Feature selection, identifying a subset of variables that are relevant for predicting a response, is an important and challenging component of many methods in statistics and machine learning. Feature selection is especially difficult and computationally intensive when the number of variables approaches or exceeds the number of samples, as is often the case for many genomic datasets. Here, we introduce a new approach -- the Bayesian Ising Approximation (BIA) -- to rapidly calculate posterior probabilities for feature relevance in L2 penalized linear regression. In the regime where the regression problem is strongly regularized by the prior, we show that computing the marginal posterior probabilities for features is equivalent to computing the magnetizations of an Ising model. Using a mean field approximation, we show it is possible to rapidly compute the feature selection path described by the posterior probabilities as a function of the L2 penalty. We present simulations and analytical results illustrating the accuracy of the BIA on some simple regression problems. Finally, we demonstrate the applicability of the BIA to high dimensional regression by analyzing a gene expression dataset with nearly 30,000 features.

We introduce a means of automating machine learning (ML) for big data tasks, by performing scalable stochastic Bayesian optimisation of ML algorithm parameters and hyper-parameters. More often than not, the critical tuning of ML algorithm parameters has relied on domain expertise from experts, along with laborious hand-tuning, brute search or lengthy sampling runs. Against this background, Bayesian optimisation is finding increasing use in automating parameter tuning, making ML algorithms accessible even to non-experts. However, the state of the art in Bayesian optimisation is incapable of scaling to the large number of evaluations of algorithm performance required to fit realistic models to complex, big data. We here describe a stochastic, sparse, Bayesian optimisation strategy to solve this problem, using many thousands of noisy evaluations of algorithm performance on subsets of data in order to effectively train algorithms for big data. We provide a comprehensive benchmarking of possible sparsification strategies for Bayesian optimisation, concluding that a Nystrom approximation offers the best scaling and performance for real tasks. Our proposed algorithm demonstrates substantial improvement over the state of the art in tuning the parameters of a Gaussian Process time series prediction task on real, big data.

We consider a discriminative learning (regression) problem, whereby the regression function is a convex combination of k linear classifiers. Existing approaches are based on the EM algorithm, or similar techniques, without provable guarantees. We develop a simple method based on spectral techniques and a `mirroring' trick, that discovers the subspace spanned by the classifiers' parameter vectors. Under a probabilistic assumption on the feature vector distribution, we prove that this approach has nearly optimal statistical efficiency.

Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method's performance.

Matrix factorization (MF) has become a common approach to collaborative filtering, due to ease of implementation and scalability to large data sets. Two existing drawbacks of the basic model is that it does not incorporate side information on either users or items, and assumes a common variance for all users. We extend the work of constrained probabilistic matrix factorization by deriving the Gibbs updates for the side feature vectors for items (Salakhutdinov and Minh, 2008). We show that this Bayesian treatment to the constrained PMF model outperforms simple MAP estimation. We also consider extensions to heteroskedastic precision introduced in the literature (Lakshminarayanan, Bouchard, and Archambeau, 2011). We show that this tends result in overfitting for deterministic approximation algorithms (ex: Variational inference) when the observed entries in the user / item matrix are distributed in an non-uniform manner. In light of this, we propose a truncated precision model. Our experimental results suggest that this model tends to delay overfitting.

We propose {graphical sure screening}, or GRASS, a very simple and computationally-efficient screening procedure for recovering the structure of a Gaussian graphical model in the high-dimensional setting. The GRASS estimate of the conditional dependence graph is obtained by thresholding the elements of the sample covariance matrix. The proposed approach possesses the sure screening property: with very high probability, the GRASS estimated edge set contains the true edge set. Furthermore, with high probability, the size of the estimated edge set is controlled. We provide a choice of threshold for GRASS that can control the expected false positive rate. We illustrate the performance of GRASS in a simulation study and on a gene expression data set, and show that in practice it performs quite competitively with more complex and computationally-demanding techniques for graph estimation.

Non-negative blind source separation (non-negative BSS), which is also referred to as non-negative matrix factorization (NMF), is a very active field in domains as different as astrophysics, audio processing or biomedical signal processing. In this context, the efficient retrieval of the sources requires the use of signal priors such as sparsity. If NMF has now been well studied with sparse constraints in the direct domain, only very few algorithms can encompass non-negativity together with sparsity in a transformed domain since simultaneously dealing with two priors in two different domains is challenging. In this article, we show how a sparse NMF algorithm coined non-negative generalized morphological component analysis (nGMCA) can be extended to impose non-negativity in the direct domain along with sparsity in a transformed domain, with both analysis and synthesis formulations. To our knowledge, this work presents the first comparison of analysis and synthesis priors ---as well as their reweighted versions--- in the context of blind source separation. Comparisons with state-of-the-art NMF algorithms on realistic data show the efficiency as well as the robustness of the proposed algorithms.

We propose a new approach to solve optimal stopping problems via simulation. Working within the backward dynamic programming/Snell envelope framework, we augment the methodology of Longstaff-Schwartz that focuses on approximating the stopping strategy. Namely, we introduce adaptive generation of the stochastic grids anchoring the simulated sample paths of the underlying state process. This allows for active learning of the classifiers partitioning the state space into the continuation and stopping regions. To this end, we examine sequential design schemes that adaptively place new design points close to the stopping boundaries. We then discuss dynamic regression algorithms that can implement such recursive estimation and local refinement of the classifiers. The new algorithm is illustrated with a variety of numerical experiments, showing that an order of magnitude savings in terms of design size can be achieved. We also compare with existing benchmarks in the context of pricing multi-dimensional Bermudan options.

In this paper we study lifted inference for the Weighted First-Order Model Counting problem (WFOMC), which counts the assignments that satisfy a given sentence in first-order logic (FOL); it has applications in Statistical Relational Learning (SRL) and Probabilistic Databases (PDB). We present several results. First, we describe a lifted inference algorithm that generalizes prior approaches in SRL and PDB. Second, we provide a novel dichotomy result for a non-trivial fragment of FO CNF sentences, showing that for each sentence the WFOMC problem is either in PTIME or #P-hard in the size of the input domain; we prove that, in the first case our algorithm solves the WFOMC problem in PTIME, and in the second case it fails. Third, we present several properties of the algorithm. Finally, we discuss limitations of lifted inference for symmetric probabilistic databases (where the weights of ground literals depend only on the relation name, and not on the constants of the domain), and prove the impossibility of a dichotomy result for the complexity of probabilistic inference for the entire language FOL.

We study propagation for the Sequence constraint in the context of constraint programming based on limited-width MDDs. Our first contribution is proving that establishing MDD-consistency for Sequence is NP-hard. Yet, we also show that this task is fixed parameter tractable with respect to the length of the sub-sequences. In addition, we propose a partial filtering algorithm that relies on a specific decomposition of the constraint and a novel extension of MDD filtering to node domains. We experimentally evaluate the performance of our proposed filtering algorithm, and demonstrate that the strength of the MDD propagation increases as the maximum width is increased. In particular, MDD propagation can outperform conventional domain propagation for Sequence by reducing the search tree size and solving time by several orders of magnitude. Similar improvements are observed with respect to the current best MDD approach that applies the decomposition of Sequence into Among constraints.