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Register a new userBayesian Inference in High-Dimensional Time-Serieswith the Orthogonal Stochastic Linear Mixing Model
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Many modern time-series datasets contain large numbers of output response variables sampled for prolonged periods of time. For example, in neuroscience, the activities of 100s-1000s of neurons are recorded during behaviors and in response to sensory stimuli. Multi-output Gaussian process models leverage the nonparametric nature of Gaussian processes to capture structure across multiple outputs. However, this class of models typically assumes that the correlations between the output response variables are invariant in the input space. Stochastic linear mixing models (SLMM) assume the mixture coefficients depend on input, making them more flexible and effective to capture complex output dependence. However, currently, the inference for SLMMs is intractable for large datasets, making them inapplicable to several modern time-series problems. In this paper, we propose a new regression framework, the orthogonal stochastic linear mixing model (OSLMM) that introduces an orthogonal constraint amongst the mixing coefficients. This constraint reduces the computational burden of inference while retaining the capability to handle complex output dependence. We provide Markov chain Monte Carlo inference procedures for both SLMM and OSLMM and demonstrate superior model scalability and reduced prediction error of OSLMM compared with state-of-the-art methods on several real-world applications. In neurophysiology recordings, we use the inferred latent functions for compact visualization of population responses to auditory stimuli, and demonstrate superior results compared to a competing method (GPFA). Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale time-series datasets.
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Spike-and-slab priors are popular Bayesian solutions for high-dimensional linear regression problems. Previous theoretical studies on spike-and-slab methods focus on specific prior formulations and use prior-dependent conditions and analyses, and thus can not be generalized directly. In this paper, we propose a class of generic spike-and-slab priors and develop a unified framework to rigorously assess their theoretical properties. Technically, we provide general conditions under which generic spike-and-slab priors can achieve the nearly-optimal posterior contraction rate and the model selection consistency. Our results include those of Narisetty and He (2014) and Castillo et al. (2015) as special cases.
We describe a series of algorithms that efficiently implement Gaussian model-X knockoffs to control the false discovery rate on large scale feature selection problems. Identifying the knockoff distribution requires solving a large scale semidefinite program for which we derive several efficient methods. One handles generic covariance matrices, has a complexity scaling as $O(p^3)$ where $p$ is the ambient dimension, while another assumes a rank $k$ factor model on the covariance matrix to reduce this complexity bound to $O(pk^2)$. We also derive efficient procedures to both estimate factor models and sample knockoff covariates with complexity linear in the dimension. We test our methods on problems with $p$ as large as $500,000$.
Many scientific problems require identifying a small set of covariates that are associated with a target response and estimating their effects. Often, these effects are nonlinear and include interactions, so linear and additive methods can lead to poor estimation and variable selection. The Bayesian framework makes it straightforward to simultaneously express sparsity, nonlinearity, and interactions in a hierarchical model. But, as for the few other methods that handle this trifecta, inference is computationally intractable - with runtime at least quadratic in the number of covariates, and often worse. In the present work, we solve this computational bottleneck. We first show that suitable Bayesian models can be represented as Gaussian processes (GPs). We then demonstrate how a kernel trick can reduce computation with these GPs to O(# covariates) time for both variable selection and estimation. Our resulting fit corresponds to a sparse orthogonal decomposition of the regression function in a Hilbert space (i.e., a functional ANOVA decomposition), where interaction effects represent all variation that cannot be explained by lower-order effects. On a variety of synthetic and real datasets, our approach outperforms existing methods used for large, high-dimensional datasets while remaining competitive (or being orders of magnitude faster) in runtime.
We study high-dimensional regression with missing entries in the covariates. A common strategy in practice is to emph{impute} the missing entries with an appropriate substitute and then implement a standard statistical procedure acting as if the covariates were fully observed. Recent literature on this subject proposes instead to design a specific, often complicated or non-convex, algorithm tailored to the case of missing covariates. We investigate a simpler approach where we fill-in the missing entries with their conditional mean given the observed covariates. We show that this imputation scheme coupled with standard off-the-shelf procedures such as the LASSO and square-root LASSO retains the minimax estimation rate in the random-design setting where the covariates are i.i.d. sub-Gaussian. We further show that the square-root LASSO remains emph{pivotal} in this setting. It is often the case that the conditional expectation cannot be computed exactly and must be approximated from data. We study two cases where the covariates either follow an autoregressive (AR) process, or are jointly Gaussian with sparse precision matrix. We propose tractable estimators for the conditional expectation and then perform linear regression via LASSO, and show similar estimation rates in both cases. We complement our theoretical results with simulations on synthetic and semi-synthetic examples, illustrating not only the sharpness of our bounds, but also the broader utility of this strategy beyond our theoretical assumptions.
We study high-dimensional Bayesian linear regression with product priors. Using the nascent theory of non-linear large deviations (Chatterjee and Dembo,2016), we derive sufficient conditions for the leading-order correctness of the naive mean-field approximation to the log-normalizing constant of the posterior distribution. Subsequently, assuming a true linear model for the observed data, we derive a limiting infinite dimensional variational formula for the log normalizing constant of the posterior. Furthermore, we establish that under an additional separation condition, the variational problem has a unique optimizer, and this optimizer governs the probabilistic properties of the posterior distribution. We provide intuitive sufficient conditions for the validity of this separation condition. Finally, we illustrate our results on concrete examples with specific design matrices.
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