We present an approach for penalized tensor decomposition (PTD) that estimates smoothly varying latent factors in multi-way data. This generalizes existing work on sparse tensor decomposition and penalized matrix decompositions, in a manner parallel to the generalized lasso for regression and smoothing problems. Our approach presents many nontrivial challenges at the intersection of modeling and computation, which are studied in detail. An efficient coordinate-wise optimization algorithm for (PTD) is presented, and its convergence properties are characterized. The method is applied both to simulated data and real data on flu hospitalizations in Texas. These results show that our penalized tensor decomposition can offer major improvements on existing methods for analyzing multi-way data that exhibit smooth spatial or temporal features.
We study estimators with generalized lasso penalties within the computational sufficiency framework introduced by Vu (2018, arXiv:1807.05985). By representing these penalties as support functions of zonotopes and more generally Minkowski sums of line segments and rays, we show that there is a natural reflection group associated with the underlying optimization problem. A consequence of this point of view is that for large classes of estimators sharing the same penalty, the penalized least squares estimator is computationally minimal sufficient. This means that all such estimators can be comput…
Using a multiplicative reparametrization, I show that a subclass of $L_q$ penalties with $q\leq 1$ can be expressed as sums of $L_2$ penalties. It follows that the lasso and other norm-penalized regression estimates may be obtained using a very simple and intuitive alternating ridge regression algorithm. As compared to a similarly intuitive EM algorithm for $L_q$ optimization, the proposed algorithm avoids some numerical instability issues and is also competitive in terms of speed. Furthermore, the proposed algorithm can be extended to accommodate sparse high-dimensional scenarios, generalized…
Recent work has focused on the problem of conducting linear regression when the number of covariates is very large, potentially greater than the sample size. To facilitate this, one useful tool is to assume that the model can be well approximated by a fit involving only a small number of covariates -- a so called sparsity assumption, which leads to the Lasso and other methods. In many situations, however, the covariates can be considered to be structured, in that the selection of some variables favours the selection of others -- with variables organised into groups entering or leaving the mode…
In high dimensional regression settings, sparsity enforcing penalties have proved useful to regularize the data-fitting term. A recently introduced technique called screening rules propose to ignore some variables in the optimization leveraging the expected sparsity of the solutions and consequently leading to faster solvers. When the procedure is guaranteed not to discard variables wrongly the rules are said to be safe. In this work, we propose a unifying framework for generalized linear models regularized with standard sparsity enforcing penalties such as $\ell_1$ or $\ell_1/\ell_2$ norms. O…
Despite its prevalence in statistical datasets, heteroscedasticity (non-constant sample variances) has been largely ignored in the high-dimensional statistics literature. Recently, studies have shown that the Lasso can accommodate heteroscedastic errors, with minor algorithmic modifications (Belloni et al., 2012; Gautier and Tsybakov, 2013). In this work, we study heteroscedastic regression with linear mean model and log-linear variances model with sparse high-dimensional parameters. In this work, we propose estimating variances in a post-Lasso fashion, which is followed by weighted-least squa…
Graphical models are frequently used to explore networks, such as genetic networks, among a set of variables. This is usually carried out via exploring the sparsity of the precision matrix of the variables under consideration. Penalized likelihood methods are often used in such explorations. Yet, positive-definiteness constraints of precision matrices make the optimization problem challenging. We introduce nonconcave penalties and the adaptive LASSO penalty to attenuate the bias problem in the network estimation. Through the local linear approximation to the nonconcave penalty functions, the p…
Penalized regression is an attractive framework for variable selection problems. Often, variables possess a grouping structure, and the relevant selection problem is that of selecting groups, not individual variables. The group lasso has been proposed as a way of extending the ideas of the lasso to the problem of group selection. Nonconvex penalties such as SCAD and MCP have been proposed and shown to have several advantages over the lasso; these penalties may also be extended to the group selection problem, giving rise to group SCAD and group MCP methods. Here, we describe algorithms for fitt…
Nonconvex penalty methods for sparse modeling in linear regression have been a topic of fervent interest in recent years. Herein, we study a family of nonconvex penalty functions that we call the trimmed Lasso and that offers exact control over the desired level of sparsity of estimators. We analyze its structural properties and in doing so show the following: 1) Drawing parallels between robust statistics and robust optimization, we show that the trimmed-Lasso-regularized least squares problem can be viewed as a generalized form of total least squares under a specific model of uncertainty. In…
We propose the Bayesian adaptive Lasso (BaLasso) for variable selection and coefficient estimation in linear regression. The BaLasso is adaptive to the signal level by adopting different shrinkage for different coefficients. Furthermore, we provide a model selection machinery for the BaLasso by assessing the posterior conditional mode estimates, motivated by the hierarchical Bayesian interpretation of the Lasso. Our formulation also permits prediction using a model averaging strategy. We discuss other variants of this new approach and provide a unified framework for variable selection using fl…
This paper proposes a new interpretation of sparse penalties such as the elastic-net and the group-lasso. Beyond providing a new viewpoint on these penalization schemes, our approach results in a unified optimization strategy. Our experiments demonstrate that this strategy, implemented on the elastic-net, is computationally extremely efficient for small to medium size problems. Our accompanying software solves problems very accurately, at machine precision, in the time required to get a rough estimate with competing state-of-the-art algorithms. We illustrate on real and artificial datasets tha…
Estimation in generalized linear models (GLM) is complicated by the presence of constraints. One can handle constraints by maximizing a penalized log-likelihood. Penalties such as the lasso are effective in high dimensions, but often lead to unwanted shrinkage. This paper explores instead penalizing the squared distance to constraint sets. Distance penalties are more flexible than algebraic and regularization penalties, and avoid the drawback of shrinkage. To optimize distance penalized objectives, we make use of the majorization-minimization principle. Resulting algorithms constructed within …
It has been shown in literature that the Lasso estimator, or l1-penalized least squares estimator, enjoys good oracle properties. This paper examines which special properties of the l1-penalty allow for sharp oracle results, and then extends the situation to general norm-based penalties that satisfy a weak decomposability condition.
Regularized regression has become very popular nowadays, particularly on high-dimensional problems where the addition of a penalty term to the log-likelihood allows inference where traditional methods fail. A number of penalties have been proposed in the literature, such as lasso, SCAD, ridge and elastic net to name a few. Despite their advantages and remarkable performance in rather extreme settings, where $p \gg n$, all these penalties, with the exception of ridge, are non-differentiable at zero. This can be a limitation in certain cases, such as computational efficiency of parameter estimat…
In this paper, we propose a framework for automatic classification of patients from multimodal genetic and brain imaging data by optimally combining them. Additive models with unadapted penalties (such as the classical group lasso penalty or $L_1$-multiple kernel learning) treat all modalities in the same manner and can result in undesirable elimination of specific modalities when their contributions are unbalanced. To overcome this limitation, we introduce a multilevel model that combines imaging and genetics and that considers joint effects between these two modalities for diagnosis predicti…
There have been many attempts to identify high-dimensional network features via multivariate approaches. Specifically, when the number of voxels or nodes, denoted as p, are substantially larger than the number of images, denoted as n, it produces an under-determined model with infinitely many possible solutions. The small-n large-p problem is often remedied by regularizing the under-determined system with additional sparse penalties. Popular sparse network models include sparse correlations, LASSO, sparse canonical correlations and graphical-LASSO. These popular sparse models require optimizin…
We study the problem of estimating high-dimensional regression models regularized by a structured sparsity-inducing penalty that encodes prior structural information on either the input or output variables. We consider two widely adopted types of penalties of this kind as motivating examples: (1) the general overlapping-group-lasso penalty, generalized from the group-lasso penalty; and (2) the graph-guided-fused-lasso penalty, generalized from the fused-lasso penalty. For both types of penalties, due to their nonseparability and nonsmoothness, developing an efficient optimization method remain…
When the design matrix has orthonormal columns, "soft thresholding" the ordinary least squares (OLS) solution produces the Lasso solution [Tibshirani, 1996]. If one uses the Puffer preconditioned Lasso [Jia and Rohe, 2012], then this result generalizes from orthonormal designs to full rank designs (Theorem 1). Theorem 2 refines the Puffer preconditioner to make the Lasso select the same model as removing the elements of the OLS solution with the largest p-values. Using a generalized Puffer preconditioner, Theorem 3 relates ridge regression to the preconditioned Lasso; this result is for the hi…
Directed acyclic graphs (DAGs) are commonly used to represent causal relationships among random variables in graphical models. Applications of these models arise in the study of physical, as well as biological systems, where directed edges between nodes represent the influence of components of the system on each other. The general problem of estimating DAGs from observed data is computationally NP-hard, Moreover two directed graphs may be observationally equivalent. When the nodes exhibit a natural ordering, the problem of estimating directed graphs reduces to the problem of estimating the str…
LLM-Lasso: A Robust Framework for Domain-Informed Feature Selection and Regularization
Stanford University School of Engineering（斯坦福大学工程学院）；Stanford University School of Medicine（斯坦福大学医学院）；Stanford University Department of Statistics（斯坦福大学统计学系）；University of Wisconsin-Madison（威斯康星大学麦迪逊分校）
In this paper, we are concerned with regularized regression problems where the prior regularizer is a proper lower semicontinuous and convex function which is also partly smooth relative to a Riemannian submanifold. This encompasses as special cases several known penalties such as the Lasso ($\ell^1$-norm), the group Lasso ($\ell^1-\ell^2$-norm), the $\ell^\infty$-norm, and the nuclear norm. This also includes so-called analysis-type priors, i.e. composition of the previously mentioned penalties with linear operators, typical examples being the total variation or fused Lasso penalties.We study…
Many least squares problems involve affine equality and inequality constraints. Although there are variety of methods for solving such problems, most statisticians find constrained estimation challenging. The current paper proposes a new path following algorithm for quadratic programming based on exact penalization. Similar penalties arise in $l_1$ regularization in model selection. Classical penalty methods solve a sequence of unconstrained problems that put greater and greater stress on meeting the constraints. In the limit as the penalty constant tends to $\infty$, one recovers the constrai…
We propose a new approach, along with refinements, based on $L_1$ penalties and aimed at jointly estimating several related regression models. Its main interest is that it can be rewritten as a weighted lasso on a simple transformation of the original data set. In particular, it does not need new dedicated algorithms and is ready to implement under a variety of regression models, {\em e.g.}, using standard R packages. Moreover, asymptotic oracle properties are derived along with preliminary non-asymptotic results, suggesting good theoretical properties. Our approach is further compared with st…
Penalized selection criteria like AIC or BIC are among the most popular methods for variable selection. Their theoretical properties have been studied intensively and are well understood, but making use of them in case of high-dimensional data is difficult due to the non-convex optimization problem induced by L0 penalties. An elegant solution to this problem is provided by the multi-step adaptive lasso, where iteratively weighted lasso problems are solved, whose weights are updated in such a way that the procedure converges towards selection with L0 penalties. In this paper we introduce an ada…
In response to the challenges of data mining, discriminant analysis continues to evolve as a vital branch of statistics. Our recently introduced method of vertex discriminant analysis (VDA) is ideally suited to handle multiple categories and an excess of predictors over training cases. The current paper explores an elaboration of VDA that conducts classification and variable selection simultaneously. Adding lasso ($\ell_1$-norm) and Euclidean penalties to the VDA loss function eliminates unnecessary predictors. Lasso penalties apply to each predictor coefficient separately; Euclidean penalties…
We consider estimation of undirected Gaussian graphical models and inverse covariances in high-dimensional scenarios by penalizing the corresponding precision matrix. While single $L_1$ (Graphical Lasso) and $L_2$ (Graphical Ridge) penalties for the precision matrix have already been studied, we propose the combination of both, yielding an Elastic Net type penalty. We enable additional flexibility by allowing to include diagonal target matrices for the precision matrix. We generalize existing algorithms for the Graphical Lasso and provide corresponding software with an efficient implementation…
In this paper, we propose an unifying view of several recently proposed structured sparsity-inducing norms. We consider the situation of a model simultaneously (a) penalized by a set- function de ned on the support of the unknown parameter vector which represents prior knowledge on supports, and (b) regularized in Lp-norm. We show that the natural combinatorial optimization problems obtained may be relaxed into convex optimization problems and introduce a notion, the lower combinatorial envelope of a set-function, that characterizes the tightness of our relaxations. We moreover establish links…
In sparse regression modeling via regularization such as the lasso, it is important to select appropriate values of tuning parameters including regularization parameters. The choice of tuning parameters can be viewed as a model selection and evaluation problem. Mallows' $C_p$ type criteria may be used as a tuning parameter selection tool in lasso-type regularization methods, for which the concept of degrees of freedom plays a key role. In the present paper, we propose an efficient algorithm that computes the degrees of freedom by extending the generalized path seeking algorithm. Our procedure …
A new estimator, named S-LASSO, is proposed for the coefficient function of the Function-on-Function linear regression model. The S-LASSO estimator is shown to be able to increase the interpretability of the model, by better locating regions where the coefficient function is zero, and to smoothly estimate non-zero values of the coefficient function. The sparsity of the estimator is ensured by a \textit{functional LASSO penalty}, which pointwise shrinks toward zero the coefficient function, while the smoothness is provided by two roughness penalties that penalize the curvature of the final esti…
We consider the augmented Lagrangian method (ALM) as a solver for the fused lasso signal approximator (FLSA) problem. The ALM is a dual method in which squares of the constraint functions are added as penalties to the Lagrangian. In order to apply this method to FLSA, two types of auxiliary variables are introduced to transform the original unconstrained minimization problem into a linearly constrained minimization problem. Each updating in this iterative algorithm consists of just a simple one-dimensional convex programming problem, with closed form solution in many cases. While the existing …
Radiogenomics is an emerging field in cancer research that combines medical imaging data with genomic data to predict patients clinical outcomes. In this paper, we propose a multivariate sparse group lasso joint model to integrate imaging and genomic data for building prediction models. Specifically, we jointly consider two models, one regresses imaging features on genomic features, and the other regresses patients clinical outcomes on genomic features. The regularization penalties through sparse group lasso allow incorporation of intrinsic group information, e.g. biological pathway and imagin…
This work proposes a new algorithm for solving the graph-fused lasso (GFL), a method for parameter estimation that operates under the assumption that the signal tends to be locally constant over a predefined graph structure. The proposed method applies the alternating direction method of multipliers (ADMM) algorithm and is based on the decomposition of the objective function into two components. While ADMM has been widely used in this problem, existing works such as network lasso decompose the objective function into the loss function component and the total variation penalty component. In com…
University of Science and Technology of China（中国科学技术大学）；Peking University（北京大学）；Central China Normal University（华中师范大学）
When we are interested in high-dimensional system and focus on classification performance, the $\ell_{1}$-penalized logistic regression is becoming important and popular. However, the Lasso estimates could be problematic when penalties of different coefficients are all the same and not related to the data. We proposed two types of weighted Lasso estimates depending on covariates by the McDiarmid inequality. Given sample size $n$ and dimension of covariates $p$, the finite sample behavior of our proposed methods with a diverging number of predictors is illustrated by non-asymptotic oracle inequ…
This paper proposes a general framework for penalized convex empirical criteria and a new version of the Sparse-Group LASSO (SGL, Simon and al., 2013), called the adaptive SGL, where both penalties of the SGL are weighted by preliminary random coefficients. We explore extensively its asymptotic properties and prove that this estimator satisfies the so-called oracle property (Fan and Li, 2001), that is the sparsity based estimator recovers the true underlying sparse model and is asymptotically normally distributed. Then we study its asymptotic properties in a double-asymptotic framework, where …
We focus on solving the clustered lasso problem, which is a least squares problem with the $\ell_1$-type penalties imposed on both the coefficients and their pairwise differences to learn the group structure of the regression parameters. Here we first reformulate the clustered lasso regularizer as a weighted ordered-lasso regularizer, which is essential in reducing the computational cost from $O(n^2)$ to $O(n\log (n))$. We then propose an inexact semismooth Newton augmented Lagrangian ({\sc Ssnal}) algorithm to solve the clustered lasso problem or its dual via this equivalent formulation, depe…
In some supervised learning settings, the practitioner might have additional information on the features used for prediction. We propose a new method which leverages this additional information for better prediction. The method, which we call the feature-weighted elastic net ("fwelnet"), uses these "features of features" to adapt the relative penalties on the feature coefficients in the elastic net penalty. In our simulations, fwelnet outperforms the lasso in terms of test mean squared error and usually gives an improvement in true positive rate or false positive rate for feature selection. We…
We consider the problems of variable selection and estimation in nonparametric additive regression models for high-dimensional data. In recent years, several methods have been proposed to model nonlinear relationships when the number of covariates exceeds the number of observations by using spline basis functions and group penalties. Nonlinear {\it monotone} effects on the response play a central role in many situations, in particular in medicine and biology. We construct the monotone splines lasso (MS-lasso) to select variables and estimate effects using monotone spline (I-splines). The addit…
We consider the problem of estimating multiple related but distinct graphical models on the basis of a high-dimensional data set with observations that belong to distinct classes. A motivating example occurs in the analysis of gene expression data for tissue samples with and without cancer. In this case, we might wish to estimate a gene expression network for the normal tissue and a gene expression network for the tumor tissue. We expect the two gene expression networks to be similar but not identical to each other, and so more accurate estimation of these two networks may be possible using a …
Extracting useful information from high-dimensional data is an important focus of today's statistical research and practice. Penalized loss function minimization has been shown to be effective for this task both theoretically and empirically. With the virtues of both regularization and sparsity, the $L_1$-penalized squared error minimization method Lasso has been popular in regression models and beyond. In this paper, we combine different norms including $L_1$ to form an intelligent penalty in order to add side information to the fitting of a regression or classification model to obtain reason…
This work addresses the issue of large covariance matrix estimation in high-dimensional statistical analysis. Recently, improved iterative algorithms with positive-definite guarantee have been developed. However, these algorithms cannot be directly extended to use a nonconvex penalty for sparsity inducing. Generally, a nonconvex penalty has the capability of ameliorating the bias problem of the popular convex lasso penalty, and thus is more advantageous. In this work, we propose a class of positive-definite covariance estimators using generalized nonconvex penalties. We develop a first-order a…
Sparse Group LASSO (SGL) is a regularized model for high-dimensional linear regression problems with grouped covariates. SGL applies $l_1$ and $l_2$ penalties on the individual predictors and group predictors, respectively, to guarantee sparse effects both on the inter-group and within-group levels. In this paper, we apply the approximate message passing (AMP) algorithm to efficiently solve the SGL problem under Gaussian random designs. We further use the recently developed state evolution analysis of AMP to derive an asymptotically exact characterization of SGL solution. This allows us to con…
