Warped Gaussian processes (WGP) [1] model output observations in regression tasks as a parametric nonlinear transformation of a Gaussian process (GP). The use of this nonlinear transformation, which is included as part of the probabilistic model, was shown to enhance performance by providing a better prior model on several data sets. In order to learn its parameters, maximum likelihood was used. In this work we show that it is possible to use a non-parametric nonlinear transformation in WGP and variationally integrate it out. The resulting Bayesian WGP is then able to work in scenarios in which the maximum likelihood WGP failed: Low data regime, data with censored values, classification, etc. We demonstrate the superior performance of Bayesian warped GPs on several real data sets.

We develop a new algorithm to cluster sparse unweighted graphs -- i.e. partition the nodes into disjoint clusters so that there is higher density within clusters, and low across clusters. By sparsity we mean the setting where both the in-cluster and across cluster edge densities are very small, possibly vanishing in the size of the graph. Sparsity makes the problem noisier, and hence more difficult to solve. Any clustering involves a tradeoff between minimizing two kinds of errors: missing edges within clusters and present edges across clusters. Our insight is that in the sparse case, these must be {\em penalized differently}. We analyze our algorithm's performance on the natural, classical and widely studied ``planted partition'' model (also called the stochastic block model); we show that our algorithm can cluster sparser graphs, and with smaller clusters, than all previous methods. This is seen empirically as well.

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.

We develop a novel approach for supervised learning based on adaptively partitioning the feature space into different regions and learning local region-specific classifiers. We formulate an empirical risk minimization problem that incorporates both partitioning and classification in to a single global objective. We show that space partitioning can be equivalently reformulated as a supervised learning problem and consequently any discriminative learning method can be utilized in conjunction with our approach. Nevertheless, we consider locally linear schemes by learning linear partitions and linear region classifiers. Locally linear schemes can not only approximate complex decision boundaries and ensure low training error but also provide tight control on over-fitting and generalization error. We train locally linear classifiers by using LDA, logistic regression and perceptrons, and so our scheme is scalable to large data sizes and high-dimensions. We present experimental results demonstrating improved performance over state of the art classification techniques on benchmark datasets. We also show improved robustness to label noise.

In many practical machine learning problems, the acquisition of labeled data is often expensive and/or time consuming. This motivates us to study a problem as follows: given a label budget, how to select data points to label such that the learning performance is optimized. We propose a selective labeling method by analyzing the generalization error of Laplacian regularized Least Squares (LapRLS). In particular, we derive a deterministic generalization error bound for LapRLS trained on subsampled data, and propose to select a subset of data points to label by minimizing this upper bound. Since the minimization is a combinational problem, we relax it into continuous domain and solve it by projected gradient descent. Experiments on benchmark datasets show that the proposed method outperforms the state-of-the-art methods.

A patient's risk for adverse events is affected by temporal processes including the nature and timing of diagnostic and therapeutic activities, and the overall evolution of the patient's pathophysiology over time. Yet many investigators ignore this temporal aspect when modeling patient risk, considering only the patient's current or aggregate state. We explore representing patient risk as a time series. In doing so, patient risk stratification becomes a time-series classification task. The task differs from most applications of time-series analysis, like speech processing, since the time series itself must first be extracted. Thus, we begin by defining and extracting approximate \textit{risk processes}, the evolving approximate daily risk of a patient. Once obtained, we use these signals to explore different approaches to time-series classification with the goal of identifying high-risk patterns. We apply the classification to the specific task of identifying patients at risk of testing positive for hospital acquired colonization with \textit{Clostridium Difficile}. We achieve an area under the receiver operating characteristic curve of 0.79 on a held-out set of several hundred patients. Our two-stage approach to risk stratification outperforms classifiers that consider only a patient's current state (p$<$0.05).

We propose a simple and novel framework for MCMC inference in continuous-time discrete-state systems with pure jump trajectories. We construct an exact MCMC sampler for such systems by alternately sampling a random discretization of time given a trajectory of the system, and then a new trajectory given the discretization. The first step can be performed efficiently using properties of the Poisson process, while the second step can avail of discrete-time MCMC techniques based on the forward-backward algorithm. We compare our approach to particle MCMC and a uniformization-based sampler, and show its advantages.

W e propose a multiresolution Gaussian process to capture lo ng-range, non-Markovian dependencies while allowing for abrupt changes a nd non-stationarity. The multiresolution GP hierarchically couples a collectio n of smooth GPs, each defined over an element of a random nested partition. Long-ra nge dependencies are captured by the top-level GP while the partition poi nts define the abrupt changes. Due to the inherent conjugacy of the GPs, one can analytically marginalize the GPs and compute the marginal likelihood of the observations given the partition tree. This property allows for efficient inference of the partition itself, for which we employ graph-theoretic techniques. W e apply the multiresolution GP to the analysis of magnetoencephalography (MEG) recordings of brain activity.

We theoretically analyze and compare the following five popular multiclass classification methods: One vs. All, All Pairs, Tree-based classifiers, Error Correcting Output Codes (ECOC) with randomly generated code matrices, and Multiclass SVM. In the first four methods, the classification is based on a reduction to binary classification. We consider the case where the binary classifier comes from a class of VC dimension $d$, and in particular from the class of halfspaces over $\reals^d$. We analyze both the estimation error and the approximation error of these methods. Our analysis reveals interesting conclusions of practical relevance, regarding the success of the different approaches under various conditions. Our proof technique employs tools from VC theory to analyze the \emph{approximation error} of hypothesis classes. This is in sharp contrast to most, if not all, previous uses of VC theory, which only deal with estimation error.

Both random Fourier features and the Nyström method have been successfully applied to efficient kernel learning. In this work, we investigate the fundamental difference between these two approaches, and how the difference could affect their generalization performances. Unlike approaches based on random Fourier features where the basis functions (i.e., cosine and sine functions) are sampled from a distribution {\it independent} from the training data, basis functions used by the Nyström method are randomly sampled from the training examples and are therefore {\it data dependent}. By exploring this difference, we show that when there is a large gap in the eigen-spectrum of the kernel matrix, approaches based the Nyström method can yield impressively better generalization error bound than random Fourier features based approach. We empirically verify our theoretical findings on a wide range of large data sets.