Many relations of scientific interest are nonlinear, and even in linear systems distributions are often non-Gaussian, for example in fMRI BOLD data. A class of search procedures for causal relations in high dimensional data relies on sample derived conditional independence decisions. The most common applications rely on Gaussian tests that can be systematically erroneous in nonlinear non-Gaussian cases. Recent work (Gretton et al. (2009), Tillman et al. (2009), Zhang et al. (2011)) has proposed conditional independence tests using Reproducing Kernel Hilbert Spaces (RKHS). Among these, perhaps the most efficient has been KCI (Kernel Conditional Independence, Zhang et al. (2011)), with computational requirements that grow effectively at least as O(N3), placing it out of range of large sample size analysis, and restricting its applicability to high dimensional data sets. We propose a class of O(N2) tests using conditional correlation independence (CCI) that require a few seconds on a standard workstation for tests that require tens of minutes to hours for the KCI method, depending on degree of parallelization, with similar accuracy. For accuracy on difficult nonlinear, non-Gaussian data sets, we also compare a recent test due to Harris & Drton (2012), applicable to nonlinear, non-Gaussian distributions in the Gaussian copula, as well as to partial correlation, a linear Gaussian test.

One of the earliest conjectures in computational learning theory-the Sample Compression conjecture-asserts that concept classes (equivalently set systems) admit compression schemes of size linear in their VC dimension. To-date this statement is known to be true for maximum classes---those that possess maximum cardinality for their VC dimension. The most promising approach to positively resolving the conjecture is by embedding general VC classes into maximum classes without super-linear increase to their VC dimensions, as such embeddings would extend the known compression schemes to all VC classes. We show that maximum classes can be characterised by a local-connectivity property of the graph obtained by viewing the class as a cubical complex. This geometric characterisation of maximum VC classes is applied to prove a negative embedding result which demonstrates VC-d classes that cannot be embedded in any maximum class of VC dimension lower than 2d. On the other hand, we show that every VC-d class C embeds in a VC-(d+D) maximum class where D is the deficiency of C, i.e., the difference between the cardinalities of a maximum VC-d class and of C. For VC-2 classes in binary n-cubes for 4 <= n <= 6, we give best possible results on embedding into maximum classes. For some special classes of Boolean functions, relationships with maximum classes are investigated. Finally we give a general recursive procedure for embedding VC-d classes into VC-(d+k) maximum classes for smallest k.

In this paper we demonstrate that tempering Markov chain Monte Carlo samplers for Bayesian models by recursively subsampling observations without replacement can improve the performance of baseline samplers in terms of effective sample size per computation. We present two tempering by subsampling algorithms, subsampled parallel tempering and subsampled tempered transitions. We provide an asymptotic analysis of the computational cost of tempering by subsampling, verify that tempering by subsampling costs less than traditional tempering, and demonstrate both algorithms on Bayesian approaches to learning the mean of a high dimensional multivariate Normal and estimating Gaussian process hyperparameters.

The normalized maximized likelihood (NML) provides the minimax regret solution in universal data compression, gambling, and prediction, and it plays an essential role in the minimum description length (MDL) method of statistical modeling and estimation. Here we show that the normalized maximum likelihood has a Bayes-like representation as a mixture of the component models, even in finite samples, though the weights of linear combination may be both positive and negative. This representation addresses in part the relationship between MDL and Bayes modeling. This representation has the advantage of speeding the calculation of marginals and conditionals required for coding and prediction applications.

We present a Bayesian nonparametric framework for multilevel clustering which utilizes group-level context information to simultaneously discover low-dimensional structures of the group contents and partitions groups into clusters. Using the Dirichlet process as the building block, our model constructs a product base-measure with a nested structure to accommodate content and context observations at multiple levels. The proposed model possesses properties that link the nested Dirichlet processes (nDP) and the Dirichlet process mixture models (DPM) in an interesting way: integrating out all contents results in the DPM over contexts, whereas integrating out group-specific contexts results in the nDP mixture over content variables. We provide a Polya-urn view of the model and an efficient collapsed Gibbs inference procedure. Extensive experiments on real-world datasets demonstrate the advantage of utilizing context information via our model in both text and image domains.

A deep belief network (DBN) (Hinton et al., 2006) is a layered stochastic network with undirected bipartite interactions between the units in the top two layers, and directed bipartite interactions between the units in all other subsequent pairs of layers, directed towards the bottom layer. The top two layers form a restricted Boltzmann machine (RBM) (Smolensky, 1986). The entire network defines a model of probability distributions on the states of the units in the bottom layer, the visible layer. When the number of units in every layer has the same order of magnitude, the network is called narrow . The depth refers to the number of layers. Deep network architectures are believed to play a key role in information processing of intelligent agents, see (Bengio, 2009) for an overview on this exciting topic. DBNs were the first deep architectures to be envisaged together with an efficient unsupervised training algorithm (Hinton et al., 2006).

Partitioning a graph into groups of vertices such that those within each group are more densely connected than vertices assigned to different groups, known as graph clustering, is often used to gain insight into the organisation of large scale networks and for visualisation purposes. Whereas a large number of dedicated techniques have been recently proposed for static graphs, the design of on-line graph clustering methods tailored for evolving networks is a challenging problem, and much less documented in the literature. Motivated by the broad variety of applications concerned, ranging from the study of biological networks to the analysis of networks of scientific references through the exploration of communications networks such as the World Wide Web, it is the main purpose of this paper to introduce a novel, computationally efficient, approach to graph clustering in the evolutionary context. Namely, the method promoted in this article can be viewed as an incremental eigenvalue solution for the spectral clustering method described by Ng. et al. (2001). The incremental eigenvalue solution is a general technique for finding the approximate eigenvectors of a symmetric matrix given a change. As well as outlining the approach in detail, we present a theoretical bound on the quality of the approximate eigenvectors using perturbation theory. We then derive a novel spectral clustering algorithm called Incremental Approximate Spectral Clustering (IASC). The IASC algorithm is simple to implement and its efficacy is demonstrated on both synthetic and real datasets modelling the evolution of a HIV epidemic, a citation network and the purchase history graph of an e-commerce website.

We present the first public release of our generic neural network training algorithm, called SkyNet. This efficient and robust machine learning tool is able to train large and deep feed-forward neural networks, including autoencoders, for use in a wide range of supervised and unsupervised learning applications, such as regression, classification, density estimation, clustering and dimensionality reduction. SkyNet uses a `pre-training' method to obtain a set of network parameters that has empirically been shown to be close to a good solution, followed by further optimisation using a regularised variant of Newton's method, where the level of regularisation is determined and adjusted automatically; the latter uses second-order derivative information to improve convergence, but without the need to evaluate or store the full Hessian matrix, by using a fast approximate method to calculate Hessian-vector products. This combination of methods allows for the training of complicated networks that are difficult to optimise using standard backpropagation techniques. SkyNet employs convergence criteria that naturally prevent overfitting, and also includes a fast algorithm for estimating the accuracy of network outputs. The utility and flexibility of SkyNet are demonstrated by application to a number of toy problems, and to astronomical problems focusing on the recovery of structure from blurred and noisy images, the identification of gamma-ray bursters, and the compression and denoising of galaxy images. The SkyNet software, which is implemented in standard ANSI C and fully parallelised using MPI, is available at http://www.mrao.cam.ac.uk/software/skynet/.

Graphical models are popular statistical tools which are used to represent dependent or causal complex systems. Statistically equivalent causal or directed graphical models are said to belong to a Markov equivalent class. It is of great interest to describe and understand the space of such classes. However, with currently known algorithms, sampling over such classes is only feasible for graphs with fewer than approximately 20 vertices. In this paper, we design reversible irreducible Markov chains on the space of Markov equivalent classes by proposing a perfect set of operators that determine the transitions of the Markov chain. The stationary distribution of a proposed Markov chain has a closed form and can be computed easily. Specifically, we construct a concrete perfect set of operators on sparse Markov equivalence classes by introducing appropriate conditions on each possible operator. Algorithms and their accelerated versions are provided to efficiently generate Markov chains and to explore properties of Markov equivalence classes of sparse directed acyclic graphs (DAGs) with thousands of vertices. We find experimentally that in most Markov equivalence classes of sparse DAGs, (1) most edges are directed, (2) most undirected subgraphs are small and (3) the number of these undirected subgraphs grows approximately linearly with the number of vertices. The article contains supplement arXiv:1303.0632, http://dx.doi.org/10.1214/13-AOS1125SUPP

Sparse classifiers such as the support vector machines (SVM) are efficient in test-phases because the classifier is characterized only by a subset of the samples called support vectors (SVs), and the rest of the samples (non SVs) have no influence on the classification result. However, the advantage of the sparsity has not been fully exploited in training phases because it is generally difficult to know which sample turns out to be SV beforehand. In this paper, we introduce a new approach called safe sample screening that enables us to identify a subset of the non-SVs and screen them out prior to the training phase. Our approach is different from existing heuristic approaches in the sense that the screened samples are guaranteed to be non-SVs at the optimal solution. We investigate the advantage of the safe sample screening approach through intensive numerical experiments, and demonstrate that it can substantially decrease the computational cost of the state-of-the-art SVM solvers such as LIBSVM. In the current big data era, we believe that safe sample screening would be of great practical importance since the data size can be reduced without sacrificing the optimality of the final solution.