Gaussian processes (GP) are powerful tools for probabilistic modeling purposes. They can be used to define prior distributions over latent functions in hierarchical Bayesian models. The prior over functions is defined implicitly by the mean and covariance function, which determine the smoothness and variability of the function. The inference can then be conducted directly in the function space by evaluating or approximating the posterior process. Despite their attractive theoretical properties GPs provide practical challenges in their implementation. GPstuff is a versatile collection of computational tools for GP models compatible with Linux and Windows MATLAB and Octave. It includes, among others, various inference methods, sparse approximations and tools for model assessment. In this work, we review these tools and demonstrate the use of GPstuff in several models.

Bayesian optimization is an effective methodology for the global optimization of functions with expensive evaluations. It relies on querying a distribution over functions defined by a relatively cheap surrogate model. An accurate model for this distribution over functions is critical to the effectiveness of the approach, and is typically fit using Gaussian processes (GPs). However, since GPs scale cubically with the number of observations, it has been challenging to handle objectives whose optimization requires many evaluations, and as such, massively parallelizing the optimization. In this work, we explore the use of neural networks as an alternative to GPs to model distributions over functions. We show that performing adaptive basis function regression with a neural network as the parametric form performs competitively with state-of-the-art GP-based approaches, but scales linearly with the number of data rather than cubically. This allows us to achieve a previously intractable degree of parallelism, which we apply to large scale hyperparameter optimization, rapidly finding competitive models on benchmark object recognition tasks using convolutional networks, and image caption generation using neural language models.

We define a family of probability distributions for random count matrices with a potentially unbounded number of rows and columns. The three distributions we consider are derived from the gamma-Poisson, gamma-negative binomial, and beta-negative binomial processes. Because the models lead to closed-form Gibbs sampling update equations, they are natural candidates for nonparametric Bayesian priors over count matrices. A key aspect of our analysis is the recognition that, although the random count matrices within the family are defined by a row-wise construction, their columns can be shown to be i.i.d. This fact is used to derive explicit formulas for drawing all the columns at once. Moreover, by analyzing these matrices' combinatorial structure, we describe how to sequentially construct a column-i.i.d. random count matrix one row at a time, and derive the predictive distribution of a new row count vector with previously unseen features. We describe the similarities and differences between the three priors, and argue that the greater flexibility of the gamma- and beta- negative binomial processes, especially their ability to model over-dispersed, heavy-tailed count data, makes these well suited to a wide variety of real-world applications. As an example of our framework, we construct a naive-Bayes text classifier to categorize a count vector to one of several existing random count matrices of different categories. The classifier supports an unbounded number of features, and unlike most existing methods, it does not require a predefined finite vocabulary to be shared by all the categories, and needs neither feature selection nor parameter tuning. Both the gamma- and beta- negative binomial processes are shown to significantly outperform the gamma-Poisson process for document categorization, with comparable performance to other state-of-the-art supervised text classification algorithms.

Given data sampled from a number of variables, one is often interested in the underlying causal relationships in the form of a directed acyclic graph. In the general case, without interventions on some of the variables it is only possible to identify the graph up to its Markov equivalence class. However, in some situations one can find the true causal graph just from observational data, for example in structural equation models with additive noise and nonlinear edge functions. Most current methods for achieving this rely on nonparametric independence tests. One of the problems there is that the null hypothesis is independence, which is what one would like to get evidence for. We take a different approach in our work by using a penalized likelihood as a score for model selection. This is practically feasible in many settings and has the advantage of yielding a natural ranking of the candidate models. When making smoothness assumptions on the probability density space, we prove consistency of the penalized maximum likelihood estimator. We also present empirical results for simulated scenarios and real two-dimensional data sets (cause-effect pairs) where we obtain similar results as other state-of-the-art methods.

We study a statistical model for the tensor principal component analysis problem introduced by Montanari and Richard: Given a order-$3$ tensor $T$ of the form $T = \tau \cdot v_0^{\otimes 3} + A$, where $\tau \geq 0$ is a signal-to-noise ratio, $v_0$ is a unit vector, and $A$ is a random noise tensor, the goal is to recover the planted vector $v_0$. For the case that $A$ has iid standard Gaussian entries, we give an efficient algorithm to recover $v_0$ whenever $\tau \geq \omega(n^{3/4} \log(n)^{1/4})$, and certify that the recovered vector is close to a maximum likelihood estimator, all with high probability over the random choice of $A$. The previous best algorithms with provable guarantees required $\tau \geq \Omega(n)$. In the regime $\tau \leq o(n)$, natural tensor-unfolding-based spectral relaxations for the underlying optimization problem break down (in the sense that their integrality gap is large). To go beyond this barrier, we use convex relaxations based on the sum-of-squares method. Our recovery algorithm proceeds by rounding a degree-$4$ sum-of-squares relaxations of the maximum-likelihood-estimation problem for the statistical model. To complement our algorithmic results, we show that degree-$4$ sum-of-squares relaxations break down for $\tau \leq O(n^{3/4}/\log(n)^{1/4})$, which demonstrates that improving our current guarantees (by more than logarithmic factors) would require new techniques or might even be intractable. Finally, we show how to exploit additional problem structure in order to solve our sum-of-squares relaxations, up to some approximation, very efficiently. Our fastest algorithm runs in nearly-linear time using shifted (matrix) power iteration and has similar guarantees as above. The analysis of this algorithm also confirms a variant of a conjecture of Montanari and Richard about singular vectors of tensor unfoldings.

Networks capture our intuition about relationships in the world. They describe the friendships between Facebook users, interactions in financial markets, and synapses connecting neurons in the brain. These networks are richly structured with cliques of friends, sectors of stocks, and a smorgasbord of cell types that govern how neurons connect. Some networks, like social network friendships, can be directly observed, but in many cases we only have an indirect view of the network through the actions of its constituents and an understanding of how the network mediates that activity. In this work, we focus on the problem of latent network discovery in the case where the observable activity takes the form of a mutually-excitatory point process known as a Hawkes process. We build on previous work that has taken a Bayesian approach to this problem, specifying prior distributions over the latent network structure and a likelihood of observed activity given this network. We extend this work by proposing a discrete-time formulation and developing a computationally efficient stochastic variational inference (SVI) algorithm that allows us to scale the approach to long sequences of observations. We demonstrate our algorithm on the calcium imaging data used in the Chalearn neural connectomics challenge.

In spite of the recent surge of interest in quantile regression, joint estimation of linear quantile planes remains a great challenge in statistics and econometrics. We propose a novel parametrization that characterizes any collection of non-crossing quantile planes over arbitrarily shaped convex predictor domains in any dimension by means of unconstrained scalar, vector and function valued parameters. Statistical models based on this parametrization inherit a fast computation of the likelihood function, enabling penalized likelihood or Bayesian approaches to model fitting. We introduce a complete Bayesian methodology by using Gaussian process prior distributions on the function valued parameters and develop a robust and efficient Markov chain Monte Carlo parameter estimation. The resulting method is shown to offer posterior consistency under mild tail and regularity conditions. We present several illustrative examples where the new method is compared against existing approaches and is found to offer better accuracy, coverage and model fit.

Nonnegative Matrix Factorization (NMF) aims to factorize a matrix into two optimized nonnegative matrices appropriate for the intended applications. The method has been widely used for unsupervised learning tasks, including recommender systems (rating matrix of users by items) and document clustering (weighting matrix of papers by keywords). However, traditional NMF methods typically assume the number of latent factors (i.e., dimensionality of the loading matrices) to be fixed. This assumption makes them inflexible for many applications. In this paper, we propose a nonparametric NMF framework to mitigate this issue by using dependent Indian Buffet Processes (dIBP). In a nutshell, we apply a correlation function for the generation of two stick weights associated with each pair of columns of loading matrices, while still maintaining their respective marginal distribution specified by IBP. As a consequence, the generation of two loading matrices will be column-wise (indirectly) correlated. Under this same framework, two classes of correlation function are proposed (1) using Bivariate beta distribution and (2) using Copula function. Both methods allow us to adopt our work for various applications by flexibly choosing an appropriate parameter settings. Compared with the other state-of-the art approaches in this area, such as using Gaussian Process (GP)-based dIBP, our work is seen to be much more flexible in terms of allowing the two corresponding binary matrix columns to have greater variations in their non-zero entries. Our experiments on the real-world and synthetic datasets show that three proposed models perform well on the document clustering task comparing standard NMF without predefining the dimension for the factor matrices, and the Bivariate beta distribution-based and Copula-based models have better flexibility than the GP-based model.

We propose an efficient ADMM method with guarantees for high-dimensional problems. We provide explicit bounds for the sparse optimization problem and the noisy matrix decomposition problem. For sparse optimization, we establish that the modified ADMM method has an optimal convergence rate of $\mathcal{O}(s\log d/T)$, where $s$ is the sparsity level, $d$ is the data dimension and $T$ is the number of steps. This matches with the minimax lower bounds for sparse estimation. For matrix decomposition into sparse and low rank components, we provide the first guarantees for any online method, and prove a convergence rate of $\tilde{\mathcal{O}}((s+r)\beta^2(p) /T) + \mathcal{O}(1/p)$ for a $p\times p$ matrix, where $s$ is the sparsity level, $r$ is the rank and $\Theta(\sqrt{p})\leq \beta(p)\leq \Theta(p)$. Our guarantees match the minimax lower bound with respect to $s,r$ and $T$. In addition, we match the minimax lower bound with respect to the matrix dimension $p$, i.e. $\beta(p)=\Theta(\sqrt{p})$, for many important statistical models including the independent noise model, the linear Bayesian network and the latent Gaussian graphical model under some conditions. Our ADMM method is based on epoch-based annealing and consists of inexpensive steps which involve projections on to simple norm balls. Experiments show that for both sparse optimization and matrix decomposition problems, our algorithm outperforms the state-of-the-art methods. In particular, we reach higher accuracy with same time complexity.

Bayesian models provide a framework for probabilistic modelling of complex datasets. However, many of such models are computationally demanding especially in the presence of large datasets. On the other hand, in sensor network applications, statistical (Bayesian) parameter estimation usually needs distributed algorithms, in which both data and computation are distributed across the nodes of the network. In this paper we propose a general framework for distributed Bayesian learning using Bregman Alternating Direction Method of Multipliers (B-ADMM). We demonstrate the utility of our framework, with Mean Field Variational Bayes (MFVB) as the primitive for distributed Matrix Factorization (MF) and distributed affine structure from motion (SfM).