It is well known in the literature that the problem of learning the structure of Bayesian networks is very hard to tackle: its computational complexity is super-exponential in the number of nodes in the worst case and polynomial in most real-world scenarios. Efficient implementations of score-based structure learning benefit from past and current research in optimisation theory, which can be adapted to the task by using the network score as the objective function to maximise. This is not true for approaches based on conditional independence tests, called constraint-based learning algorithms. The only optimisation in widespread use, backtracking, leverages the symmetries implied by the definitions of neighbourhood and Markov blanket. In this paper we illustrate how backtracking is implemented in recent versions of the bnlearn R package, and how it degrades the stability of Bayesian network structure learning for little gain in terms of speed. As an alternative, we describe a software architecture and framework that can be used to parallelise constraint-based structure learning algorithms (also implemented in bnlearn) and we demonstrate its performance using four reference networks and two real-world data sets from genetics and systems biology. We show that on modern multi-core or multiprocessor hardware parallel implementations are preferable over backtracking, which was developed when single-processor machines were the norm.

Models of complex systems are often formalized as sequential software simulators: computationally intensive programs that iteratively build up probable system configurations given parameters and initial conditions. These simulators enable modelers to capture effects that are difficult to characterize analytically or summarize statistically. However, in many real-world applications, these simulations need to be inverted to match the observed data. This typically requires the custom design, derivation and implementation of sophisticated inversion algorithms. Here we give a framework for inverting a broad class of complex software simulators via probabilistic programming and automatic inference, using under 20 lines of probabilistic code. Our approach is based on a formulation of inversion as approximate inference in a simple sequential probabilistic model. We implement four inference strategies, including Metropolis-Hastings, a sequentialized Metropolis-Hastings scheme, and a particle Markov chain Monte Carlo scheme, requiring 4 or fewer lines of probabilistic code each. We demonstrate our framework by applying it to invert a real geological software simulator from the oil and gas industry.

It is well known that Principal Component Analysis (PCA) is strongly affected by outliers and a lot of effort has been put into robustification of PCA. In this paper we present a new algorithm for robust PCA minimizing the trimmed reconstruction error. By directly minimizing over the Stiefel manifold, we avoid deflation as often used by projection pursuit methods. In distinction to other methods for robust PCA, our method has no free parameter and is computationally very efficient. We illustrate the performance on various datasets including an application to background modeling and subtraction. Our method performs better or similar to current state-of-the-art methods while being faster.

Low dimensional representations of words allow accurate NLP models to be trained on limited annotated data. While most representations ignore words' local context, a natural way to induce context-dependent representations is to perform inference in a probabilistic latent-variable sequence model. Given the recent success of continuous vector space word representations, we provide such an inference procedure for continuous states, where words' representations are given by the posterior mean of a linear dynamical system. Here, efficient inference can be performed using Kalman filtering. Our learning algorithm is extremely scalable, operating on simple cooccurrence counts for both parameter initialization using the method of moments and subsequent iterations of EM. In our experiments, we employ our inferred word embeddings as features in standard tagging tasks, obtaining significant accuracy improvements. Finally, the Kalman filter updates can be seen as a linear recurrent neural network. We demonstrate that using the parameters of our model to initialize a non-linear recurrent neural network language model reduces its training time by a day and yields lower perplexity.

Spectral methods that are based on eigenvectors and eigenvalues of discrete graph Laplacians, such as Diffusion Maps and Laplacian Eigenmaps are often used for manifold learning and non-linear dimensionality reduction. It was previously shown by Belkin and Niyogi \cite{belkin_niyogi:2007} that the eigenvectors and eigenvalues of the graph Laplacian converge to the eigenfunctions and eigenvalues of the Laplace-Beltrami operator of the manifold in the limit of infinitely many data points sampled independently from the uniform distribution over the manifold. Recently, we introduced Vector Diffusion Maps and showed that the connection Laplacian of the tangent bundle of the manifold can be approximated from random samples. In this paper, we present a unified framework for approximating other connection Laplacians over the manifold by considering its principle bundle structure. We prove that the eigenvectors and eigenvalues of these Laplacians converge in the limit of infinitely many independent random samples. We generalize the spectral convergence results to the case where the data points are sampled from a non-uniform distribution, and for manifolds with and without boundary.

Inspired by recent successes of deep learning in computer vision, we propose a novel framework for encoding time series as different types of images, namely, Gramian Angular Summation/Difference Fields (GASF/GADF) and Markov Transition Fields (MTF). This enables the use of techniques from computer vision for time series classification and imputation. We used Tiled Convolutional Neural Networks (tiled CNNs) on 20 standard datasets to learn high-level features from the individual and compound GASF-GADF-MTF images. Our approaches achieve highly competitive results when compared to nine of the current best time series classification approaches. Inspired by the bijection property of GASF on 0/1 rescaled data, we train Denoised Auto-encoders (DA) on the GASF images of four standard and one synthesized compound dataset. The imputation MSE on test data is reduced by 12.18%-48.02% when compared to using the raw data. An analysis of the features and weights learned via tiled CNNs and DAs explains why the approaches work.

This paper presents a novel method for the reconstruction of a neural network connectivity using calcium fluorescence data. We introduce a fast unsupervised method to integrate different networks that reconstructs structural connectivity from neuron activity. Our method improves the state-of-the-art reconstruction method General Transfer Entropy (GTE). We are able to better eliminate indirect links, improving therefore the quality of the network via a normalization and ensemble process of GTE and three new informative features. The approach is based on a simple combination of networks, which is remarkably fast. The performance of our approach is benchmarked on simulated time series provided at the connectomics challenge and also submitted at the public competition.

In this paper we develop proximal methods for statistical learning. Proximal point algorithms are useful in statistics and machine learning for obtaining optimization solutions for composite functions. Our approach exploits closed-form solutions of proximal operators and envelope representations based on the Moreau, Forward-Backward, Douglas-Rachford and Half-Quadratic envelopes. Envelope representations lead to novel proximal algorithms for statistical optimisation of composite objective functions which include both non-smooth and non-convex objectives. We illustrate our methodology with regularized Logistic and Poisson regression and non-convex bridge penalties with a fused lasso norm. We provide a discussion of convergence of non-descent algorithms with acceleration and for non-convex functions. Finally, we provide directions for future research.

Cortana is taking the war of words to Siri's home turf, Amazon amazes us with its tax return, and we find out why the record industry has a love-hate relationship with YouTube. Microsoft is challenging Apple's voice-activated personal assistant Siri by bringing its own voice control system Cortana to iPhones, not to mention Android devices too. It's all part of the build-up to Windows 10, but will iPhone owners switch allegiance? Amazon is changing the way it operates in Europe to pay more taxes in individual countries, ending its much-criticised wheeze of exploiting the tax haven of Luxembourg. Tax doesn't have to be taxing.

We study the computational complexity of Markov chain Monte Carlo (MCMC) methods for high-dimensional Bayesian linear regression under sparsity constraints. We first show that a Bayesian approach can achieve variable-selection consistency under relatively mild conditions on the design matrix. We then demonstrate that the statistical criterion of posterior concentration need not imply the computational desideratum of rapid mixing of the MCMC algorithm. By introducing a truncated sparsity prior for variable selection, we provide a set of conditions that guarantee both variable-selection consistency and rapid mixing of a particular Metropolis-Hastings algorithm. The mixing time is linear in the number of covariates up to a logarithmic factor. Our proof controls the spectral gap of the Markov chain by constructing a canonical path ensemble that is inspired by the steps taken by greedy algorithms for variable selection.