Bayesian Compressed Regression

As an alternative to variable selection or shrinkage in high dimensional regression, we propose to randomly compress the predictors prior to analysis. This dramatically reduces storage and computational bottlenecks, performing well when the predictors can be projected to a low dimensional linear subspace with minimal loss of information about the response. As opposed to existing Bayesian dimensionality reduction approaches, the exact posterior distribution conditional on the compressed data is available analytically, speeding up computation by many orders of magnitude while also bypassing robustness issues due to convergence and mixing problems with MCMC. Model averaging is used to reduce sensitivity to the random projection matrix, while accommodating uncertainty in the subspace dimension. Strong theoretical support is provided for the approach by showing near parametric convergence rates for the predictive density in the large p small n asymptotic paradigm. Practical performance relative to competitors is illustrated in simulations and real data applications.Comment: 29 pages, 4 figure

A Method for Compressing Parameters in Bayesian Models with Application to Logistic Sequence Prediction Models

Bayesian classification and regression with high order interactions is largely infeasible because Markov chain Monte Carlo (MCMC) would need to be applied with a great many parameters, whose number increases rapidly with the order. In this paper we show how to make it feasible by effectively reducing the number of parameters, exploiting the fact that many interactions have the same values for all training cases. Our method uses a single ``compressed'' parameter to represent the sum of all parameters associated with a set of patterns that have the same value for all training cases. Using symmetric stable distributions as the priors of the original parameters, we can easily find the priors of these compressed parameters. We therefore need to deal only with a much smaller number of compressed parameters when training the model with MCMC. The number of compressed parameters may have converged before considering the highest possible order. After training the model, we can split these compressed parameters into the original ones as needed to make predictions for test cases. We show in detail how to compress parameters for logistic sequence prediction models. Experiments on both simulated and real data demonstrate that a huge number of parameters can indeed be reduced by our compression method.Comment: 29 page

Sparse Probit Linear Mixed Model

Linear Mixed Models (LMMs) are important tools in statistical genetics. When used for feature selection, they allow to find a sparse set of genetic traits that best predict a continuous phenotype of interest, while simultaneously correcting for various confounding factors such as age, ethnicity and population structure. Formulated as models for linear regression, LMMs have been restricted to continuous phenotypes. We introduce the Sparse Probit Linear Mixed Model (Probit-LMM), where we generalize the LMM modeling paradigm to binary phenotypes. As a technical challenge, the model no longer possesses a closed-form likelihood function. In this paper, we present a scalable approximate inference algorithm that lets us fit the model to high-dimensional data sets. We show on three real-world examples from different domains that in the setup of binary labels, our algorithm leads to better prediction accuracies and also selects features which show less correlation with the confounding factors.Comment: Published version, 21 pages, 6 figure

Structured Sparse Modelling with Hierarchical GP

In this paper a new Bayesian model for sparse linear regression with a spatio-temporal structure is proposed. It incorporates the structural assumptions based on a hierarchical Gaussian process prior for spike and slab coefficients. We design an inference algorithm based on Expectation Propagation and evaluate the model over the real data.Comment: SPARS 201

Statistical Mechanics of High-Dimensional Inference

To model modern large-scale datasets, we need efficient algorithms to infer a set of $P$ unknown model parameters from $N$ noisy measurements. What are fundamental limits on the accuracy of parameter inference, given finite signal-to-noise ratios, limited measurements, prior information, and computational tractability requirements? How can we combine prior information with measurements to achieve these limits? Classical statistics gives incisive answers to these questions as the measurement density $\alpha = \frac{N}{P}\rightarrow \infty$. However, these classical results are not relevant to modern high-dimensional inference problems, which instead occur at finite $\alpha$. We formulate and analyze high-dimensional inference as a problem in the statistical physics of quenched disorder. Our analysis uncovers fundamental limits on the accuracy of inference in high dimensions, and reveals that widely cherished inference algorithms like maximum likelihood (ML) and maximum-a posteriori (MAP) inference cannot achieve these limits. We further find optimal, computationally tractable algorithms that can achieve these limits. Intriguingly, in high dimensions, these optimal algorithms become computationally simpler than MAP and ML, while still outperforming them. For example, such optimal algorithms can lead to as much as a 20% reduction in the amount of data to achieve the same performance relative to MAP. Moreover, our analysis reveals simple relations between optimal high dimensional inference and low dimensional scalar Bayesian inference, insights into the nature of generalization and predictive power in high dimensions, information theoretic limits on compressed sensing, phase transitions in quadratic inference, and connections to central mathematical objects in convex optimization theory and random matrix theory.Comment: See http://ganguli-gang.stanford.edu/pdf/HighDimInf.Supp.pdf for supplementary materia