We present a Bayesian nonparametric model for genetic sequence data in which a set of genetic sequences is modelled using a Markov model of partitions. The partitions at consecutive locations in the genome are related by their clusters first splitting and then merging. Our model can be thought of as a discrete time analogue of continuous time fragmentation-coagulation processes [Teh et al 2011], preserving the important properties of projectivity, exchangeability and reversibility, while being more scalable. We apply this model to the problem of genotype imputation, showing improved computational efficiency while maintaining the same accuracies as in [Teh et al 2011].

Clustering is a key component in data analysis toolbox. Despite its importance, scalable algorithms often eschew rich statistical models in favor of simpler descriptions such as $k$-means clustering. In this paper we present a sampler, capable of estimating mixtures of exponential families. At its heart lies a novel proposal distribution using random projections to achieve high throughput in generating proposals, which is crucial for clustering models with large numbers of clusters.

In this paper, we consider the problem of clustering data points into lowdimensional subspacesin the presence of outliers. We pose the problem using a density estimation formulation with an associated generative model. Based on this probability model, we first develop an iterative expectation-maximization (EM) algorithm andthen derive its global solution. In addition, we develop two Bayesian methods based on variational Bayesian (VB) approximation, which are capable of automatic dimensionality selection. While the first method is based on an alternating optimizationscheme for all unknowns, the second method makes use of recent results in VB matrix factorization leading to fast and effective estimation. Both methods are extended to handle sparse outliers for robustness and can handle missingvalues. Experimental results suggest that proposed methods are very effective in subspace clustering and identifying outliers.

We describe a new model for learning meaningful representations of text documents from an unlabeled collection of documents. This model is inspired by the recently proposed Replicated Softmax, an undirected graphical model of word counts that was shown to learn a better generative model and more meaningful document representations. Specifically, we take inspiration from the conditional mean-field recursive equations of the Replicated Softmax in order to define a neural network architecture that estimates the probability of observing a new word in a given document given the previously observed words. This paradigm also allows us to replace the expensive softmax distribution over words with a hierarchical distribution over paths in a binary tree of words. The end result is a model whose training complexity scales logarithmically with the vocabulary size instead of linearly as in the Replicated Softmax. Our experiments show that our model is competitive both as a generative model of documents and as a document representation learning algorithm.

Variational methods provide a computationally scalable alternative to Monte Carlo methods for large-scale, Bayesian nonparametric learning. In practice, however, conventional batch and online variational methods quickly become trapped in local optima. In this paper, we consider a nonparametric topic model based on the hierarchical Dirichlet process (HDP), and develop a novel online variational inference algorithm based on split-merge topic updates. We derive a simpler and faster variational approximation of the HDP, and show that by intelligently splitting and merging components of the variational posterior, we can achieve substantially better predictions of test data than conventional online and batch variational algorithms. For streaming analysis of large datasets where batch analysis is infeasible, we show that our split-merge updates better capture the nonparametric properties of the underlying model, allowing continual learning of new topics.

In this paper, we present a Bayesian framework for multilabel classification using compressed sensing. The key idea in compressed sensing for multilabel classification is to first project the label vector to a lower dimensional space using a random transformation and then learn regression functions over these projections. Our approach considers both of these components in a single probabilistic model, thereby jointly optimizing over compression as well as learning tasks. We then derive an efficient variational inference scheme that provides joint posterior distribution over all the unobserved labels. The two key benefits of the model are that a) it can naturally handle datasets that have missing labels and b) it can also measure uncertainty in prediction. The uncertainty estimate provided by the model naturally allows for active learning paradigms where an oracle provides information about labels that promise to be maximally informative for the prediction task. Our experiments show significant boost over prior methods in terms of prediction performance over benchmark datasets, both in the fully labeled and the missing labels case. Finally, we also highlight various useful active learning scenarios that are enabled by the probabilistic model.

Rich and complex time-series data, such as those generated from engineering systems, financialmarkets, videos, or neural recordings are now a common feature of modern data analysis. Explaining the phenomena underlying these diverse data sets requires flexible and accurate models. In this paper, we promote Gaussian process dynamical systems as a rich model class that is appropriate for such an analysis. We present a new approximate message-passing algorithm for Bayesian state estimation and inference in Gaussian process dynamical systems, a nonparametric probabilisticgeneralization of commonly used state-space models. We derive our message-passing algorithm using Expectation Propagation and provide a unifying perspective on message passing in general state-space models. We show that existing Gaussian filters and smoothers appear as special cases within our inference framework, and that these existing approaches can be improved upon using iterated message passing. Using both synthetic and real-world data, we demonstrate that iterated message passing can improve inference in a wide range of tasks in Bayesian state estimation, thus leading to improved predictions and more effective decision making.

We present a Bayesian nonparametric model that discovers implicit social structure from interaction time-series data. Social groups are often formed implicitly, through actions among members of groups. Yet many models of social networks use explicitly declared relationships to infer social structure. We consider a particular class of Hawkes processes, a doubly stochastic point process, that is able to model reciprocity between groups of individuals. We then extend the Infinite Relational Model by using these reciprocating Hawkes processes to parameterise its edges, making events associated with edges co-dependent through time. Our model outperforms general, unstructured Hawkes processes as well as structured Poisson process-based models at predicting verbal and email turn-taking, and military conflicts among nations.

We study how to automatically select and adapt multiple abstractions or representations of the world to support model-based reinforcement learning. We address the challenges of transfer learning in heterogeneous environments with varying tasks. We present an efficient, online framework that, through a sequence of tasks, learns a set of relevant representations to be used in future tasks. Without pre-defined mapping strategies, we introduce a general approach to support transfer learning across different state spaces. We demonstrate the potential impact of our system through improved jumpstart and faster convergence to near optimum policy in two benchmark domains.

A challenging problem in hierarchical classification is to leverage the hierarchical relations among classes for improving classification performance. An even greater challenge is to do so in a manner that is computationally feasible for the large scale problems usually encountered in practice. This paper proposes a set of Bayesian methods to model hierarchical dependencies among class labels using multivari- ate logistic regression. Specifically, the parent-child relationships are modeled by placing a hierarchical prior over the children nodes centered around the parame- ters of their parents; thereby encouraging classes nearby in the hierarchy to share similar model parameters. We present new, efficient variational algorithms for tractable posterior inference in these models, and provide a parallel implementa- tion that can comfortably handle large-scale problems with hundreds of thousands of dimensions and tens of thousands of classes. We run a comparative evaluation on multiple large-scale benchmark datasets that highlights the scalability of our approach, and shows a significant performance advantage over the other state-of- the-art hierarchical methods.