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Register a new userProbing for sparse and fast variable selection with model-based boosting
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Added by
Janek Thomas
Publication date
2017
fields
Mathematical Statistics
and research's language is
English
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We present a new variable selection method based on model-based gradient boosting and randomly permuted variables. Model-based boosting is a tool to fit a statistical model while performing variable selection at the same time. A drawback of the fitting lies in the need of multiple model fits on slightly altered data (e.g. cross-validation or bootstrap) to find the optimal number of boosting iterations and prevent overfitting. In our proposed approach, we augment the data set with randomly permut
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We develop a Bayesian variable selection method, called SVEN, based on a hierarchical Gaussian linear model with priors placed on the regression coefficients as well as on the model space. Sparsity is achieved by using degenerate spike priors on inactive variables, whereas Gaussian slab priors are placed on the coefficients for the important predictors making the posterior probability of a model available in explicit form (up to a normalizing constant). The strong model selection consistency is shown to be attained when the number of predictors grows nearly exponentially with the sample size and even when the norm of mean effects solely due to the unimportant variables diverge, which is a novel attractive feature. An appealing byproduct of SVEN is the construction of novel model weight adjusted prediction intervals. Embedding a unique model based screening and using fast Cholesky updates, SVEN produces a highly scalable computational framework to explore gigantic model spaces, rapidly identify the regions of high posterior probabilities and make fast inference and prediction. A temperature schedule guided by our model selection consistency derivations is used to further mitigate multimodal posterior distributions. The performance of SVEN is demonstrated through a number of simulation experiments and a real data example from a genome wide association study with over half a million markers.
This paper proposes a canonical-correlation-based filter method for feature selection. The sum of squared canonical correlation coefficients is adopted as the feature ranking criterion. The proposed method boosts the computational speed of the ranking criterion in greedy search. The supporting theorems developed for the feature selection method are fundamental to the understanding of the canonical correlation analysis. In empirical studies, a synthetic dataset is used to demonstrate the speed advantage of the proposed method, and eight real datasets are applied to show the effectiveness of the proposed feature ranking criterion in both classification and regression. The results show that the proposed method is considerably faster than the definition-based method, and the proposed ranking criterion is competitive compared with the seven mutual-information-based criteria.
In this paper, we consider the Graphical Lasso (GL), a popular optimization problem for learning the sparse representations of high-dimensional datasets, which is well-known to be computationally expensive for large-scale problems. Recently, we have shown that the sparsity pattern of the optimal solution of GL is equivalent to the one obtained from simply thresholding the sample covariance matrix, for sparse graphs under different conditions. We have also derived a closed-form solution that is optimal when the thresholded sample covariance matrix has an acyclic structure. As a major generalization of the previous result, in this paper we derive a closed-form solution for the GL for graphs with chordal structures. We show that the GL and thresholding equivalence conditions can significantly be simplified and are expected to hold for high-dimensional problems if the thresholded sample covariance matrix has a chordal structure. We then show that the GL and thresholding equivalence is enough to reduce the GL to a maximum determinant matrix completion problem and drive a recursive closed-form solution for the GL when the thresholded sample covariance matrix has a chordal structure. For large-scale problems with up to 450 million variables, the proposed method can solve the GL problem in less than 2 minutes, while the state-of-the-art methods converge in more than 2 hours.
Modern computing and communication technologies can make data collection procedures very efficient. However, our ability to analyze large data sets and/or to extract information out from them is hard-pressed to keep up with our capacities for data collection. Among these huge data sets, some of them are not collected for any particular research purpose. For a classification problem, this means that the essential label information may not be readily obtainable, in the data set in hands, and an extra labeling procedure is required such that we can have enough label information to be used for constructing a classification model. When the size of a data set is huge, to label each subject in it will cost a lot in both capital and time. Thus, it is an important issue to decide which subjects should be labeled first in order to efficiently reduce the training cost/time. Active learning method is a promising outlet for this situation, because with the active learning ideas, we can select the unlabeled subjects sequentially without knowing their label information. In addition, there will be no confirmed information about the essential variables for constructing an efficient classification rule. Thus, how to merge a variable selection scheme with an active learning procedure is of interest. In this paper, we propose a procedure for building binary classification models when the complete label information is not available in the beginning of the training stage. We study an model-based active learning procedure with sequential variable selection schemes, and discuss the results of the proposed procedure from both theoretical and numerical aspects.
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not straightforward. We therefore require suitable statistical tools that allow us to choose rationally between different mechanistic models of e.g. signal transduction or gene regulation networks. This is particularly challenging in systems biology where only a small number of molecular species can be assayed at any given time and all measurements are subject to measurement uncertainty. Here we develop such a model selection framework based on approximate Bayesian computation and employing sequential Monte Carlo sampling. We show that our approach can be applied across a wide range of biological scenarios, and we illustrate its use on real data describing influenza dynamics and the JAK-STAT signalling pathway. Bayesian model selection strikes a balance between the complexity of the simulation models and their ability to describe observed data. The present approach enables us to employ the whole formal apparatus to any system that can be (efficiently) simulated, even when exact likelihoods are computationally intractable.
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