Determining interactions between entities and the overall organization and clustering of nodes in networks is a major challenge when analyzing biological and social network data. Here we extend the Indian Buffet Process (IBP), a nonparametric Bayesian model, to integrate noisy interaction scores with properties of individual entities for inferring interaction networks and clustering nodes within these networks. We present an application of this method to study how microR-NAs regulate mRNAs in cells. Analysis of synthetic and real data indicates that the method improves upon prior methods, correctly recovers interactions and clusters, and provides accurate biological predictions.

We introduce the Piecewise-Constant Conditional Intensity Model, a model for learning temporal dependencies in event streams. We describe a closed-form Bayesian approach to learning these models, and describe an importance sampling algorithm for forecasting future events using these models, using a proposal distribution based on Poisson superposition. We then use synthetic data, supercomputer event logs, and web search query logs to illustrate that our learning algorithm can efficiently learn nonlinear temporal dependencies, and that our importance sampling algorithm can effectively forecast future events.

We present an asymptotic analysis of Viterbi Training (VT) and contrast it with a more conventional Maximum Likelihood (ML) approach to parameter estimation in Hidden Markov Models. While ML estimator works by (locally) maximizing the likelihood of the observed data, VT seeks to maximize the probability of the most likely hidden state sequence. We develop an analytical framework based on a generating function formalism and illustrate it on an exactly solvable model of HMM with one unambiguous symbol. For this particular model the ML objective function is continuously degenerate. VT objective, in contrast, is shown to have only finite degeneracy.

Is it possible to crowdsource categorization? Amongst the challenges: (a) each worker has only a partial view of the data, (b) different workers may have different clustering criteria and may produce different numbers of categories, (c) the underlying category structure may be hierarchical. We propose a Bayesian model of how workers may approach clustering and show how one may infer clusters / categories, as well as worker parameters, using this model. Our experiments, carried out on large collections of images, suggest that Bayesian crowdclustering works well and may be superior to single-expert annotations.

For many real-world applications, we often need to select correlated variables-- such as genetic variations and imaging features associated with Alzheimer's disease--in a high dimensional space. The correlation between variables presents a challenge to classical variable selection methods. To address this challenge, the elastic net has been developed and successfully applied to many applications. Despite its great success, the elastic net does not exploit the correlation information embedded in the data to select correlated variables. To overcome this limitation, we present a novel hybrid model, EigenNet, that uses the eigenstructures of data to guide variable selection.

Inferring key unobservable features of individuals is an important task in the applied sciences. In particular, an important source of data in fields such as marketing, social sciences and medicine is questionnaires: answers in such questionnaires are noisy measures of target unobserved features. While comprehensive surveys help to better estimate the latent variables of interest, aiming at a high number of questions comes at a price: refusal to participate in surveys can go up, as well as the rate of missing data; quality of answers can decline; costs associated with applying such questionnaires can also increase. In this paper, we cast the problem of refining existing models for questionnaire data as follows: solve a constrained optimization problem of preserving the maximum amount of information found in a latent variable model using only a subset of existing questions. The goal is to find an optimal subset of a given size. For that, we first define an information theoretical measure for quantifying the quality of a reduced questionnaire. Three different approximate inference methods are introduced to solve this problem. Comparisons against a simple but powerful heuristic are presented.

Kernel-based reinforcement-learning (KBRL) is a method for learning a decision policy from a set of sample transitions which stands out for its strong theoretical guarantees. However, the size of the approximator grows with the number of transitions, which makes the approach impractical for large problems. In this paper we introduce a novel algorithm to improve the scalability of KBRL. We resort to a special decomposition of a transition matrix, called stochastic factorization, to fix the size of the approximator while at the same time incorporating all the information contained in the data. The resulting algorithm, kernel-based stochastic factorization (KBSF), is much faster but still converges to a unique solution. We derive a theoretical upper bound for the distance between the value functions computed by KBRL and KBSF. The effectiveness of our method is illustrated with computational experiments on four reinforcement-learning problems, including a difficult task in which the goal is to learn a neurostimulation policy to suppress the occurrence of seizures in epileptic rat brains. We empirically demonstrate that the proposed approach is able to compress the information contained in KBRL's model. Also, on the tasks studied, KBSF outperforms two of the most prominent reinforcement-learning algorithms, namely least-squares policy iteration and fitted Q-iteration.

It has been argued that perceptual multistability reflects probabilistic inference performed by the brain when sensory input is ambiguous. Alternatively, more traditional explanations of multistability refer to low-level mechanisms such as neuronal adaptation. We employ a Deep Boltzmann Machine (DBM) model of cortical processing to demonstrate that these two different approaches can be combined in the same framework. Based on recent developments in machine learning, we show how neuronal adaptation can be understood as a mechanism that improves probabilistic, sampling-based inference. Using the ambiguous Necker cube image, we analyze the perceptual switching exhibited by the model. We also examine the influence of spatial attention, and explore how binocular rivalry can be modeled with the same approach. Our work joins earlier studies in demonstrating how the principles underlying DBMs relate to cortical processing, and offers novel perspectives on the neural implementation of approximate probabilistic inference in the brain.

We introduce a variational Bayesian inference algorithm which can be widely applied to sparse linear models. The algorithm is based on the spike and slab prior which, from a Bayesian perspective, is the golden standard for sparse inference. We apply the method to a general multi-task and multiple kernel learning model in which a common set of Gaussian process functions is linearly combined with task-specific sparse weights, thus inducing relation between tasks. This model unifies several sparse linear models, such as generalized linear models, sparse factor analysis and matrix factorization with missing values, so that the variational algorithm can be applied to all these cases. We demonstrate our approach in multioutput Gaussian process regression, multi-class classification, image processing applications and collaborative filtering.

In recent years, a rich variety of shrinkage priors have been proposed that have great promise in addressing massive regression problems. In general, these new priors can be expressed as scale mixtures of normals, but have more complex forms and better properties than traditional Cauchy and double exponential priors. We first propose a new class of normal scale mixtures through a novel generalized beta distribution that encompasses many interesting priors as special cases. This encompassing framework should prove useful in comparing competing priors, considering properties and revealing close connections. We then develop a class of variational Bayes approximations through the new hierarchy presented that will scale more efficiently to the types of truly massive data sets that are now encountered routinely.