Journal of Machine Learning Research

The ℓ1-penalized method, or the Lasso, has emerged as an important tool for the analysis of large data sets. Many important results have been obtained for the Lasso in linear regression which have led to a deeper understanding of high-dimensional statistical problems. In this article, we consider a class of weighted ℓ1-penalized estimators for convex loss functions of a general form, including the generalized linear models. We study the estimation, prediction, selection and sparsity properties of the weighted ℓ1-penalized estimator in sparse, high-dimensional settings where the number of predictors p can be much larger than the sample size n. Adaptive Lasso is considered as a special case. A multistage method is developed to approximate concave regularized estimation by applying an adaptive Lasso recursively. We provide prediction and estimation oracle inequalities for single- and multi-stage estimators, a general selection consistency theorem, and an upper bound for the dimension of the Lasso estimator. Important models including the linear regression, logistic regression and log-linear models are used throughout to illustrate the applications of the general results.

We use convex relaxation techniques to provide a sequence of regularized low-rank solutions for large-scale matrix completion problems. Using the nuclear norm as a regularizer, we provide a simple and very efficient convex algorithm for minimizing the reconstruction error subject to a bound on the nuclear norm. Our algorithm Soft-Impute iteratively replaces the missing elements with those obtained from a soft-thresholded SVD. With warm starts this allows us to efficiently compute an entire regularization path of solutions on a grid of values of the regularization parameter. The computationally intensive part of our algorithm is in computing a low-rank SVD of a dense matrix. Exploiting the problem structure, we show that the task can be performed with a complexity linear in the matrix dimensions. Our semidefinite-programming algorithm is readily scalable to large matrices: for example it can obtain a rank-80 approximation of a 10(6) × 10(6) incomplete matrix with 10(5) observed entries in 2.5 hours, and can fit a rank 40 approximation to the full Netflix training set in 6.6 hours. Our methods show very good performance both in training and test error when compared to other competitive state-of-the art techniques.

We describe a class of sparse latent factor models, called graphical factor models (GFMs), and relevant sparse learning algorithms for posterior mode estimation. Linear, Gaussian GFMs have sparse, orthogonal factor loadings matrices, that, in addition to sparsity of the implied covariance matrices, also induce conditional independence structures via zeros in the implied precision matrices. We describe the models and their use for robust estimation of sparse latent factor structure and data/signal reconstruction. We develop computational algorithms for model exploration and posterior mode search, addressing the hard combinatorial optimization involved in the search over a huge space of potential sparse configurations. A mean-field variational technique coupled with annealing is developed to successively generate "artificial" posterior distributions that, at the limiting temperature in the annealing schedule, define required posterior modes in the GFM parameter space. Several detailed empirical studies and comparisons to related approaches are discussed, including analyses of handwritten digit image and cancer gene expression data.

In this paper, we introduce PEBL, a Python library and application for learning Bayesian network structure from data and prior knowledge that provides features unmatched by alternative software packages: the ability to use interventional data, flexible specification of structural priors, modeling with hidden variables and exploitation of parallel processing. PEBL is released under the MIT open-source license, can be installed from the Python Package Index and is available at http://pebl-project.googlecode.com.

Variable selection in high-dimensional space characterizes many contemporary problems in scientific discovery and decision making. Many frequently-used techniques are based on independence screening; examples include correlation ranking (Fan and Lv, 2008) or feature selection using a two-sample t-test in high-dimensional classification (Tibshirani et al., 2003). Within the context of the linear model, Fan and Lv (2008) showed that this simple correlation ranking possesses a sure independence screening property under certain conditions and that its revision, called iteratively sure independent screening (ISIS), is needed when the features are marginally unrelated but jointly related to the response variable. In this paper, we extend ISIS, without explicit definition of residuals, to a general pseudo-likelihood framework, which includes generalized linear models as a special case. Even in the least-squares setting, the new method improves ISIS by allowing feature deletion in the iterative process. Our technique allows us to select important features in high-dimensional classification where the popularly used two-sample t-method fails. A new technique is introduced to reduce the false selection rate in the feature screening stage. Several simulated and two real data examples are presented to illustrate the methodology.

We consider the problems of estimating the parameters as well as the structure of binary-valued Markov networks. For maximizing the penalized log-likelihood, we implement an approximate procedure based on the pseudo-likelihood of Besag (1975) and generalize it to a fast exact algorithm. The exact algorithm starts with the pseudo-likelihood solution and then adjusts the pseudo-likelihood criterion so that each additional iterations moves it closer to the exact solution. Our results show that this procedure is faster than the competing exact method proposed by Lee, Ganapathi, and Koller (2006a). However, we also find that the approximate pseudo-likelihood as well as the approaches of Wainwright et al. (2006), when implemented using the coordinate descent procedure of Friedman, Hastie, and Tibshirani (2008b), are much faster than the exact methods, and only slightly less accurate.

Chain graphs present a broad class of graphical models for description of conditional independence structures, including both Markov networks and Bayesian networks as special cases. In this paper, we propose a computationally feasible method for the structural learning of chain graphs based on the idea of decomposing the learning problem into a set of smaller scale problems on its decomposed subgraphs. The decomposition requires conditional independencies but does not require the separators to be complete subgraphs. Algorithms for both skeleton recovery and complex arrow orientation are presented. Simulations under a variety of settings demonstrate the competitive performance of our method, especially when the underlying graph is sparse.

A non-parametric hierarchical Bayesian framework is developed for designing a classifier, based on a mixture of simple (linear) classifiers. Each simple classifier is termed a local "expert", and the number of experts and their construction are manifested via a Dirichlet process formulation. The simple form of the "experts" allows analytical handling of incomplete data. The model is extended to allow simultaneous design of classifiers on multiple data sets, termed multi-task learning, with this also performed non-parametrically via the Dirichlet process. Fast inference is performed using variational Bayesian (VB) analysis, and example results are presented for several data sets. We also perform inference via Gibbs sampling, to which we compare the VB results.

Clustering analysis is widely used in many fields. Traditionally clustering is regarded as unsupervised learning for its lack of a class label or a quantitative response variable, which in contrast is present in supervised learning such as classification and regression. Here we formulate clustering as penalized regression with grouping pursuit. In addition to the novel use of a non-convex group penalty and its associated unique operating characteristics in the proposed clustering method, a main advantage of this formulation is its allowing borrowing some well established results in classification and regression, such as model selection criteria to select the number of clusters, a difficult problem in clustering analysis. In particular, we propose using the generalized cross-validation (GCV) based on generalized degrees of freedom (GDF) to select the number of clusters. We use a few simple numerical examples to compare our proposed method with some existing approaches, demonstrating our method's promising performance.

We apply a variational method to automatically determine the number of mixtures of independent components in high-dimensional datasets, in which the sources may be nonsymmetrically distributed. The data are modeled by clusters where each cluster is described as a linear mixture of independent factors. The variational Bayesian method yields an accurate density model for the observed data without overfitting problems. This allows the dimensionality of the data to be identified for each cluster. The new method was successfully applied to a difficult real-world medical dataset for diagnosing glaucoma.

We study the variability of predictions made by bagged learners and random forests, and show how to estimate standard errors for these methods. Our work builds on variance estimates for bagging proposed by Efron (1992, 2013) that are based on the jackknife and the infinitesimal jackknife (IJ). In practice, bagged predictors are computed using a finite number B of bootstrap replicates, and working with a large B can be computationally expensive. Direct applications of jackknife and IJ estimators to bagging require B = Θ(n (1.5)) bootstrap replicates to converge, where n is the size of the training set. We propose improved versions that only require B = Θ(n) replicates. Moreover, we show that the IJ estimator requires 1.7 times less bootstrap replicates than the jackknife to achieve a given accuracy. Finally, we study the sampling distributions of the jackknife and IJ variance estimates themselves. We illustrate our findings with multiple experiments and simulation studies.

We present a novel method for estimating tree-structured covariance matrices directly from observed continuous data. Specifically, we estimate a covariance matrix from observations of p continuous random variables encoding a stochastic process over a tree with p leaves. A representation of these classes of matrices as linear combinations of rank-one matrices indicating object partitions is used to formulate estimation as instances of well-studied numerical optimization problems.In particular, our estimates are based on projection, where the covariance estimate is the nearest tree-structured covariance matrix to an observed sample covariance matrix. The problem is posed as a linear or quadratic mixed-integer program (MIP) where a setting of the integer variables in the MIP specifies a set of tree topologies of the structured covariance matrix. We solve these problems to optimality using efficient and robust existing MIP solvers.We present a case study in phylogenetic analysis of gene expression and a simulation study comparing our method to distance-based tree estimating procedures.

In cognitive science and neuroscience, there have been two leading models describing how humans perceive and classify facial expressions of emotion-the continuous and the categorical model. The continuous model defines each facial expression of emotion as a feature vector in a face space. This model explains, for example, how expressions of emotion can be seen at different intensities. In contrast, the categorical model consists of C classifiers, each tuned to a specific emotion category. This model explains, among other findings, why the images in a morphing sequence between a happy and a surprise face are perceived as either happy or surprise but not something in between. While the continuous model has a more difficult time justifying this latter finding, the categorical model is not as good when it comes to explaining how expressions are recognized at different intensities or modes. Most importantly, both models have problems explaining how one can recognize combinations of emotion categories such as happily surprised versus angrily surprised versus surprise. To resolve these issues, in the past several years, we have worked on a revised model that justifies the results reported in the cognitive science and neuroscience literature. This model consists of C distinct continuous spaces. Multiple (compound) emotion categories can be recognized by linearly combining these C face spaces. The dimensions of these spaces are shown to be mostly configural. According to this model, the major task for the classification of facial expressions of emotion is precise, detailed detection of facial landmarks rather than recognition. We provide an overview of the literature justifying the model, show how the resulting model can be employed to build algorithms for the recognition of facial expression of emotion, and propose research directions in machine learning and computer vision researchers to keep pushing the state of the art in these areas. We also discuss how the model can aid in studies of human perception, social interactions and disorders.

Planning problems that involve learning a policy from a single training set of finite horizon trajectories arise in both social science and medical fields. We consider Q-learning with function approximation for this setting and derive an upper bound on the generalization error. This upper bound is in terms of quantities minimized by a Q-learning algorithm, the complexity of the approximation space and an approximation term due to the mismatch between Q-learning and the goal of learning a policy that maximizes the value function.

We develop an R package fastclime for solving a family of regularized linear programming (LP) problems. Our package efficiently implements the parametric simplex algorithm, which provides a scalable and sophisticated tool for solving large-scale linear programs. As an illustrative example, one use of our LP solver is to implement an important sparse precision matrix estimation method called CLIME (Constrained L 1 Minimization Estimator). Compared with existing packages for this problem such as clime and flare, our package has three advantages: (1) it efficiently calculates the full piecewise-linear regularization path; (2) it provides an accurate dual certificate as stopping criterion; (3) it is completely coded in C and is highly portable. This package is designed to be useful to statisticians and machine learning researchers for solving a wide range of problems.

We present a general and detailed development of an algorithm for finite-horizon fitted-Q iteration with an arbitrary number of reward signals and linear value function approximation using an arbitrary number of state features. This includes a detailed treatment of the 3-reward function case using triangulation primitives from computational geometry and a method for identifying globally dominated actions. We also present an example of how our methods can be used to construct a real-world decision aid by considering symptom reduction, weight gain, and quality of life in sequential treatments for schizophrenia. Finally, we discuss future directions in which to take this work that will further enable our methods to make a positive impact on the field of evidence-based clinical decision support.

Hard and soft classifiers are two important groups of techniques for classification problems. Logistic regression and Support Vector Machines are typical examples of soft and hard classifiers respectively. The essential difference between these two groups is whether one needs to estimate the class conditional probability for the classification task or not. In particular, soft classifiers predict the label based on the obtained class conditional probabilities, while hard classifiers bypass the estimation of probabilities and focus on the decision boundary. In practice, for the goal of accurate classification, it is unclear which one to use in a given situation. To tackle this problem, the Large-margin Unified Machine (LUM) was recently proposed as a unified family to embrace both groups. The LUM family enables one to study the behavior change from soft to hard binary classifiers. For multicategory cases, however, the concept of soft and hard classification becomes less clear. In that case, class probability estimation becomes more involved as it requires estimation of a probability vector. In this paper, we propose a new Multicategory LUM (MLUM) framework to investigate the behavior of soft versus hard classification under multicategory settings. Our theoretical and numerical results help to shed some light on the nature of multicategory classification and its transition behavior from soft to hard classifiers. The numerical results suggest that the proposed tuned MLUM yields very competitive performance.

The problem of selecting a subset of relevant features in a potentially overwhelming quantity of data is classic and found in many branches of science including - examples in computer vision, text processing and more recently bioinformatics are abundant. We present a definition of "relevancy" based on spectral properties of the Affinity (or Laplacian) of the features' measurement matrix. The feature selection process is then based on a continuous ranking of the features defined by a least-squares optimization process. A remarkable property of the feature relevance function is that sparse solutions for the ranking values naturally emerge as a result of a "biased nonnegativity" of a key matrix in the process. As a result, a simple least-squares optimization process converges onto a sparse solution, i.e., a selection of a subset of features which form a local maxima over the relevance function. The feature selection algorithm can be embedded in both unsupervised and supervised inference problems and empirical evidence shows that the feature selections typically achieve high accuracy even when only a small fraction of the features are relevant.

In the context of independent components analysis (ICA), the mutual information (MI) of the extracted components is one of the most desirable measures of independence, due to its special properties. This paper presents a method for performing linear and nonlinear ICA based on MI, with few approximations. The use of MI as an objective function for ICA requires the estimation of the statistical distributions of the separated components. In this work, both the extraction of independent components and the estimation of their distributions are performed simultaneously, by a single network with a specialized structure, trained with a single objective function

This paper comments on the published work dealing with robustness and regularization of support vector machines (Journal of Machine Learning Research, vol. 10, pp. 1485-1510, 2009) [arXiv:0803.3490] by H. Xu, etc. They proposed a theorem to show that it is possible to relate robustness in the feature space and robustness in the sample space directly. In this paper, we propose a counter example that rejects their theorem.

Hierarchical statistical models are widely employed in information science and data engineering. The models consist of two types of variables: observable variables that represent the given data and latent variables for the unobservable labels. An asymptotic analysis of the models plays an important role in evaluating the learning process; the result of the analysis is applied not only to theoretical but also to practical situations, such as optimal model selection and active learning. There are many studies of generalization errors, which measure the prediction accuracy of the observable variables. However, the accuracy of estimating the latent variables has not yet been elucidated. For a quantitative evaluation of this, the present paper formulates distribution-based functions for the errors in the estimation of the latent variables. The asymptotic behavior is analyzed for both the maximum likelihood and the Bayes methods.

We study the theoretical advantages of active learning over passive learning. Specifically, we prove that, in noise-free classifier learning for VC classes, any passive learning algorithm can be transformed into an active learning algorithm with asymptotically strictly superior label complexity for all nontrivial target functions and distributions. We further provide a general characterization of the magnitudes of these improvements in terms of a novel generalization of the disagreement coefficient. We also extend these results to active learning in the presence of label noise, and find that even under broad classes of noise distributions, we can typically guarantee strict improvements over the known results for passive learning.

Actor-Critic based approaches were among the first to address reinforcement learning in a general setting. Recently, these algorithms have gained renewed interest due to their generality, good convergence properties, and possible biological relevance. In this paper, we introduce an online temporal difference based actor-critic algorithm which is proved to converge to a neighborhood of a local maximum of the average reward. Linear function approximation is used by the critic in order estimate the value function, and the temporal difference signal, which is passed from the critic to the actor. The main distinguishing feature of the present convergence proof is that both the actor and the critic operate on a similar time scale, while in most current convergence proofs they are required to have very different time scales in order to converge. Moreover, the same temporal difference signal is used to update the parameters of both the actor and the critic. A limitation of the proposed approach, compared to results available for two time scale convergence, is that convergence is guaranteed only to a neighborhood of an optimal value, rather to an optimal value itself. The single time scale and identical temporal difference signal used by the actor and the critic, may provide a step towards constructing more biologically realistic models of reinforcement learning in the brain.

The investigation of directed acyclic graphs (DAGs) encoding the same Markov property, that is the same conditional independence relations of multivariate observational distributions, has a long tradition; many algorithms exist for model selection and structure learning in Markov equivalence classes. In this paper, we extend the notion of Markov equivalence of DAGs to the case of interventional distributions arising from multiple intervention experiments. We show that under reasonable assumptions on the intervention experiments, interventional Markov equivalence defines a finer partitioning of DAGs than observational Markov equivalence and hence improves the identifiability of causal models. We give a graph theoretic criterion for two DAGs being Markov equivalent under interventions and show that each interventional Markov equivalence class can, analogously to the observational case, be uniquely represented by a chain graph called interventional essential graph (also known as CPDAG in the observational case). These are key insights for deriving a generalization of the Greedy Equivalence Search algorithm aimed at structure learning from interventional data. This new algorithm is evaluated in a simulation study.

We consider the PC-algorithm Spirtes et. al. (2000) for estimating the skeleton of a very high-dimensional acyclic directed graph (DAG) with corresponding Gaussian distribution. The PC-algorithm is computationally feasible for sparse problems with many nodes, i.e. variables, and it has the attractive property to automatically achieve high computational efficiency as a function of sparseness of the true underlying DAG. We prove consistency of the algorithm for very high-dimensional, sparse DAGs where the number of nodes is allowed to quickly grow with sample size n, as fast as O(n^a) for any 0<a<infinity. The sparseness assumption is rather minimal requiring only that the neighborhoods in the DAG are of lower order than sample size n. We empirically demonstrate the PC-algorithm for simulated data and argue that the algorithm is rather insensitive to the choice of its single tuning parameter.