thus allowing for structural changes. The regimes are identified through prior constraints on the mixing probability of the zero-inflated model. Finally, we model the jointly dynamics of the network and of a set of variables of interest. We follow a Bayesian approach to inference, exploiting the Pólya-Gamma data augmentation scheme for logit models in order to provide an efficient Gibbs sampler for posterior approximation. We show the effectiveness of the sampler on simulated datasets of medium-big sizes, finally we apply the methodology to a real dataset of financial networks.

inefficiency of data augmentation for large samples

Posted in Books, pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , on May 31, 2016 by xi'an

On Monday, James Johndrow, Aaron Smith, Natesh Pillai, and David Dunson arXived a paper on the diminishing benefits of using data augmentation for large and highly imbalanced categorical data. They reconsider the data augmentation scheme of Tanner and Wong (1987), surprisingly not mentioned, used in the first occurrences of the Gibbs sampler like Albert and Chib’s (1993) or our mixture estimation paper with Jean Diebolt (1990). The central difficulty with data augmentation is that the distribution to be simulated operates on a space that is of order O(n), even when the original distribution covers a single parameter. As illustrated by the coalescent in population genetics (and the subsequent intrusion of the ABC methodology), there are well-known cases when the completion is near to impossible and clearly inefficient (as again illustrated by the failure of importance sampling strategies on the coalescent). The paper provides spectral gaps for the logistic and probit regression completions, which are of order a power of log(n) divided by √n, when all observations are equal to one. In a somewhat related paper with Jim Hobert and Vivek Roy, we studied the spectral gap for mixtures with a small number of observations: I wonder at the existence of a similar result in this setting, when all observations stem from one component of the mixture, when all observations are one. The result in this paper is theoretically appealing, the more because the posteriors associated with such models are highly regular and very close to Gaussian (and hence not that challenging as argued by Chopin and Ridgway). And because the data augmentation algorithm is uniformly ergodic in this setting (as we established with Jean Diebolt  and later explored with Richard Tweedie). As demonstrated in the  experiment produced in the paper, when comparing with HMC and Metropolis-Hastings (same computing times?), which produce much higher effective sample sizes.

corrected MCMC samplers for multivariate probit models

Posted in Books, pictures, R, Statistics, University life with tags , , , , , , , , on May 6, 2015 by xi'an

“Moreover, IvD point out an error in Nobile’s derivation which can alter its stationary distribution. Ironically, as we shall see, the algorithms of IvD also contain an error.”

 Xiyun Jiao and David A. van Dyk arXived a paper correcting an MCMC sampler and R package MNP for the multivariate probit model, proposed by Imai and van Dyk in 2005. [Hence the abbreviation IvD in the above quote.] Earlier versions of the Gibbs sampler for the multivariate probit model by Rob McCulloch and Peter Rossi in 1994, with a Metropolis update added by Agostino Nobile, and finally an improved version developed by Imai and van Dyk in 2005. As noted in the above quote, Jiao and van Dyk have discovered two mistakes in this latest version, jeopardizing the validity of the output.

IvDykThe multivariate probit model considered here is a multinomial model where the occurrence of the k-th category is represented as the k-th component of a (multivariate) normal (correlated) vector being the largest of all components. The latent normal model being non-identifiable since invariant by either translation or scale, identifying constraints are used in the literature. This means using a covariance matrix of the form Σ/trace(Σ), where Σ is an inverse Wishart random matrix. In their 2005 implementation, relying on marginal data augmentation—which essentially means simulating the non-identifiable part repeatedly at various steps of the data augmentation algorithm—, Imai and van Dyk missed a translation term and a constraint on the simulated matrices that lead to simulations outside the rightful support, as illustrated from the above graph [snapshot from the arXived paper].

IvDyk1Since the IvD method is used in many subsequent papers, it is quite important that these mistakes are signalled and corrected. [Another snapshot above shows how much both algorithm differ!] Without much thinking about this, I [thus idly] wonder why an identifying prior is not taking the place of a hard identifying constraint, as it should solve the issue more nicely. In that it would create less constraints and more entropy (!) in exploring the augmented space, while theoretically providing a convergent approximation of the identifiable parts. I may (must!) however miss an obvious constraint preventing this implementation.

recycling accept-reject rejections (#2)

Posted in R, Statistics, University life with tags , , , , , , on July 2, 2014 by xi'an

Following yesterday’s post on Rao’s, Liu’s, and Dunson’s paper on a new approach to intractable normalising constants, and taking advantage of being in Warwick, I tested the method on a toy model, namely the posterior associated with n Student’s t observations with unknown location parameter μ and a flat prior,

x_1,\ldots,x_n \sim p(x|\mu) \propto \left[ 1+(x-\mu)^2/\nu \right]^{-(\nu+1)/2}

which is “naturally” bounded by a Cauchy density with scale √ν. The constant M is then easily derived and running the new algorithm follows from a normal random walk proposal targeting the augmented likelihood (R code below).

dunsonAs shown by the above graph, the completion-by-rejection scheme produces a similar outcome (tomato) as the one based on the sole observations (steelblue). With a similar acceptance rate. However, the computing time is much much degraded:

> system.time(g8())
   user  system elapsed
 53.751   0.056  54.103
> system.time(g9())
   user  system elapsed
  1.156   0.000   1.161

when compared with the no-completion version. Here is the entire R code that produced both MCMC samples: Continue reading

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