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].

We address a central problem of neuroanatomy, namely, the automatic segmentation of neuronal structures depicted in stacks of electron microscopy (EM) images. This is necessary to efficiently map 3D brain structure and connectivity. To segment {\em biological} neuron membranes, we use a special type of deep {\em artificial} neural network as a pixel classifier. The label of each pixel (membrane or non-membrane) is predicted from raw pixel values in a square window centered on it. The input layer maps each window pixel to a neuron. It is followed by a succession of convolutional and max-pooling layers which preserve 2D information and extract features with increasing levels of abstraction. The output layer produces a calibrated probability for each class. The classifier is trained by plain gradient descent on a $512 \times 512 \times 30$ stack with known ground truth, and tested on a stack of the same size (ground truth unknown to the authors) by the organizers of the ISBI 2012 EM Segmentation Challenge. Even without problem-specific post-processing, our approach outperforms competing techniques by a large margin in all three considered metrics, i.e. \emph{rand error}, \emph{warping error} and \emph{pixel error}. For pixel error, our approach is the only one outperforming a second human observer.

In the paper, we consider the problem of link prediction in time-evolving graphs. We assume that certain graph features, such as the node degree, follow a vector autoregressive (VAR) model and we propose to use this information to improve the accuracy of prediction. Our strategy involves a joint optimization procedure over the space of adjacency matrices and VAR matrices which takes into account both sparsity and low rank properties of the matrices. Oracle inequalities are derived and illustrate the trade-offs in the choice of smoothing parameters when modeling the joint effect of sparsity and low rank property. The estimate is computed efficiently using proximal methods through a generalized forward-backward agorithm.

Linear Support Vector Machines (SVMs) have become very popular in vision as part of state-of-the-art object recognition and other classification tasks but require high dimensional feature spaces for good performance. Deep learning methods can find more compact representations but current methods employ multilayer perceptrons that require solving a difficult, non-convex optimization problem. We propose a deep non-linear classifier whose layers are SVMs and which incorporates random projection as its core stacking element. Our method learns layers of linear SVMs recursively transforming the original data manifold through a random projection of the weak prediction computed from each layer. Our method scales as linear SVMs, does not rely on any kernel computations or nonconvex optimization, and exhibits better generalization ability than kernel-based SVMs. This is especially true when the number of training samples is smaller than the dimensionality of data, a common scenario in many real-world applications. The use of random projections is key to our method, as we show in the experiments section, in which we observe a consistent improvement over previous --often more complicated-- methods on several vision and speech benchmarks.

User preferences for items can be inferred from either explicit feedback, such as item ratings, or implicit feedback, such as rental histories. Research in collaborative filtering has concentrated on explicit feedback, resulting in the development of accurate and scalable models. However, since explicit feedback is often difficult to collect it is important to develop effective models that take advantage of the more widely available implicit feedback. We introduce a probabilistic approach to collaborative filtering with implicit feedback based on modelling the user's item selection process. In the interests of scalability, we restrict our attention to tree-structured distributions over items and develop a principled and efficient algorithm for learning item trees from data. We also identify a problem with a widely used protocol for evaluating implicit feedback models and propose a way of addressing it using a small quantity of explicit feedback data.

We introduce a new Bayesian admixture model intended for exploratory analysis ofcommunication networks--specifically, the discovery and visualization of topic-specific subnetworks in email data sets. Our model produces principled visualizations ofemail networks, i.e., visualizations that have precise mathematical interpretations in terms of our model and its relationship to the observed data. We validate our modeling assumptions by demonstrating that our model achieves better link prediction performance than three state-of-the-art network models and exhibits topic coherence comparable to that of latent Dirichlet allocation. We showcase our model's ability to discover and visualize topic-specific communication patternsusing a new email data set: the New Hanover County email network. We provide an extensive analysis of these communication patterns, leading us to recommend our model for any exploratory analysis of email networks or other similarly-structured communication data. Finally, we advocate for principled visualization asa primary objective in the development of new network models.

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.

Information, disease, and influence diffuse over networks of entities in both natural systems and human society. Analyzing these transmission networks plays an important role in understanding the diffusion processes and predicting events in the future. However, the underlying transmission networks are often hidden and incomplete, and we observe only the time stamps when cascades of events happen. In this paper, we attempt to address the challenging problem of uncovering the hidden network only from the cascades. The structure discovery problem is complicated by the fact that the influence among different entities in a network are heterogeneous, which can not be described by a simple parametric model. Therefore, we propose a kernel-based method which can capture a diverse range of different types of influence without any prior assumption. In both synthetic and real cascade data, we show that our model can better recover the underlying diffusion network and drastically improve the estimation of the influence functions between networked entities.

We develop a probabilistic model of legislative data that uses the text of the bills to uncover lawmakers' positions on specific political issues. Our model can be used to explore how a lawmaker's voting patterns deviate from what is expected and how that deviation depends on what is being voted on. We derive approximate posterior inference algorithms based on variational methods. Across 12 years of legislative data, we demonstrate both improvement in heldout predictive performance and the model's utility in interpreting an inherently multi-dimensional space.

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.