More Like this

1. Large-scale model selection in misspecified generalized linear models

   https://doi.org/10.1093/biomet/asab005  

   Demirkaya, Emre; Feng, Yang; Basu, Pallavi; Lv, Jinchi (January 2021, Biometrika)

   Summary Model selection is crucial both to high-dimensional learning and to inference for contemporary big data applications in pinpointing the best set of covariates among a sequence of candidate interpretable models. Most existing work implicitly assumes that the models are correctly specified or have fixed dimensionality, yet both model misspecification and high dimensionality are prevalent in practice. In this paper, we exploit the framework of model selection principles under the misspecified generalized linear models presented in Lv & Liu (2014), and investigate the asymptotic expansion of the posterior model probability in the setting of high-dimensional misspecified models. With a natural choice of prior probabilities that encourages interpretability and incorporates the Kullback–Leibler divergence, we suggest using the high-dimensional generalized Bayesian information criterion with prior probability for large-scale model selection with misspecification. Our new information criterion characterizes the impacts of both model misspecification and high dimensionality on model selection. We further establish the consistency of covariance contrast matrix estimation and the model selection consistency of the new information criterion in ultrahigh dimensions under some mild regularity conditions. Our numerical studies demonstrate that the proposed method enjoys improved model selection consistency over its main competitors. 

   more » « less
2. Statistical Optimality and Stability of Tangent Transform Algorithms in Logit Models

   Ghosh, I. (July 2022, Journal of machine learning research)

   Pierre Alquier (Ed.)

   A systematic approach to finding variational approximation in an otherwise intractable non-conjugate model is to exploit the general principle of convex duality by minorizing the marginal likelihood that renders the problem tractable. While such approaches are popular in the context of variational inference in non-conjugate Bayesian models, theoretical guarantees on statistical optimality and algorithmic convergence are lacking. Focusing on logistic regression models, we provide mild conditions on the data generating process to derive non-asymptotic upper bounds to the risk incurred by the variational optima. We demonstrate that these assumptions can be completely relaxed if one considers a slight variation of the algorithm by raising the likelihood to a fractional power. Next, we utilize the theory of dynamical systems to provide convergence guarantees for such algorithms in logistic and multinomial logit regression. In particular, we establish local asymptotic stability of the algorithm without any assumptions on the data-generating process. We explore a special case involving a semi-orthogonal design under which a global convergence is obtained. The theory is further illustrated using several numerical studies. 

   more » « less
3. Bayesian inference: more than Bayes’s theorem

   https://doi.org/10.3389/fspas.2024.1326926  

   Loredo, Thomas J; Wolpert, Robert L (October 2024, Frontiers in Astronomy and Space Sciences)

   Bayesian inference gets its name fromBayes’s theorem, expressing posterior probabilities for hypotheses about a data generating process as the (normalized) product of prior probabilities and a likelihood function. But Bayesian inference uses all of probability theory, not just Bayes’s theorem. Many hypotheses of scientific interest arecomposite hypotheses, with the strength of evidence for the hypothesis dependent on knowledge about auxiliary factors, such as the values of nuisance parameters (e.g., uncertain background rates or calibration factors). Many important capabilities of Bayesian methods arise from use of the law of total probability, which instructs analysts to compute probabilities for composite hypotheses bymarginalizationover auxiliary factors. This tutorial targets relative newcomers to Bayesian inference, aiming to complement tutorials that focus on Bayes’s theorem and how priors modulate likelihoods. The emphasis here is on marginalization over parameter spaces—both how it is the foundation for important capabilities, and how it may motivate caution when parameter spaces are large. Topics covered include the difference between likelihood and probability, understanding the impact of priors beyond merely shifting the maximum likelihood estimate, and the role of marginalization in accounting for uncertainty in nuisance parameters, systematic error, and model misspecification. 

   more » « less
4. Approximate Post-Selective Inference for Regression with the Group LASSO

   Panigrahi, Snigdha; MacDonald, Peter W; Kessler, Daniel (March 2023, Journal of machine learning research)

   After selection with the Group LASSO (or generalized variants such as the overlapping, sparse, or standardized Group LASSO), inference for the selected parameters is unreliable in the absence of adjustments for selection bias. In the penalized Gaussian regression setup, existing approaches provide adjustments for selection events that can be expressed as linear inequalities in the data variables. Such a representation, however, fails to hold for selection with the Group LASSO and substantially obstructs the scope of subsequent post-selective inference. Key questions of inferential interest—for example, inference for the effects of selected variables on the outcome—remain unanswered. In the present paper, we develop a consistent, post-selective, Bayesian method to address the existing gaps by deriving a likelihood adjustment factor and an approximation thereof that eliminates bias from the selection of groups. Experiments on simulated data and data from the Human Connectome Project demonstrate that our method recovers the effects of parameters within the selected groups while paying only a small price for bias adjustment. 

   more » « less
5. Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

   https://doi.org/10.1093/sysbio/syad074  

   Thompson, Ammon; Liebeskind, Benjamin J; Scully, Erik J; Landis, Michael J (January 2024, Systematic Biology)

   Perez, Manolo (Ed.)

   Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models. 

   more » « less