Manifold Elastic Net: A Unified Framework for Sparse Dimension Reduction

It is difficult to find the optimal sparse solution of a manifold learning based dimensionality reduction algorithm. The lasso or the elastic net penalized manifold learning based dimensionality reduction is not directly a lasso penalized least square problem and thus the least angle regression (LARS) (Efron et al. \cite{LARS}), one of the most popular algorithms in sparse learning, cannot be applied. Therefore, most current approaches take indirect ways or have strict settings, which can be inconvenient for applications. In this paper, we proposed the manifold elastic net or MEN for short. MEN incorporates the merits of both the manifold learning based dimensionality reduction and the sparse learning based dimensionality reduction. By using a series of equivalent transformations, we show MEN is equivalent to the lasso penalized least square problem and thus LARS is adopted to obtain the optimal sparse solution of MEN. In particular, MEN has the following advantages for subsequent classification: 1) the local geometry of samples is well preserved for low dimensional data representation, 2) both the margin maximization and the classification error minimization are considered for sparse projection calculation, 3) the projection matrix of MEN improves the parsimony in computation, 4) the elastic net penalty reduces the over-fitting problem, and 5) the projection matrix of MEN can be interpreted psychologically and physiologically. Experimental evidence on face recognition over various popular datasets suggests that MEN is superior to top level dimensionality reduction algorithms.Comment: 33 pages, 12 figure

Pathway-Based Genomics Prediction using Generalized Elastic Net.

We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers solutions toward sets of mechanistically interlinked genes. Using experiments on synthetic data, we demonstrate that pathway-guided results maintain, and often improve, the accuracy of predictors even in cases where the full gene network is unknown. We apply the method to predict the drug response of breast cancer cell lines. GELnet is able to reveal genetic determinants of sensitivity and resistance for several compounds. In particular, for an EGFR/HER2 inhibitor, it finds a possible trans-differentiation resistance mechanism missed by the corresponding pathway agnostic approach

SpaSM: A MATLAB Toolbox for Sparse Statistical Modeling

Applications in biotechnology such as gene expression analysis and image processing have led to a tremendous development of statistical methods with emphasis on reliable solutions to severely underdetermined systems. Furthermore, interpretations of such solutions are of importance, meaning that the surplus of inputs has been reduced to a concise model. At the core of this development are methods which augment the standard linear models for regression, classification and decomposition such that sparse solutions are obtained. This toolbox aims at making public available carefully implemented and well-tested variants of the most popular of such methods for the MATLAB programming environment. These methods consist of easy-to-read yet efficient implementations of various coefficient-path following algorithms and implementations of sparse principal component analysis and sparse discriminant analysis which are not available in MATLAB. The toolbox builds on code made public in 2005 and which has since been used in several studies

Feature selection guided by structural information

In generalized linear regression problems with an abundant number of features, lasso-type regularization which imposes an $\ell^1$-constraint on the regression coefficients has become a widely established technique. Deficiencies of the lasso in certain scenarios, notably strongly correlated design, were unmasked when Zou and Hastie [J. Roy. Statist. Soc. Ser. B 67 (2005) 301--320] introduced the elastic net. In this paper we propose to extend the elastic net by admitting general nonnegative quadratic constraints as a second form of regularization. The generalized ridge-type constraint will typically make use of the known association structure of features, for example, by using temporal- or spatial closeness. We study properties of the resulting "structured elastic net" regression estimation procedure, including basic asymptotics and the issue of model selection consistency. In this vein, we provide an analog to the so-called "irrepresentable condition" which holds for the lasso. Moreover, we outline algorithmic solutions for the structured elastic net within the generalized linear model family. The rationale and the performance of our approach is illustrated by means of simulated and real world data, with a focus on signal regression.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS302 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org