The fundamental aim of clustering algorithms is to partition data points. We consider tasks where the discovered partition is allowed to vary with some covariate such as space or time. One approach would be to use fragmentation-coagulation processes, but these, being Markov processes, are restricted to linear or tree structured covariate spaces. We define a partition-valued process on an arbitrary covariate space using Gaussian processes. We use the process to construct a multitask clustering model which partitions datapoints in a similar way across multiple data sources, and a time series model of network data which allows cluster assignments to vary over time. We describe sampling algorithms for inference and apply our method to defining cancer subtypes based on different types of cellular characteristics, finding regulatory modules from gene expression data from multiple human populations, and discovering time varying community structure in a social network.

We present an automatic classification method for astronomical catalogs with missing data. We use Bayesian networks, a probabilistic graphical model, that allows us to perform inference to pre- dict missing values given observed data and dependency relationships between variables. To learn a Bayesian network from incomplete data, we use an iterative algorithm that utilises sampling methods and expectation maximization to estimate the distributions and probabilistic dependencies of variables from data with missing values. To test our model we use three catalogs with missing data (SAGE, 2MASS and UBVI) and one complete catalog (MACHO). We examine how classification accuracy changes when information from missing data catalogs is included, how our method compares to traditional missing data approaches and at what computational cost. Integrating these catalogs with missing data we find that classification of variable objects improves by few percent and by 15% for quasar detection while keeping the computational cost the same.

Significant success has been reported recently using deep neural networks for classification. Such large networks can be computationally intensive, even after training is over. Implementing these trained networks in hardware chips with a limited precision of synaptic weights may improve their speed and energy efficiency by several orders of magnitude, thus enabling their integration into small and low-power electronic devices. With this motivation, we develop a computationally efficient learning algorithm for multilayer neural networks with binary weights, assuming all the hidden neurons have a fan-out of one. This algorithm, derived within a Bayesian probabilistic online setting, is shown to work well for both synthetic and real-world problems, performing comparably to algorithms with real-valued weights, while retaining computational tractability.

In this work, we propose a PAC-Bayes bound for the generalization risk of the Gibbs classifier in the multi-class classification framework. The novelty of our work is the critical use of the confusion matrix of a classifier as an error measure; this puts our contribution in the line of work aiming at dealing with performance measure that are richer than mere scalar criterion such as the misclassification rate. Thanks to very recent and beautiful results on matrix concentration inequalities, we derive two bounds showing that the true confusion risk of the Gibbs classifier is upper-bounded by its empirical risk plus a term depending on the number of training examples in each class. To the best of our knowledge, this is the first PAC-Bayes bounds based on confusion matrices.

We consider discrete graphical models Markov with respect to a graph $G$ and propose two distributed marginal methods to estimate the maximum likelihood estimate of the canonical parameter of the model. Both methods are based on a relaxation of the marginal likelihood obtained by considering the density of the variables represented by a vertex $v$ of $G$ and a neighborhood. The two methods differ by the size of the neighborhood of $v$. We show that the estimates are consistent and that those obtained with the larger neighborhood have smaller asymptotic variance than the ones obtained through the smaller neighborhood.

The kernel least mean squares (KLMS) algorithm is a computationally efficient nonlinear adaptive filtering method that "kernelizes" the celebrated (linear) least mean squares algorithm. We demonstrate that the least mean squares algorithm is closely related to the Kalman filtering, and thus, the KLMS can be interpreted as an approximate Bayesian filtering method. This allows us to systematically develop extensions of the KLMS by modifying the underlying state-space and observation models. The resulting extensions introduce many desirable properties such as "forgetting", and the ability to learn from discrete data, while retaining the computational simplicity and time complexity of the original algorithm.

In this paper, learning a Bayesian network structure that optimizes a scoring function for a given dataset is viewed as a shortest path problem in an implicit state-space search graph. This perspective highlights the importance of two research issues: the development of search strategies for solving the shortest path problem, and the design of heuristic functions for guiding the search. This paper introduces several techniques for addressing the issues. One is an A* search algorithm that learns an optimal Bayesian network structure by only searching the most promising part of the solution space. The others are mainly two heuristic functions. The first heuristic function represents a simple relaxation of the acyclicity constraint of a Bayesian network. Although admissible and consistent, the heuristic may introduce too much relaxation and result in a loose bound. The second heuristic function reduces the amount of relaxation by avoiding directed cycles within some groups of variables. Empirical results show that these methods constitute a promising approach to learning optimal Bayesian network structures.

We consider the prediction of weak effects in a multiple-output regression setup, when covariates are expected to explain a small amount, less than $\approx 1%$, of the variance of the target variables. To facilitate the prediction of the weak effects, we constrain our model structure by introducing a novel Bayesian approach of sharing information between the regression model and the noise model. Further reduction of the effective number of parameters is achieved by introducing an infinite shrinkage prior and group sparsity in the context of the Bayesian reduced rank regression, and using the Bayesian infinite factor model as a flexible low-rank noise model. In our experiments the model incorporating the novelties outperformed alternatives in genomic prediction of rich phenotype data. In particular, the information sharing between the noise and regression models led to significant improvement in prediction accuracy.

The cumulative distribution network (CDN) is a recently developed class of probabilistic graphical models (PGMs) permitting a copula factorization, in which the CDF, rather than the density, is factored. Despite there being much recent interest within the machine learning community about copula representations, there has been scarce research into the CDN, its amalgamation with copula theory, and no evaluation of its performance. Algorithms for inference, sampling, and learning in these models are underdeveloped compared those of other PGMs, hindering widerspread use. One advantage of the CDN is that it allows the factors to be parameterized as copulae, combining the benefits of graphical models with those of copula theory. In brief, the use of a copula parameterization enables greater modelling flexibility by separating representation of the marginals from the dependence structure, permitting more efficient and robust learning. Another advantage is that the CDN permits the representation of implicit latent variables, whose parameterization and connectivity are not required to be specified. Unfortunately, that the model can encode only latent relationships between variables severely limits its utility. In this thesis, we present inference, learning, and sampling for CDNs, and further the state-of-the-art. First, we explain the basics of copula theory and the representation of copula CDNs. Then, we discuss inference in the models, and develop the first sampling algorithm. We explain standard learning methods, propose an algorithm for learning from data missing completely at random (MCAR), and develop a novel algorithm for learning models of arbitrary treewidth and size. Properties of the models and algorithms are investigated through Monte Carlo simulations. We conclude with further discussion of the advantages and limitations of CDNs, and suggest future work.

Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease diagnosis and ii) to identify associations between genetic and phenotypical data. These two tasks are tightly coupled because underlying associations between genetic variations and phenotypical features contain the biological basis for a disease. While a variety of sparse models have been applied for disease diagnosis and canonical correlation analysis and its extensions have bee widely used in association studies (e.g., eQTL analysis), these two tasks have been treated separately. To unify these two tasks, we present a new sparse Bayesian approach for joint association study and disease diagnosis. In this approach, common latent features are extracted from different data sources based on sparse projection matrices and used to predict multiple disease severity levels based on Gaussian process ordinal regression; in return, the disease status is used to guide the discovery of relationships between the data sources. The sparse projection matrices not only reveal interactions between data sources but also select groups of biomarkers related to the disease. To learn the model from data, we develop an efficient variational expectation maximization algorithm. Simulation results demonstrate that our approach achieves higher accuracy in both predicting ordinal labels and discovering associations between data sources than alternative methods. We apply our approach to an imaging genetics dataset for the study of Alzheimer's Disease (AD). Our method identifies biologically meaningful relationships between genetic variations, MRI features, and AD status, and achieves significantly higher accuracy for predicting ordinal AD stages than the competing methods.