We present the Parallel, Forward-Backward with Pruning (PFBP) algorithm for feature selection (FS) in Big Data settings (high dimensionality and or sample size). To tackle the challenges of Big Data FS PFBP partitions the data matrix both in terms of rows (samples, training examples) as well as columns (features). By employing the concepts of p-values of conditional independence tests and meta-analysis techniques PFBP manages to rely only on computations local to a partition while minimizing communication costs. Then, it employs powerful and safe (asymptotically sound) heuristics to make early, approximate decisions, such as Early Dropping of features from consideration in subsequent iterations, Early Stopping of consideration of features within the same iteration, or Early Return of the winner in each iteration. PFBP provides asymptotic guarantees of optimal-ity for data distributions faithfully representable by a causal network (Bayesian network or maximal ancestral graph). Our empirical analysis confirms a super-linear speedup of the algorithm with increasing sample size, linear scalability with respect to the number of features and processing cores, while dominating other competitive algorithms in its class.
In extensive simulations it has been shown that causal-based feature selection methods are competitive with Lasso on classification and survival analysis tasks on many real datasets @cite_51 @cite_16 @cite_31 @cite_49 . Furthermore, the non-parallel version of PFBP (called Forward-Backward Selection with Early Dropping) as well as the standard Forward-Backward Selection algorithm have been shown to perform as well as Lasso if restricted to select the same number of variables @cite_12 .
@cite_49 @cite_31 @cite_16 @cite_51 @cite_12
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Forward-backward selection is one of the most basic and commonly-used feature selection algorithms available. It is also general and conceptually applicable to many different types of data. In this paper, we propose a heuristic that significantly improves its running time, while preserving predictive accuracy. The idea is to temporarily discard the variables that are conditionally independent with the outcome given the selected variable set. Depending on how those variables are reconsidered and reintroduced, this heuristic gives rise to a family of algorithms with increasingly stronger theoretical guarantees. In distributions that can be faithfully represented by Bayesian networks or maximal ancestral graphs, members of this algorithmic family are able to correctly identify the Markov blanket in the sample limit. In experiments we show that the proposed heuristic increases computational efficiency by about two orders of magnitude in high-dimensional problems, while selecting fewer variables and retaining predictive performance. Furthermore, we show that the proposed algorithm and feature selection with LASSO perform similarly when restricted to select the same number of variables, making the proposed algorithm an attractive alternative for problems where no (efficient) algorithm for LASSO exists. We consider the least-square linear regression problem with regularization by the l1-norm, a problem usually referred to as the Lasso. In this paper, we present a detailed asymptotic analysis of model consistency of the Lasso. For various decays of the regularization parameter, we compute asymptotic equivalents of the probability of correct model selection (i.e., variable selection). For a specific rate decay, we show that the Lasso selects all the variables that should enter the model with probability tending to one exponentially fast, while it selects all other variables with strictly positive probability. We show that this property implies that if we run the Lasso for several bootstrapped replications of a given sample, then intersecting the supports of the Lasso bootstrap estimates leads to consistent model selection. This novel variable selection algorithm, referred to as the Bolasso, is compared favorably to other linear regression methods on synthetic data and datasets from the UCI machine learning repository. 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 computes multiple exact local minimizers of a possibly nonconvex penalized loss function in a certain main branch of the graph of critical points of the penalized loss. Its output is a continuous piecewise linear path encompassing from the origin for infinite penalty to a least squares solution for zero penalty. We prove that at a universal penalty level, the MC+ has high probability of matching the signs of the unknowns, and thus correct selection, without assuming the strong irrepresentable condition required by the LASSO. This selection consistency applies to the case of p » n, and is proved to hold for exactly the MC+ solution among possibly many local minimizers. We prove that the MC+ attains certain minimax convergence rates in probability for the estimation of regression coefficients in l r balls. We use the SURE method to derive degrees of freedom and C p -type risk estimates for general penalized LSE, including the LASSO and MC+ estimators, and prove their unbiasedness. Based on the estimated degrees of freedom, we propose an estimator of the noise level for proper choice of the penalty level. For full rank designs and general sub-quadratic penalties, we provide necessary and sufficient conditions for the continuity of the penalized LSE. Simulation results overwhelmingly support our claim of superior variable selection properties and demonstrate the computational efficiency of the proposed method. Summary. We consider the problem of selecting grouped variables (factors) for accurate prediction in regression. Such a problem arises naturally in many practical situations with the multifactor analysis-of-variance problem as the most important and well-known example. Instead of selecting factors by stepwise backward elimination, we focus on the accuracy of estimation and consider extensions of the lasso, the LARS algorithm and the non-negative garrotte for factor selection. The lasso, the LARS algorithm and the non-negative garrotte are recently proposed regression methods that can be used to select individual variables. We study and propose efficient algorithms for the extensions of these methods for factor selection and show that these extensions give superior performance to the traditional stepwise backward elimination method in factor selection problems. We study the similarities and the differences between these methods. Simulations and real examples are used to illustrate the methods.