A novel extrapolation method is proposed for longitudinal forecasting. A hierarchical Gaussian process model is used to combine nonlinear population change and individual memory of the past to make prediction. The prediction error is minimized through the hierarchical design. The method is further extended to joint modeling of continuous measurements and survival events. The baseline hazard, covariate and joint effects are conveniently modeled in this hierarchical structure. The estimation and inference are implemented in fully Bayesian framework using the objective and shrinkage priors. In simulation studies, this model shows robustness in latent estimation, correlation detection and high accuracy in forecasting. The model is illustrated with medical monitoring data from cystic fibrosis (CF) patients. Estimation and forecasts are obtained in the measurement of lung function and records of acute respiratory events. Keyword: Extrapolation, Joint Model, Longitudinal Model, Hierarchical Gaussian Process, Cystic Fibrosis, Medical Monitoring

We consider the problem of maximizing a real-valued continuous function $f$ using a Bayesian approach. Since the early work of Jonas Mockus and Antanas \v{Z}ilinskas in the 70's, the problem of optimization is usually formulated by considering the loss function $\max f - M_n$ (where $M_n$ denotes the best function value observed after $n$ evaluations of $f$). This loss function puts emphasis on the value of the maximum, at the expense of the location of the maximizer. In the special case of a one-step Bayes-optimal strategy, it leads to the classical Expected Improvement (EI) sampling criterion. This is a special case of a Stepwise Uncertainty Reduction (SUR) strategy, where the risk associated to a certain uncertainty measure (here, the expected loss) on the quantity of interest is minimized at each step of the algorithm. In this article, assuming that $f$ is defined over a measure space $(\mathbb{X}, \lambda)$, we propose to consider instead the integral loss function $\int_{\mathbb{X}} (f - M_n)_{+}\, d\lambda$, and we show that this leads, in the case of a Gaussian process prior, to a new numerically tractable sampling criterion that we call $\rm EI^2$ (for Expected Integrated Expected Improvement). A numerical experiment illustrates that a SUR strategy based on this new sampling criterion reduces the error on both the value and the location of the maximizer faster than the EI-based strategy.

In the big data era, scalability has become a crucial requirement for any useful computational model. Probabilistic graphical models are very useful for mining and discovering data insights, but they are not scalable enough to be suitable for big data problems. Bayesian Networks particularly demonstrate this limitation when their data is represented using few random variables while each random variable has a massive set of values. With hierarchical data - data that is arranged in a treelike structure with several levels - one would expect to see hundreds of thousands or millions of values distributed over even just a small number of levels. When modeling this kind of hierarchical data across large data sets, Bayesian networks become infeasible for representing the probability distributions for the following reasons: i) Each level represents a single random variable with hundreds of thousands of values, ii) The number of levels is usually small, so there are also few random variables, and iii) The structure of the network is predefined since the dependency is modeled top-down from each parent to each of its child nodes, so the network would contain a single linear path for the random variables from each parent to each child node. In this paper we present a scalable probabilistic graphical model to overcome these limitations for massive hierarchical data. We believe the proposed model will lead to an easily-scalable, more readable, and expressive implementation for problems that require probabilistic-based solutions for massive amounts of hierarchical data. We successfully applied this model to solve two different challenging probabilistic-based problems on massive hierarchical data sets for different domains, namely, bioinformatics and latent semantic discovery over search logs.

This paper presents a Bayesian image segmentation model based on Potts prior and loopy belief propagation. The proposed Bayesian model involves several terms, including the pairwise interactions of Potts models, and the average vectors and covariant matrices of Gauss distributions in color image modeling. These terms are often referred to as hyperparameters in statistical machine learning theory. In order to determine these hyperparameters, we propose a new scheme for hyperparameter estimation based on conditional maximization of entropy in the Potts prior. The algorithm is given based on loopy belief propagation. In addition, we compare our conditional maximum entropy framework with the conventional maximum likelihood framework, and also clarify how the first order phase transitions in LBP's for Potts models influence our hyperparameter estimation procedures.

In this paper, we investigate the statistical convergence rate of a Bayesian low-rank tensor estimator. Our problem setting is the regression problem where a tensor structure underlying the data is estimated. This problem setting occurs in many practical applications, such as collaborative filtering, multi-task learning, and spatio-temporal data analysis. The convergence rate is analyzed in terms of both in-sample and out-of-sample predictive accuracies. It is shown that a near optimal rate is achieved without any strong convexity of the observation. Moreover, we show that the method has adaptivity to the unknown rank of the true tensor, that is, the near optimal rate depending on the true rank is achieved even if it is not known a priori.

We consider distributed estimation of the inverse covariance matrix, also called the concentration or precision matrix, in Gaussian graphical models. Traditional centralized estimation often requires global inference of the covariance matrix, which can be computationally intensive in large dimensions. Approximate inference based on message-passing algorithms, on the other hand, can lead to unstable and biased estimation in loopy graphical models. In this paper, we propose a general framework for distributed estimation based on a maximum marginal likelihood (MML) approach. This approach computes local parameter estimates by maximizing marginal likelihoods defined with respect to data collected from local neighborhoods. Due to the non-convexity of the MML problem, we introduce and solve a convex relaxation. The local estimates are then combined into a global estimate without the need for iterative message-passing between neighborhoods. The proposed algorithm is naturally parallelizable and computationally efficient, thereby making it suitable for high-dimensional problems. In the classical regime where the number of variables $p$ is fixed and the number of samples $T$ increases to infinity, the proposed estimator is shown to be asymptotically consistent and to improve monotonically as the local neighborhood size increases. In the high-dimensional scaling regime where both $p$ and $T$ increase to infinity, the convergence rate to the true parameters is derived and is seen to be comparable to centralized maximum likelihood estimation. Extensive numerical experiments demonstrate the improved performance of the two-hop version of the proposed estimator, which suffices to almost close the gap to the centralized maximum likelihood estimator at a reduced computational cost.

Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the phylogeny and genotype of major subclonal lineages represented in the population of cancer cells. We also propose new split-merge updates tailored to the subclonal reconstruction problem that improve the mixing time of Markov chains. In comparisons with the tree-structured stick breaking prior used in PhyloSub, we demonstrate superior mixing and running time using the treeCRP with our new split-merge procedures. We also show that given the same number of samples, TSSB and treeCRP have similar ability to recover the subclonal structure of a tumor.

We consider the problem of estimating the conditional probability of a label in time O(log n), where n is the number of possible labels. We analyze a natural reduction of this problem to a set of binary regression problems organized in a tree structure, proving a regret bound that scales with the depth of the tree. Motivated by this analysis, we propose the first online algorithm which provably constructs a logarithmic depth tree on the set of labels to solve this problem. We test the algorithm empirically, showing that it works succesfully on a dataset with roughly 106 labels.

We consider the problem of learning a high-dimensional graphical model in which certain hub nodes are highly-connected to many other nodes. Many authors have studied the use of an l1 penalty in order to learn a sparse graph in high-dimensional setting. However, the l1 penalty implicitly assumes that each edge is equally likely and independent of all other edges. We propose a general framework to accommodate more realistic networks with hub nodes, using a convex formulation that involves a row-column overlap norm penalty. We apply this general framework to three widely-used probabilistic graphical models: the Gaussian graphical model, the covariance graph model, and the binary Ising model. An alternating direction method of multipliers algorithm is used to solve the corresponding convex optimization problems. On synthetic data, we demonstrate that our proposed framework outperforms competitors that do not explicitly model hub nodes. We illustrate our proposal on a webpage data set and a gene expression data set.

A mixture of Gaussians fit to a single curved or heavy-tailed cluster will report that the data contains many clusters. To produce more appropriate clusterings, we introduce a model which warps a latent mixture of Gaussians to produce nonparametric cluster shapes. The possibly low-dimensional latent mixture model allows us to summarize the properties of the high-dimensional clusters (or density manifolds) describing the data. The number of manifolds, as well as the shape and dimension of each manifold is automatically inferred. We derive a simple inference scheme for this model which analytically integrates out both the mixture parameters and the warping function. We show that our model is effective for density estimation, performs better than infinite Gaussian mixture models at recovering the true number of clusters, and produces interpretable summaries of high-dimensional datasets.