The paper proposes a new covariance estimator for large covariance matrices when the variables have a natural ordering. Using the Cholesky decomposition of the inverse, we impose a banded structure on the Cholesky factor, and select the bandwidth adaptively for each row of the Cholesky factor, using a novel penalty we call nested Lasso. This structure has more flexibility than regular banding, but, unlike regular Lasso applied to the entries of the Cholesky factor, results in a sparse estimator for the inverse of the covariance matrix. An iterative algorithm for solving the optimization problem is developed. The estimator is compared to a number of other covariance estimators and is shown to do best, both in simulations and on a real data example. Simulations show that the margin by which the estimator outperforms its competitors tends to increase with dimension.
Imposition of a lasso penalty shrinks parameter estimates toward zero and performs continuous model selection. Lasso penalized regression is capable of handling linear regression problems where the number of predictors far exceeds the number of cases. This paper tests two exceptionally fast algorithms for estimating regression coefficients with a lasso penalty. The previously known $\ell_2$ algorithm is based on cyclic coordinate descent. Our new $\ell_1$ algorithm is based on greedy coordinate descent and Edgeworth's algorithm for ordinary $\ell_1$ regression. Each algorithm relies on a tunin…
Comparison of the LASSO and Integrative LASSO with Penalty Factors (IPF-LASSO) methods for multi-omics data: Variable selection with Type I error control
In this work, we consider a manufactory process which can be described by a multiple-instance logistic regression model. In order to compute the maximum likelihood estimation of the unknown coefficient, an expectation-maximization algorithm is proposed, and the proposed modeling approach can be extended to identify the important covariates by adding the coefficient penalty term into the likelihood function. In addition to essential technical details, we demonstrate the usefulness of the proposed method by simulations and real examples.
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…
We investigate properties of estimators obtained by minimization of U-processes with the Lasso penalty in high-dimensional settings. Our attention is focused on the ranking problem that is popular in machine learning. It is related to guessing the ordering between objects on the basis of their observed predictors. We prove the oracle inequality for the excess risk of the considered estimator as well as the bound for the l1 distance between the estimator and the oracle.
We consider the group lasso penalty for the linear model. We note that the standard algorithm for solving the problem assumes that the model matrices in each group are orthonormal. Here we consider a more general penalty that blends the lasso (L1) with the group lasso ("two-norm"). This penalty yields solutions that are sparse at both the group and individual feature levels. We derive an efficient algorithm for the resulting convex problem based on coordinate descent. This algorithm can also be used to solve the general form of the group lasso, with non-orthonormal model matrices.
We propose a convex formulation of the fused lasso signal approximation problem consisting of non-convex penalty functions. The fused lasso signal model aims to estimate a sparse piecewise constant signal from a noisy observation. Originally, the $\ell_1$ norm was used as a sparsity-inducing convex penalty function for the fused lasso signal approximation problem. However, the $\ell_1$ norm underestimates signal values. Non-convex sparsity-inducing penalty functions better estimate signal values. In this paper, we show how to ensure the convexity of the fused lasso signal approximation problem…
We present a new approach to solve the sparse approximation or best subset selection problem, namely find a $k$-sparse vector ${\bf x}\in\mathbb{R}^d$ that minimizes the $\ell_2$ residual $\lVert A{\bf x}-{\bf y} \rVert_2$. We consider a regularized approach, whereby this residual is penalized by the non-convex $\textit{trimmed lasso}$, defined as the $\ell_1$-norm of ${\bf x}$ excluding its $k$ largest-magnitude entries. We prove that the trimmed lasso has several appealing theoretical properties, and in particular derive sparse recovery guarantees assuming successful optimization of the pena…
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…
In this article we study variable selection problem using LASSO with new improvisations. LASSO uses $\ell_{1}$ penalty, it shrinks most of the coefficients to zero when number of explanatory variables $(p)$ are much larger the number of observations $(N)$. Novelty of the approach developed in this article blends basic ideas behind resampling and LASSO together which provides a significant variable reduction and improved prediction accuracy in terms of mean squared error in the test sample. Different weighting schemes have been explored using Bootstrapped LASSO, the basic methodology developed …
The statistics literature of the past 15 years has established many favorable properties for sparse diminishing-bias regularization: techniques which can roughly be understood as providing estimation under penalty functions spanning the range of concavity between $L_0$ and $L_1$ norms. However, lasso $L_1$-regularized estimation remains the standard tool for industrial `Big Data' applications because of its minimal computational cost and the presence of easy-to-apply rules for penalty selection. In response, this article proposes a simple new algorithm framework that requires no more computati…
Regression with the lasso penalty is a popular tool for performing dimension reduction when the number of covariates is large. In many applications of the lasso, like in genomics, covariates are subject to measurement error. We study the impact of measurement error on linear regression with the lasso penalty, both analytically and in simulation experiments. A simple method of correction for measurement error in the lasso is then considered. In the large sample limit, the corrected lasso yields sign consistent covariate selection under conditions very similar to the lasso with perfect measureme…
We introduce a pliable lasso method for estimation of interaction effects in the Cox proportional hazards model framework. The pliable lasso is a linear model that includes interactions between covariates X and a set of modifying variables Z and assumes sparsity of the main effects and interaction effects. The hierarchical penalty excludes interaction effects when the corresponding main effects are zero: this avoids overfitting and an explosion of model complexity. We extend this method to the Cox model for survival data, incorporating modifiers that are either fixed or varying in time into th…
Istituto Italiano di Tecnologia（意大利技术研究院）；MIT（麻省理工学院）；Università di Genova（热那亚大学）
We consider a regularized least squares problem, with regularization by structured sparsity-inducing norms, which extend the usual $\ell_1$ and the group lasso penalty, by allowing the subsets to overlap. Such regularizations lead to nonsmooth problems that are difficult to optimize, and we propose in this paper a suitable version of an accelerated proximal method to solve them. We prove convergence of a nested procedure, obtained composing an accelerated proximal method with an inner algorithm for computing the proximity operator. By exploiting the geometrical properties of the penalty, we de…
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…
We describe a simple, efficient, permutation based procedure for selecting the penalty parameter in the LASSO. The procedure, which is intended for applications where variable selection is the primary focus, can be applied in a variety of structural settings, including generalized linear models. We briefly discuss connections between permutation selection and existing theory for the LASSO. In addition, we present a simulation study and an analysis of three real data sets in which permutation selection is compared with cross-validation (CV), the Bayesian information criterion (BIC), and a selec…
This paper considers a multiple regression model and compares, under full model hypothesis, analytically as well as by simulation, the performance characteristics of some popular penalty estimators such as ridge regression, LASSO, adaptive LASSO, SCAD, and elastic net versus Least Squares Estimator, restricted estimator, preliminary test estimator, and Stein-type estimators when the dimension of the parameter space is smaller than the sample space dimension. We find that RR uniformly dominates LSE, RE, PTE, SE and PRSE while LASSO, aLASSO, SCAD, and EN uniformly dominates LSE only. Further, it…
Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology. Whole-genome expression data over time provides an opportunity to determine how the expression levels of genes are affected by changes in transcription levels of other genes, and can therefore be used to discover regulatory interactions among genes. In this p…
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…
This paper considers the penalized least squares estimator with arbitrary convex penalty. When the observation noise is Gaussian, we show that the prediction error is a subgaussian random variable concentrated around its median. We apply this concentration property to derive sharp oracle inequalities for the prediction error of the LASSO, the group LASSO and the SLOPE estimators, both in probability and in expectation. In contrast to the previous work on the LASSO type methods, our oracle inequalities in probability are obtained at any confidence level for estimators with tuning parameters tha…
The Lasso is a very well known penalized regression model, which adds an $L_{1}$ penalty with parameter $λ_{1}$ on the coefficients to the squared error loss function. The Fused Lasso extends this model by also putting an $L_{1}$ penalty with parameter $λ_{2}$ on the difference of neighboring coefficients, assuming there is a natural ordering. In this paper, we develop a fast path algorithm for solving the Fused Lasso Signal Approximator that computes the solutions for all values of $λ_1$ and $λ_2$. In the supplement, we also give an algorithm for the general Fused Lasso for the case with pred…
L1 -penalized regression methods such as the Lasso (Tibshirani 1996) that achieve both variable selection and shrinkage have been very popular. An extension of this method is the Fused Lasso (Tibshirani and Wang 2007), which allows for the incorporation of external information into the model. In this article, we develop new and fast algorithms for solving the Fused Lasso which are based on coordinate-wise optimization. This class of algorithms has recently been applied very successfully to solve L1 -penalized problems very quickly (Friedman et al. 2007). As a straightforward coordinate-wise pr…
Consider the problem of estimating the entries of an unknown mean matrix or tensor given a single noisy realization. In the matrix case, this problem can be addressed by decomposing the mean matrix into a component that is additive in the rows and columns, i.e.\ the additive ANOVA decomposition of the mean matrix, plus a matrix of elementwise effects, and assuming that the elementwise effects may be sparse. Accordingly, the mean matrix can be estimated by solving a penalized regression problem, applying a lasso penalty to the elementwise effects. Although solving this penalized regression prob…
We consider the problems of estimation and selection of parameters endowed with a known group structure, when the groups are assumed to be sign-coherent, that is, gathering either nonnegative, nonpositive or null parameters. To tackle this problem, we propose the cooperative-Lasso penalty. We derive the optimality conditions defining the cooperative-Lasso estimate for generalized linear models, and propose an efficient active set algorithm suited to high-dimensional problems. We study the asymptotic consistency of the estimator in the linear regression setup and derive its irrepresentable cond…
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…
In this paper, we derive non-asymptotic error bounds for the Lasso estimator when the penalty parameter for the estimator is chosen using $K$-fold cross-validation. Our bounds imply that the cross-validated Lasso estimator has nearly optimal rates of convergence in the prediction, $L^2$, and $L^1$ norms. For example, we show that in the model with the Gaussian noise and under fairly general assumptions on the candidate set of values of the penalty parameter, the estimation error of the cross-validated Lasso estimator converges to zero in the prediction norm with the $\sqrt{s\log p / n}\times \…
Adaptive multi-penalty regularization based on a generalized Lasso path
Department of Mathematical Sciences, Norwegian University of Science and Technology（挪威科学与技术大学数学科学系）；Section for Computing and Software, Simula Research Laboratory AS（Simula研究实验室计算与软件部门）
In this paper, we consider the Group Lasso estimator of the covariance matrix of a stochastic process corrupted by an additive noise. We propose to estimate the covariance matrix in a high-dimensional setting under the assumption that the process has a sparse representation in a large dictionary of basis functions. Using a matrix regression model, we propose a new methodology for high-dimensional covariance matrix estimation based on empirical contrast regularization by a group Lasso penalty. Using such a penalty, the method selects a sparse set of basis functions in the dictionary used to app…
Regularized regression approaches such as the Lasso have been widely adopted for constructing sparse linear models in high-dimensional datasets. A complexity in fitting these models is the tuning of the parameters which control the level of introduced sparsity through penalization. The most common approach to select the penalty parameter is through $k$-fold cross-validation. While cross-validation is used to minimise the empirical prediction error, approaches such as the $m$-out-of-$n$ paired bootstrap which use smaller training datasets provide consistency in selecting the non-zero coefficien…
Large-scale {\it in vitro} drug sensitivity screens are an important tool in personalized oncology to predict the effectiveness of potential cancer drugs. The prediction of the sensitivity of cancer cell lines to a panel of drugs is a multivariate regression problem with high-dimensional heterogeneous multi-omics data as input data and with potentially strong correlations between the outcome variables which represent the sensitivity to the different drugs. We propose a joint penalized regression approach with structured penalty terms which allow us to utilize the correlation structure between …
We study uniqueness in the generalized lasso problem, where the penalty is the $\ell_1$ norm of a matrix $D$ times the coefficient vector. We derive a broad result on uniqueness that places weak assumptions on the predictor matrix $X$ and penalty matrix $D$; the implication is that, if $D$ is fixed and its null space is not too large (the dimension of its null space is at most the number of samples), and $X$ and response vector $y$ jointly follow an absolutely continuous distribution, then the generalized lasso problem has a unique solution almost surely, regardless of the number of predictors…
In this work a method to regularize Cox frailty models is proposed that accommodates time-varying covariates and time-varying coefficients and is based on the full instead of the partial likelihood. A particular advantage in this framework is that the baseline hazard can be explicitly modeled in a smooth, semi-parametric way, e.g. via P-splines. Regularization for variable selection is performed via a lasso penalty and via group lasso for categorical variables while a second penalty regularizes wiggliness of smooth estimates of time-varying coefficients and the baseline hazard. Additionally, a…
We consider the problem of learning a structured multi-task regression, where the output consists of multiple responses that are related by a graph and the correlated response variables are dependent on the common inputs in a sparse but synergistic manner. Previous methods such as l1/l2-regularized multi-task regression assume that all of the output variables are equally related to the inputs, although in many real-world problems, outputs are related in a complex manner. In this paper, we propose graph-guided fused lasso (GFlasso) for structured multi-task regression that exploits the graph st…
In this paper, we aim to give a theoretical approximation for the penalty level of $\ell_{1}$-regularization problems. This can save much time in practice compared with the traditional methods, such as cross-validation. To achieve this goal, we develop two Gaussian approximation methods, which are based on a moderate deviation theorem and Stein's method respectively. Both of them give efficient approximations and have good performances in simulations. We apply the two Gaussian approximation methods into three types of ultra-high dimensional $\ell_{1}$ penalized regressions: lasso, square-root …
We propose MC+, a fast, continuous, nearly unbiased and accurate method of penalized variable selection in high-dimensional linear regression. The LASSO is fast and continuous, but biased. The bias of the LASSO may prevent consistent variable selection. Subset selection is unbiased but computationally costly. The MC+ has two elements: a minimax concave penalty (MCP) and a penalized linear unbiased selection (PLUS) algorithm. The MCP provides the convexity of the penalized loss in sparse regions to the greatest extent given certain thresholds for variable selection and unbiasedness. The PLUS co…
We propose a new method of learning a sparse nonnegative-definite target matrix. Our primary example of the target matrix is the inverse of a population covariance or correlation matrix. The algorithm first estimates each column of the target matrix by the scaled Lasso and then adjusts the matrix estimator to be symmetric. The penalty level of the scaled Lasso for each column is completely determined by data via convex minimization, without using cross-validation. We prove that this scaled Lasso method guarantees the fastest proven rate of convergence in the spectrum norm under conditions of w…
We consider the problem of Graphical lasso with an additional $\ell_{\infty}$ element-wise norm constraint on the precision matrix. This problem has applications in high-dimensional covariance decomposition such as in \citep{Janzamin-12}. We propose an ADMM algorithm to solve this problem. We also use a continuation strategy on the penalty parameter to have a fast implemenation of the algorithm.
We propose an Exclusive Topic Modeling (ETM) for unsupervised text classification, which is able to 1) identify the field-specific keywords though less frequently appeared and 2) deliver well-structured topics with exclusive words. In particular, a weighted Lasso penalty is imposed to reduce the dominance of the frequently appearing yet less relevant words automatically, and a pairwise Kullback-Leibler divergence penalty is used to implement topics separation. Simulation studies demonstrate that the ETM detects the field-specific keywords, while LDA fails. When applying to the benchmark NIPS d…
In linear regression, SLOPE is a new convex analysis method that generalizes the Lasso via the sorted L1 penalty: larger fitted coefficients are penalized more heavily. This magnitude-dependent regularization requires an input of penalty sequence $λ$, instead of a scalar penalty as in the Lasso case, thus making the design extremely expensive in computation. In this paper, we propose two efficient algorithms to design the possibly high-dimensional SLOPE penalty, in order to minimize the mean squared error. For Gaussian data matrices, we propose a first order Projected Gradient Descent (PGD) un…
This work proposes an adaptive trace lasso regularized L1-norm based graph cut method for dimensionality reduction of Hyperspectral images, called as `Trace Lasso-L1 Graph Cut' (TL-L1GC). The underlying idea of this method is to generate the optimal projection matrix by considering both the sparsity as well as the correlation of the data samples. The conventional L2-norm used in the objective function is sensitive to noise and outliers. Therefore, in this work L1-norm is utilized as a robust alternative to L2-norm. Besides, for further improvement of the results, we use a penalty function of t…
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 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…
We consider the problem of binary classification where one can, for a particular cost, choose not to classify an observation. We present a simple proof for the oracle inequality for the excess risk of structural risk minimizers using a lasso type penalty.
Merck & Co., Inc（默沙东公司）；Georgia Institute of Technology（佐治亚理工学院）
In optimization, it is known that when the objective functions are strictly convex and well-conditioned, gradient-based approaches can be extremely effective, e.g., achieving the exponential rate of convergence. On the other hand, the existing Lasso-type estimator in general cannot achieve the optimal rate due to the undesirable behavior of the absolute function at the origin. A homotopic method is to use a sequence of surrogate functions to approximate the $\ell_1$ penalty that is used in the Lasso-type of estimators. The surrogate functions will converge to the $\ell_1$ penalty in the Lasso …
For some special data in reality, such as the genetic data, adjacent genes may have the similar function. Thus ensuring the smoothness between adjacent genes is highly necessary. But, in this case, the standard lasso penalty just doesn't seem appropriate anymore. On the other hand, in high-dimensional statistics, some datasets are easily contaminated by outliers or contain variables with heavy-tailed distributions, which makes many conventional methods inadequate. To address both issues, in this paper, we propose an adaptive Huber regression for robust estimation and inference, in which, the f…
We consider the problem of estimating sparse graphs by a lasso penalty applied to the inverse covariance matrix. Using a coordinate descent procedure for the lasso, we develop a simple algorithm that is remarkably fast: in the worst cases, it solves a 1000 node problem (~500,000 parameters) in about a minute, and is 50 to 2000 times faster than competing methods. It also provides a conceptual link between the exact problem and the approximation suggested by Meinhausen and Buhlmann (2006). We illustrate the method on some cell-signaling data from proteomics.
Covariance graphical lasso applies a lasso penalty on the elements of the covariance matrix. This method is useful because it not only produces sparse estimation of covariance matrix but also discovers marginal independence structures by generating zeros in the covariance matrix. We propose and explore two new algorithms for solving the covariance graphical lasso problem. Our new algorithms are based on coordinate descent and ECM. We show that these two algorithms are more attractive than the only existing competing algorithm of Bien and Tibshirani (2011) in terms of simplicity, speed and stab…
In many scientific studies, it becomes increasingly important to delineate the causal pathways through a large number of mediators, such as genetic and brain mediators. Structural equation modeling (SEM) is a popular technique to estimate the pathway effects, commonly expressed as products of coefficients. However, it becomes unstable to fit such models with high dimensional mediators, especially for a general setting where all the mediators are causally dependent but the exact causal relationships between them are unknown. This paper proposes a sparse mediation model using a regularized SEM a…
