In literature there are several studies on the performance of Bayesian network structure learning algorithms. The focus of these studies is almost always the heuristics the learning algorithms are based on, i.e. the maximisation algorithms (in score-based algorithms) or the techniques for learning the dependencies of each variable (in constraint-based algorithms). In this paper we investigate how the use of permutation tests instead of parametric ones affects the performance of Bayesian network structure learning from discrete data. Shrinkage tests are also covered to provide a broad overview of the techniques developed in current literature.

We present a multi-task learning approach to jointly estimate the means of multiple independent data sets. The proposed multi-task averaging (MTA) algorithm results in a convex combination of the single-task maximum likelihood estimates. We derive the optimal minimum risk estimator and the minimax estimator, and show that these estimators can be efficiently estimated. Simulations and real data experiments demonstrate that MTA estimators often outperform both single-task and James-Stein estimators.

The use of L1 regularisation for sparse learning has generated immense research interest, with successful application in such diverse areas as signal acquisition, image coding, genomics and collaborative filtering. While existing work highlights the many advantages of L1 methods, in this paper we find that L1 regularisation often dramatically underperforms in terms of predictive performance when compared with other methods for inferring sparsity. We focus on unsupervised latent variable models, and develop L1 minimising factor models, Bayesian variants of "L1", and Bayesian models with a stronger L0-like sparsity induced through spike-and-slab distributions. These spike-and-slab Bayesian factor models encourage sparsity while accounting for uncertainty in a principled manner and avoiding unnecessary shrinkage of non-zero values. We demonstrate on a number of data sets that in practice spike-and-slab Bayesian methods outperform L1 minimisation, even on a computational budget. We thus highlight the need to re-assess the wide use of L1 methods in sparsity-reliant applications, particularly when we care about generalising to previously unseen data, and provide an alternative that, over many varying conditions, provides improved generalisation performance.

Inferring probabilistic networks from data is a notoriously difficult task. Under various goodness-of-fit measures, finding an optimal network is NP-hard, even if restricted to polytrees of bounded in-degree. Polynomial-time algorithms are known only for rare special cases, perhaps most notably for branchings, that is, polytrees in which the in-degree of every node is at most one. Here, we study the complexity of finding an optimal polytree that can be turned into a branching by deleting some number of arcs or nodes, treated as a parameter. We show that the problem can be solved via a matroid intersection formulation in polynomial time if the number of deleted arcs is bounded by a constant. The order of the polynomial time bound depends on this constant, hence the algorithm does not establish fixed-parameter tractability when parameterized by the number of deleted arcs. We show that a restricted version of the problem allows fixed-parameter tractability and hence scales well with the parameter. We contrast this positive result by showing that if we parameterize by the number of deleted nodes, a somewhat more powerful parameter, the problem is not fixed-parameter tractable, subject to a complexity-theoretic assumption.

Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical model for such data, by combining assumptions from phylogenetics with Gaussian processes. We describe its use as a nonparametric Bayesian prior distribution, both for prediction (placing posterior distributions on ancestral functions) and model selection (comparing rates of evolution across a phylogeny, or identifying the most likely phylogenies consistent with the observed data). Our work is integrative, extending the popular phylogenetic Brownian Motion and Ornstein-Uhlenbeck models to functional data and Bayesian inference, and extending Gaussian Process regression to phylogenies. We provide a brief illustration of the application of our method.

We present the multidimensional membership mixture (M3) models where every dimension of the membership represents an independent mixture model and each data point is generated from the selected mixture components jointly. This is helpful when the data has a certain shared structure. For example, three unique means and three unique variances can effectively form a Gaussian mixture model with nine components, while requiring only six parameters to fully describe it. In this paper, we present three instantiations of M3 models (together with the learning and inference algorithms): infinite, finite, and hybrid, depending on whether the number of mixtures is fixed or not. They are built upon Dirichlet process mixture models, latent Dirichlet allocation, and a combination respectively. We then consider two applications: topic modeling and learning 3D object arrangements. Our experiments show that our M3 models achieve better performance using fewer topics than many classic topic models. We also observe that topics from the different dimensions of M3 models are meaningful and orthogonal to each other.

Distributions over rankings are used to model data in a multitude of real world settings such as preference analysis and political elections. Modeling such distributions presents several computational challenges, however, due to the factorial size of the set of rankings over an item set. Some of these challenges are quite familiar to the artificial intelligence community, such as how to compactly represent a distribution over a combinatorially large space, and how to efficiently perform probabilistic inference with these representations. With respect to ranking, however, there is the additional challenge of what we refer to as human task complexity -- users are rarely willing to provide a full ranking over a long list of candidates, instead often preferring to provide partial ranking information. Simultaneously addressing all of these challenges -- i.e., designing a compactly representable model which is amenable to efficient inference and can be learned using partial ranking data -- is a difficult task, but is necessary if we would like to scale to problems with nontrivial size. In this paper, we show that the recently proposed riffled independence assumptions cleanly and efficiently address each of the above challenges. In particular, we establish a tight mathematical connection between the concepts of riffled independence and of partial rankings. This correspondence not only allows us to then develop efficient and exact algorithms for performing inference tasks using riffled independence based representations with partial rankings, but somewhat surprisingly, also shows that efficient inference is not possible for riffle independent models (in a certain sense) with observations which do not take the form of partial rankings. Finally, using our inference algorithm, we introduce the first method for learning riffled independence based models from partially ranked data.

The graphical lasso (glasso) is a widely-used fast algorithm for estimating sparse inverse covariance matrices. The glasso solves an L1 penalized maximum likelihood problem and is available as an R library on CRAN. The output from the glasso, a regularized covariance matrix estimate a sparse inverse covariance matrix estimate, not only identify a graphical model but can also serve as intermediate inputs into multivariate procedures such as PCA, LDA, MANOVA, and others. The glasso indeed produces a covariance matrix estimate which solves the L1 penalized optimization problem in a dual sense; however, the method for producing the inverse covariance matrix estimator after this optimization is inexact and may produce asymmetric estimates. This problem is exacerbated when the amount of L1 regularization that is applied is small, which in turn is more likely to occur if the true underlying inverse covariance matrix is not sparse. The lack of symmetry can potentially have consequences. First, it implies that the covariance and inverse covariance estimates are not numerical inverses of one another, and second, asymmetry can possibly lead to negative or complex eigenvalues,rendering many multivariate procedures which may depend on the inverse covariance estimator unusable. We demonstrate this problem, explain its causes, and propose possible remedies.

This paper presents an unsupervised algorithm for nonlinear unmixing of hyperspectral images. The proposed model assumes that the pixel reflectances result from a nonlinear function of the abundance vectors associated with the pure spectral components. We assume that the spectral signatures of the pure components and the nonlinear function are unknown. The first step of the proposed method consists of the Bayesian estimation of the abundance vectors for all the image pixels and the nonlinear function relating the abundance vectors to the observations. The endmembers are subsequently estimated using Gaussian process regression. The performance of the unmixing strategy is evaluated with simulations conducted on synthetic and real data.

We have developed a method for statistical anomaly detection which has been deployed in a tool for condition monitoring of train fleets. The tool is currently used by several railway operators over the world to inspect and visualize the occurrence of event messages generated on the trains. The anomaly detection component helps the operators to quickly find significant deviations from normal behavior and to detect early indications for possible problems. The savings in maintenance costs comes mainly from avoiding costly breakdowns, and have been estimated to several million Euros per year for the tool. In the long run, it is expected that maintenance costs can be reduced with between 5 and 10 % by using the tool.