We consider estimation of multiple high-dimensional Gaussian graphical models corresponding to a single set of nodes under several distinct conditions. We assume that most aspects of the networks are shared, but that there are some structured differences between them. Specifically, the network differences are generated from node perturbations: a few nodes are perturbed across networks, and most or all edges stemming from such nodes differ between networks. This corresponds to a simple model for the mechanism underlying many cancers, in which the gene regulatory network is disrupted due to the aberrant activity of a few specific genes. We propose to solve this problem using the structured joint graphical lasso, a convex optimization problem that is based upon the use of a novel symmetric overlap norm penalty, which we solve using an alternating directions method of multipliers algorithm.

Stochastic differential equations (SDE) are a natural tool for modelling systems that are inherently noisy or contain uncertainties that can be modelled as stochastic processes. Crucial to the process of using SDE to build mathematical models is the ability to estimate parameters of those models from observed data. Over the past few decades, significant progress has been made on this problem, but we are still far from having a definitive solution. We describe a novel method of approximating a diffusion process that we show to be useful in Markov chain Monte-Carlo (MCMC) inference algorithms. We take the'white' noise that drives a diffusion process and decompose it into two terms.

Multiple-output regression models require estimating multiple functions, one for each output. To improve parameter estimation in such models, methods based on structural regularization of the model parameters are usually needed. In this paper, we present a multiple-output regression model that leverages the covariance structure of the functions (i.e., how the multiple functions are related with each other) as well as the conditional covariance structure of the outputs. This is in contrast with existing methods that usually take into account only one of these structures. More importantly, unlike most of the other existing methods, none of these structures need be known a priori in our model, and are learned from the data.

One of the enduring challenges in Markov chain Monte Carlo methodology is the development of proposal mechanisms to make moves distant from the current point, that are accepted with high probability and at low computational cost. The recent introduction of locally adaptive MCMC methods based on the natural underlying Riemannian geometry of such models goes some way to alleviating these problems for certain classes of models for which the metric tensor is analytically tractable, however computational efficiency is not assured due to the necessity of potentially high-dimensional matrix operations at each iteration. In this paper we firstly investigate a sampling-based approach for approximating the metric tensor and suggest a valid MCMC algorithm that extends the applicability of Riemannian Manifold MCMC methods to statistical models that do not admit an analytically computable metric tensor. Secondly, we show how the approximation scheme we consider naturally motivates the use of l1 regularisation to improve estimates and obtain a sparse approximate inverse of the metric, which enables stable and sparse approximations of the local geometry to be made. We demonstrate the application of this algorithm for inferring the parameters of a realistic system of ordinary differential equations using a biologically motivated robust student-t error model, for which the expected Fisher Information is analytically intractable.

In this paper, we introduce two novel metric learning algorithms, χ2-LMNN and GB-LMNN, which are explicitly designed to be non-linear and easy-to-use. The two approaches achieve this goal in fundamentally different ways: χ2-LMNN inherits the computational benefits of a linear mapping from linear metric learning, but uses a non-linear χ2-distance to explicitly capture similarities within histogram data sets; GB-LMNN applies gradient-boosting to learn non-linear mappings directly in function space and takes advantage of this approach's robustness, speed, parallelizability and insensitivity towards the single additional hyper-parameter. On various benchmark data sets, we demonstrate these methods not only match the current state-of-the-art in terms of kNN classification error, but in the case of χ2-LMNN, obtain best results in 19 out of 20 learning settings.

Links between probabilistic and non-probabilistic learning algorithms can arise by performing small-variance asymptotics, i.e., letting the variance of particular distributions in a graphical model go to zero. For instance, in the context of clustering, such an approach yields precise connections between the k-means and EM algorithms. In this paper, we explore small-variance asymptotics for exponential family Dirichlet process (DP) and hierarchical Dirichlet process (HDP) mixture models. Utilizing connections between exponential family distributions and Bregman divergences, we derive novel clustering algorithms from the asymptotic limit of the DP and HDP mixtures that feature the scalability of existing hard clustering methods as well as the flexibility of Bayesian nonparametric models. We focus on special cases of our analysis for discrete-data problems, including topic modeling, and we demonstrate the utility of our results by applying variants of our algorithms to problems arising in vision and document analysis.

Non-linear dynamical systems (DS) have been used extensively for building generative models of human behavior. Its applications range from modeling brain dynamics to encoding motor commands. Many schemes have been proposed for encoding robot motions using dynamical systems with a single attractor placed at a predefined target in state space. Although these enable the robots to react against sudden perturbations without any re-planning, the motions are always directed towards a single target. In this work, we focus on combining several such DS with distinct attractors, resulting in a multi-stable DS.

Undirected graphical models, or Markov networks, such as Gaussian graphical models and Ising models enjoy popularity in a variety of applications. In many settings, however, data may not follow a Gaussian or binomial distribution assumed by these models. We introduce a new class of graphical models based on generalized linear models (GLM) by assuming that node-wise conditional distributions arise from exponential families. Our models allow one to estimate networks for a wide class of exponential distributions, such as the Poisson, negative binomial, and exponential, by fitting penalized GLMs to select the neighborhood for each node. A major contribution of this paper is the rigorous statistical analysis showing that with high probability, the neighborhood of our graphical models can be recovered exactly.

The application of the maximum entropy principle to sequence modeling has been popularized by methods such as Conditional Random Fields (CRFs). However, these approaches are generally limited to modeling paths in discrete spaces of low dimensionality. We consider the problem of modeling distributions over paths in continuous spaces of high dimensionality---a problem for which inference is generally intractable. Our main contribution is to show that maximum entropy modeling of high-dimensional, continuous paths is tractable as long as the constrained features possess a certain kind of low dimensional structure. In this case, we show that the associated {\em partition function} is symmetric and that this symmetry can be exploited to compute the partition function efficiently in a compressed form. Empirical results are given showing an application of our method to maximum entropy modeling of high dimensional human motion capture data.

In this paper we apply boosting to learn complex non-linear local visual feature representations, drawing inspiration from its successful application to visual object detection. The main goal of local feature descriptors is to distinctively represent a salient image region while remaining invariant to viewpoint and illumination changes. This representation can be improved using machine learning, however, past approaches have been mostly limited to learning linear feature mappings in either the original input or a kernelized input feature space. While kernelized methods have proven somewhat effective for learning non-linear local feature descriptors, they rely heavily on the choice of an appropriate kernel function whose selection is often difficult and non-intuitive. We propose to use the boosting-trick to obtain a non-linear mapping of the input to a high-dimensional feature space.