Coordinate descent algorithms for nonconvex penalized regression, with applications to biological feature selection

A number of variable selection methods have been proposed involving nonconvex penalty functions. These methods, which include the smoothly clipped absolute deviation (SCAD) penalty and the minimax concave penalty (MCP), have been demonstrated to have attractive theoretical properties, but model fitting is not a straightforward task, and the resulting solutions may be unstable. Here, we demonstrate the potential of coordinate descent algorithms for fitting these models, establishing theoretical convergence properties and demonstrating that they are significantly faster than competing approaches. In addition, we demonstrate the utility of convexity diagnostics to determine regions of the parameter space in which the objective function is locally convex, even though the penalty is not. Our simulation study and data examples indicate that nonconvex penalties like MCP and SCAD are worthwhile alternatives to the lasso in many applications. In particular, our numerical results suggest that MCP is the preferred approach among the three methods.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS388 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Strong rules for nonconvex penalties and their implications for efficient algorithms in high-dimensional regression

We consider approaches for improving the efficiency of algorithms for fitting nonconvex penalized regression models such as SCAD and MCP in high dimensions. In particular, we develop rules for discarding variables during cyclic coordinate descent. This dimension reduction leads to a substantial improvement in the speed of these algorithms for high-dimensional problems. The rules we propose here eliminate a substantial fraction of the variables from the coordinate descent algorithm. Violations are quite rare, especially in the locally convex region of the solution path, and furthermore, may be easily detected and corrected by checking the Karush-Kuhn-Tucker conditions. We extend these rules to generalized linear models, as well as to other nonconvex penalties such as the $\ell_2$-stabilized Mnet penalty, group MCP, and group SCAD. We explore three variants of the coordinate decent algorithm that incorporate these rules and study the efficiency of these algorithms in fitting models to both simulated data and on real data from a genome-wide association study

Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors

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 fitting these models stably and efficiently. In addition, we present simulation results and real data examples comparing and contrasting the statistical properties of these methods

Likelihood Adaptively Modified Penalties

A new family of penalty functions, adaptive to likelihood, is introduced for model selection in general regression models. It arises naturally through assuming certain types of prior distribution on the regression parameters. To study stability properties of the penalized maximum likelihood estimator, two types of asymptotic stability are defined. Theoretical properties, including the parameter estimation consistency, model selection consistency, and asymptotic stability, are established under suitable regularity conditions. An efficient coordinate-descent algorithm is proposed. Simulation results and real data analysis show that the proposed method has competitive performance in comparison with existing ones.Comment: 42 pages, 4 figure

A Selective Review of Group Selection in High-Dimensional Models

Grouping structures arise naturally in many statistical modeling problems. Several methods have been proposed for variable selection that respect grouping structure in variables. Examples include the group LASSO and several concave group selection methods. In this article, we give a selective review of group selection concerning methodological developments, theoretical properties and computational algorithms. We pay particular attention to group selection methods involving concave penalties. We address both group selection and bi-level selection methods. We describe several applications of these methods in nonparametric additive models, semiparametric regression, seemingly unrelated regressions, genomic data analysis and genome wide association studies. We also highlight some issues that require further study.Comment: Published in at http://dx.doi.org/10.1214/12-STS392 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

APPLE: Approximate Path for Penalized Likelihood Estimators

In high-dimensional data analysis, penalized likelihood estimators are shown to provide superior results in both variable selection and parameter estimation. A new algorithm, APPLE, is proposed for calculating the Approximate Path for Penalized Likelihood Estimators. Both the convex penalty (such as LASSO) and the nonconvex penalty (such as SCAD and MCP) cases are considered. The APPLE efficiently computes the solution path for the penalized likelihood estimator using a hybrid of the modified predictor-corrector method and the coordinate-descent algorithm. APPLE is compared with several well-known packages via simulation and analysis of two gene expression data sets.Comment: 24 pages, 9 figure