Heavy-tailed error distributions and predictors with anomalous values are ubiquitous in high-dimensional regression problems and can seriously jeopardize the validity of statistical analyses if not properly addressed. For more reliable estimation under these adverse conditions, we propose a new robust regularized estimator for simultaneous variable selection and coefficient estimation. This estimator, called adaptive PENSE, possesses the oracle property without prior knowledge of the scale of the residuals and without any moment conditions on the error distribution. The proposed estimator gives reliable results even under very heavy-tailed error distributions and aberrant contamination in the predictors or residuals. Importantly, even in these challenging settings variable selection by adaptive PENSE remains stable. Numerical studies on simulated and real data sets highlight superior finite-sample performance in a vast range of settings compared to other robust regularized estimators in the case of contaminated samples and competitiveness compared to classical regularized estimators in clean samples.
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. Unfortunately, methods that simultaneously express sparsity, nonlinearity, and interactions are 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 show that suitable interaction models have a kernel representation, namely there exists a "kernel trick" to perform variable selection and estimation in $O$(# covariates) time. 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 data sets, our approach outperforms existing methods used for large, high-dimensional data sets while remaining competitive (or being orders of magnitude faster) in runtime.
Discovering the partial differential equations underlying spatio-temporal datasets from very limited and highly noisy observations is of paramount interest in many scientific fields. However, it remains an open question to know when model discovery algorithms based on sparse regression can actually recover the underlying physical processes. In this work, we show the design matrices used to infer the equations by sparse regression can violate the irrepresentability condition (IRC) of the Lasso, even when derived from analytical PDE solutions (i.e. without additional noise). Sparse regression techniques which can recover the true underlying model under violated IRC conditions are therefore required, leading to the introduction of the randomised adaptive Lasso. We show once the latter is integrated within the deep learning model discovery framework DeepMod, a wide variety of nonlinear and chaotic canonical PDEs can be recovered: (1) up to $\mathcal{O}(2)$ higher noise-to-sample ratios than state-of-the-art algorithms, (2) with a single set of hyperparameters, which paves the road towards truly automated model discovery.
Scoring systems are highly interpretable and widely used to evaluate time-to-event outcomes in healthcare research. However, existing time-to-event scores are predominantly created ad-hoc using a few manually selected variables based on clinician's knowledge, suggesting an unmet need for a robust and efficient generic score-generating method. AutoScore was previously developed as an interpretable machine learning score generator, integrated both machine learning and point-based scores in the strong discriminability and accessibility. We have further extended it to time-to-event data and developed AutoScore-Survival, for automatically generating time-to-event scores with right-censored survival data. Random survival forest provides an efficient solution for selecting variables, and Cox regression was used for score weighting. We illustrated our method in a real-life study of 90-day mortality of patients in intensive care units and compared its performance with survival models (i.e., Cox) and the random survival forest. The AutoScore-Survival-derived scoring model was more parsimonious than survival models built using traditional variable selection methods (e.g., penalized likelihood approach and stepwise variable selection), and its performance was comparable to survival models using the same set of variables. Although AutoScore-Survival achieved a comparable integrated area under the curve of 0.782 (95% CI: 0.767-0.794), the integer-valued time-to-event scores generated are favorable in clinical applications because they are easier to compute and interpret. Our proposed AutoScore-Survival provides an automated, robust and easy-to-use machine learning-based clinical score generator to studies of time-to-event outcomes. It provides a systematic guideline to facilitate the future development of time-to-event scores for clinical applications.
Many problems require the selection of a subset of variables from a full set of optimization variables. The computational complexity of an exhaustive search over all possible subsets of variables is, however, prohibitively expensive, necessitating more efficient but potentially suboptimal search strategies. We focus on sparse variable selection for generalized Rayleigh quotient optimization and generalized eigenvalue problems. Such problems often arise in the signal processing field, e.g., in the design of optimal data-driven filters. We extend and generalize existing work on convex optimization-based variable selection using semidefinite relaxations toward group-sparse variable selection using the $\ell_{1,\infty}$-norm. This group-sparsity allows, for instance, to perform sensor selection for spatio-temporal (instead of purely spatial) filters, and to select variables based on multiple generalized eigenvectors instead of only the dominant one. Furthermore, we extensively compare our method to state-of-the-art methods for sensor selection for spatio-temporal filter design in a simulated sensor network setting. The results show both the proposed algorithm and backward greedy selection method best approximate the exhaustive solution. However, the backward greedy selection has more specific failure cases, in particular for ill-conditioned covariance matrices. As such, the proposed algorithm is the most robust currently available method for group-sparse variable selection in generalized eigenvalue problems.
Sorted l1 regularization has been incorporated into many methods for solving high-dimensional statistical estimation problems, including the SLOPE estimator in linear regression. In this paper, we study how this relatively new regularization technique improves variable selection by characterizing the optimal SLOPE trade-off between the false discovery proportion (FDP) and true positive proportion (TPP) or, equivalently, between measures of type I error and power. Assuming a regime of linear sparsity and working under Gaussian random designs, we obtain an upper bound on the optimal trade-off for SLOPE, showing its capability of breaking the Donoho-Tanner power limit. To put it into perspective, this limit is the highest possible power that the Lasso, which is perhaps the most popular l1-based method, can achieve even with arbitrarily strong effect sizes. Next, we derive a tight lower bound that delineates the fundamental limit of sorted l1 regularization in optimally trading the FDP off for the TPP. Finally, we show that on any problem instance, SLOPE with a certain regularization sequence outperforms the Lasso, in the sense of having a smaller FDP, larger TPP and smaller l2 estimation risk simultaneously. Our proofs are based on a novel technique that reduces a calculus of variations problem to a class of infinite-dimensional convex optimization problems and a very recent result from approximate message passing theory.
It is a long-standing question to discover causal relations among a set of variables in many empirical sciences. Recently, Reinforcement Learning (RL) has achieved promising results in causal discovery from observational data. However, searching the space of directed graphs and enforcing acyclicity by implicit penalties tend to be inefficient and restrict the existing RL-based method to small scale problems. In this work, we propose a novel RL-based approach for causal discovery, by incorporating RL into the ordering-based paradigm. Specifically, we formulate the ordering search problem as a multi-step Markov decision process, implement the ordering generating process with an encoder-decoder architecture, and finally use RL to optimize the proposed model based on the reward mechanisms designed for~each ordering. A generated ordering would then be processed using variable selection to obtain the final causal graph. We analyze the consistency and computational complexity of the proposed method, and empirically show that a pretrained model can be exploited to accelerate training. Experimental results on both synthetic and real data sets shows that the proposed method achieves a much improved performance over existing RL-based method.
Best subset of groups selection (BSGS) is the process of selecting a small part of non-overlapping groups to achieve the best interpretability on the response variable. It has attracted increasing attention and has far-reaching applications in practice. However, due to the computational intractability of BSGS in high-dimensional settings, developing efficient algorithms for solving BSGS remains a research hotspot. In this paper,we propose a group-splicing algorithm that iteratively detects the relevant groups and excludes the irrelevant ones. Moreover, coupled with a novel group information criterion, we develop an adaptive algorithm to determine the optimal model size. Under mild conditions, it is certifiable that our algorithm can identify the optimal subset of groups in polynomial time with high probability. Finally, we demonstrate the efficiency and accuracy of our methods by comparing them with several state-of-the-art algorithms on both synthetic and real-world datasets.
We present a new algorithmic framework for grouped variable selection that is based on discrete mathematical optimization. While there exist several appealing approaches based on convex relaxations and nonconvex heuristics, we focus on optimal solutions for the $\ell_0$-regularized formulation, a problem that is relatively unexplored due to computational challenges. Our methodology covers both high-dimensional linear regression and nonparametric sparse additive modeling with smooth components. Our algorithmic framework consists of approximate and exact algorithms. The approximate algorithms are based on coordinate descent and local search, with runtimes comparable to popular sparse learning algorithms. Our exact algorithm is based on a standalone branch-and-bound (BnB) framework, which can solve the associated mixed integer programming (MIP) problem to certified optimality. By exploiting the problem structure, our custom BnB algorithm can solve to optimality problem instances with $5 \times 10^6$ features and $10^3$ observations in minutes to hours -- over $1000$ times larger than what is currently possible using state-of-the-art commercial MIP solvers. We also explore statistical properties of the $\ell_0$-based estimators. We demonstrate, theoretically and empirically, that our proposed estimators have an edge over popular group-sparse estimators in terms of statistical performance in various regimes. We provide an open-source implementation of our proposed framework.
The missing data issue is ubiquitous in health studies. Variable selection in the presence of both missing covariates and outcomes is an important statistical research topic but has been less studied. Existing literature focuses on parametric regression techniques that provide direct parameter estimates of the regression model. Flexible nonparametric machine learning methods considerably mitigate the reliance on the parametric assumptions, but do not provide as naturally defined variable importance measure as the covariate effect native to parametric models. We investigate a general variable selection approach when both the covariates and outcomes can be missing at random and have general missing data patterns. This approach exploits the flexibility of machine learning modeling techniques and bootstrap imputation, which is amenable to nonparametric methods in which the covariate effects are not directly available. We conduct expansive simulations investigating the practical operating characteristics of the proposed variable selection approach, when combined with four tree-based machine learning methods, XGBoost, Random Forests, Bayesian Additive Regression Trees (BART) and Conditional Random Forests, and two commonly used parametric methods, lasso and backward stepwise selection. Numeric results suggest that when combined with bootstrap imputation, XGBoost and BART have the overall best variable selection performance with respect to the $F_1$ score and Type I error across various settings. In general, there is no significant difference in the variable selection performance due to imputation methods. We further demonstrate the methods via a case study of risk factors for 3-year incidence of metabolic syndrome with data from the Study of Women's Health Across the Nation.
Various unsupervised greedy selection methods have been proposed as computationally tractable approximations to the NP-hard subset selection problem. These methods rely on sequentially selecting the variables that best improve performance with respect to a selection criterion. Theoretical results exist that provide performance bounds and enable "lazy greedy" efficient implementations for selection criteria that satisfy a diminishing returns property known as submodularity. This has motivated the development of variable selection algorithms based on mutual information and frame potential. Recently, the authors introduced Forward Selection Component Analysis (FSCA) which uses variance explained as its selection criterion. While this criterion is not submodular, FSCA has been shown to be highly effective for applications such as measurement plan optimisation. In this paper a "lazy" implementation of the FSCA algorithm (L-FSCA) is proposed, which, although not equivalent to FSCA due to the absence of submodularity, has the potential to yield comparable performance while being up to an order of magnitude faster to compute. The efficacy of L-FSCA is demonstrated by performing a systematic comparison with FSCA and five other unsupervised variable selection methods from the literature using simulated and real-world case studies. Experimental results confirm that L-FSCA yields almost identical performance to FSCA while reducing computation time by between 22% and 94% for the case studies considered.
Deep learning has been the engine powering many successes of data science. However, the deep neural network (DNN), as the basic model of deep learning, is often excessively over-parameterized, causing many difficulties in training, prediction and interpretation. We propose a frequentist-like method for learning sparse DNNs and justify its consistency under the Bayesian framework: the proposed method could learn a sparse DNN with at most $O(n/\log(n))$ connections and nice theoretical guarantees such as posterior consistency, variable selection consistency and asymptotically optimal generalization bounds. In particular, we establish posterior consistency for the sparse DNN with a mixture Gaussian prior, show that the structure of the sparse DNN can be consistently determined using a Laplace approximation-based marginal posterior inclusion probability approach, and use Bayesian evidence to elicit sparse DNNs learned by an optimization method such as stochastic gradient descent in multiple runs with different initializations. The proposed method is computationally more efficient than standard Bayesian methods for large-scale sparse DNNs. The numerical results indicate that the proposed method can perform very well for large-scale network compression and high-dimensional nonlinear variable selection, both advancing interpretable machine learning.
This work considers variational Bayesian inference as an inexpensive and scalable alternative to a fully Bayesian approach in the context of sparsity-promoting priors. In particular, the priors considered arise from scale mixtures of Normal distributions with a generalized inverse Gaussian mixing distribution. This includes the variational Bayesian LASSO as an inexpensive and scalable alternative to the Bayesian LASSO introduced in [65]. It also includes a family of priors which more strongly promote sparsity. For linear models the method requires only the iterative solution of deterministic least squares problems. Furthermore, for p unknown covariates the method can be implemented exactly online with a cost of $O(p^3)$ in computation and $O(p^2)$ in memory per iteration -- in other words, the cost per iteration is independent of n, and in principle infinite data can be considered. For large $p$ an approximation is able to achieve promising results for a cost of $O(p)$ per iteration, in both computation and memory. Strategies for hyper-parameter tuning are also considered. The method is implemented for real and simulated data. It is shown that the performance in terms of variable selection and uncertainty quantification of the variational Bayesian LASSO can be comparable to the Bayesian LASSO for problems which are tractable with that method, and for a fraction of the cost. The present method comfortably handles $n = 65536$, $p = 131073$ on a laptop in less than 30 minutes, and $n = 10^5$, $p = 2.1 \times 10^6$ overnight.
This paper develops a sparsity-inducing version of Bayesian Causal Forests, a recently proposed nonparametric causal regression model that employs Bayesian Additive Regression Trees and is specifically designed to estimate heterogeneous treatment effects using observational data. The sparsity-inducing component we introduce is motivated by empirical studies where not all the available covariates are relevant, leading to different degrees of sparsity underlying the surfaces of interest in the estimation of individual treatment effects. The extended version presented in this work, which we name Shrinkage Bayesian Causal Forest, is equipped with an additional pair of priors allowing the model to adjust the weight of each covariate through the corresponding number of splits in the tree ensemble. These priors improve the model's adaptability to sparse data generating processes and allow to perform fully Bayesian feature shrinkage in a framework for treatment effects estimation, and thus to uncover the moderating factors driving heterogeneity. In addition, the method allows prior knowledge about the relevant confounding covariates and the relative magnitude of their impact on the outcome to be incorporated in the model. We illustrate the performance of our method in simulated studies, in comparison to Bayesian Causal Forest and other state-of-the-art models, to demonstrate how it scales up with an increasing number of covariates and how it handles strongly confounded scenarios. Finally, we also provide an example of application using real-world data.
Mixed Integer Programming (MIP) solvers rely on an array of sophisticated heuristics developed with decades of research to solve large-scale MIP instances encountered in practice. Machine learning offers to automatically construct better heuristics from data by exploiting shared structure among instances in the data. This paper applies learning to the two key sub-tasks of a MIP solver, generating a high-quality joint variable assignment, and bounding the gap in objective value between that assignment and an optimal one. Our approach constructs two corresponding neural network-based components, Neural Diving and Neural Branching, to use in a base MIP solver such as SCIP. Neural Diving learns a deep neural network to generate multiple partial assignments for its integer variables, and the resulting smaller MIPs for un-assigned variables are solved with SCIP to construct high quality joint assignments. Neural Branching learns a deep neural network to make variable selection decisions in branch-and-bound to bound the objective value gap with a small tree. This is done by imitating a new variant of Full Strong Branching we propose that scales to large instances using GPUs. We evaluate our approach on six diverse real-world datasets, including two Google production datasets and MIPLIB, by training separate neural networks on each. Most instances in all the datasets combined have $10^3-10^6$ variables and constraints after presolve, which is significantly larger than previous learning approaches. Comparing solvers with respect to primal-dual gap averaged over a held-out set of instances, the learning-augmented SCIP is 2x to 10x better on all datasets except one on which it is $10^5$x better, at large time limits. To the best of our knowledge, ours is the first learning approach to demonstrate such large improvements over SCIP on both large-scale real-world application datasets and MIPLIB.
Sparse deep learning aims to address the challenge of huge storage consumption by deep neural networks, and to recover the sparse structure of target functions. Although tremendous empirical successes have been achieved, most sparse deep learning algorithms are lacking of theoretical support. On the other hand, another line of works have proposed theoretical frameworks that are computationally infeasible. In this paper, we train sparse deep neural networks with a fully Bayesian treatment under spike-and-slab priors, and develop a set of computationally efficient variational inferences via continuous relaxation of Bernoulli distribution. The variational posterior contraction rate is provided, which justifies the consistency of the proposed variational Bayes method. Notably, our empirical results demonstrate that this variational procedure provides uncertainty quantification in terms of Bayesian predictive distribution and is also capable to accomplish consistent variable selection by training a sparse multi-layer neural network.
Detecting influential features in non-linear and/or high-dimensional data is a challenging and increasingly important task in machine learning. Variable selection methods have thus been gaining much attention as well as post-selection inference. Indeed, the selected features can be significantly flawed when the selection procedure is not accounted for. We propose a selective inference procedure using the so-called model-free "HSIC-Lasso" based on the framework of truncated Gaussians combined with the polyhedral lemma. We then develop an algorithm, which allows for low computational costs and provides a selection of the regularisation parameter. The performance of our method is illustrated by both artificial and real-world data based experiments, which emphasise a tight control of the type-I error, even for small sample sizes.
Network estimation and variable selection have been extensively studied in the statistical literature, but only recently have those two challenges been addressed simultaneously. In this paper, we seek to develop a novel method to simultaneously estimate network interactions and associations to relevant covariates for count data, and specifically for compositional data, which have a fixed sum constraint. We use a hierarchical Bayesian model with latent layers and employ spike-and-slab priors for both edge and covariate selection. For posterior inference, we develop a novel variational inference scheme with an expectation maximization step, to enable efficient estimation. Through simulation studies, we demonstrate that the proposed model outperforms existing methods in its accuracy of network recovery. We show the practical utility of our model via an application to microbiome data. The human microbiome has been shown to contribute to many of the functions of the human body, and also to be linked with a number of diseases. In our application, we seek to better understand the interaction between microbes and relevant covariates, as well as the interaction of microbes with each other. We provide a Python implementation of our algorithm, called SINC (Simultaneous Inference for Networks and Covariates), available online.
A new class of Markov chain Monte Carlo (MCMC) algorithms, based on simulating piecewise deterministic Markov processes (PDMPs), have recently shown great promise: they are non-reversible, can mix better than standard MCMC algorithms, and can use subsampling ideas to speed up computation in big data scenarios. However, current PDMP samplers can only sample from posterior densities that are differentiable almost everywhere, which precludes their use for model choice. Motivated by variable selection problems, we show how to develop reversible jump PDMP samplers that can jointly explore the discrete space of models and the continuous space of parameters. Our framework is general: it takes any existing PDMP sampler, and adds two types of trans-dimensional moves that allow for the addition or removal of a variable from the model. We show how the rates of these trans-dimensional moves can be calculated so that the sampler has the correct invariant distribution. Simulations show that the new samplers can mix better than standard MCMC algorithms. Our empirical results show they are also more efficient than gradient-based samplers that avoid model choice through use of continuous spike-and-slab priors which replace a point mass at zero for each parameter with a density concentrated around zero.
Sparse models are desirable for many applications across diverse domains as they can perform automatic variable selection, aid interpretability, and provide regularization. When fitting sparse models in a Bayesian framework, however, analytically obtaining a posterior distribution over the parameters of interest is intractable for all but the simplest cases. As a result practitioners must rely on either sampling algorithms such as Markov chain Monte Carlo or variational methods to obtain an approximate posterior. Mean field variational inference is a particularly simple and popular framework that is often amenable to analytically deriving closed-form parameter updates. When all distributions in the model are members of exponential families and are conditionally conjugate, optimization schemes can often be derived by hand. Yet, I show that using standard mean field variational inference can fail to produce sensible results for models with sparsity-inducing priors, such as the spike-and-slab. Fortunately, such pathological behavior can be remedied as I show that mixtures of exponential family distributions with non-overlapping support form an exponential family. In particular, any mixture of a diffuse exponential family and a point mass at zero to model sparsity forms an exponential family. Furthermore, specific choices of these distributions maintain conditional conjugacy. I use two applications to motivate these results: one from statistical genetics that has connections to generalized least squares with a spike-and-slab prior on the regression coefficients; and sparse probabilistic principal component analysis. The theoretical results presented here are broadly applicable beyond these two examples.