In this paper we propose a new basis selection criterion for building sparse GP regression models that provides promising gains in accuracy as well as efficiency over previous methods. Our algorithm is much faster than that of Smola and Bartlett, while, in generalization it greatly outperforms the information gain approach proposed by Seeger et al, especially on the quality of predictive distributions.

We present a nonlinear, simple, yet effective, feature subset selection method for regression and use it in analyzing cortical neural activity. Our algorithm involves a feature-weighted version of the k-nearest-neighbor algorithm. It is able to capture complex dependency of the target function on its input and makes use of the leave-one-out error as a natural regularization. We explain the characteristics of our algorithm on synthetic problems and use it in the context of predicting hand velocity from spikes recorded in motor cortex of a behaving monkey. By applying feature selection we are able to improve prediction quality and suggest a novel way of exploring neural data.

We present a method for nonparametric regression that performs bandwidth selection and variable selection simultaneously. The approach is based on the technique of incrementally decreasing the bandwidth in directions where the gradient of the estimator with respect to bandwidth is large. When the unknown function satisfies a sparsity condition, our approach avoids the curse of dimensionality, achieving the optimal minimax rate of convergence, up to logarithmic factors, as if the relevant variables were known in advance. The method--called rodeo (regularization of derivative expectation operator)--conducts a sequence of hypothesis tests, and is easy to implement. A modified version that replaces hard with soft thresholding effectively solves a sequence of lasso problems.

Kernel methods make it relatively easy to define complex highdimensional feature spaces. This raises the question of how we can identify the relevant subspaces for a particular learning task. When two views of the same phenomenon are available kernel Canonical Correlation Analysis (KCCA) has been shown to be an effective preprocessing step that can improve the performance of classification algorithms such as the Support Vector Machine (SVM). This paper takes this observation to its logical conclusion and proposes a method that combines this two stage learning (KCCA followed by SVM) into a single optimisation termed SVM-2K. We present both experimental and theoretical analysis of the approach showing encouraging results and insights.

This paper presents a new sampling algorithm for approximating functions of variables representable as undirected graphical models of arbitrary connectivity with pairwise potentials, as well as for estimating the notoriously difficult partition function of the graph. The algorithm fits into the framework of sequential Monte Carlo methods rather than the more widely used MCMC, and relies on constructing a sequence of intermediate distributions which get closer to the desired one. While the idea of using "tempered" proposals is known, we construct a novel sequence of target distributions where, rather than dropping a global temperature parameter, we sequentially couple individual pairs of variables that are, initially, sampled exactly from a spanning tree of the variables.

We show how to learn a Mahanalobis distance metric for k-nearest neighbor (kNN) classification by semidefinite programming. The metric is trained with the goal that the k-nearest neighbors always belong to the same class while examples from different classes are separated by a large margin. On seven data sets of varying size and difficulty, we find that metrics trained in this way lead to significant improvements in kNN classification--for example, achieving a test error rate of 1.3% on the MNIST handwritten digits. As in support vector machines (SVMs), the learning problem reduces to a convex optimization based on the hinge loss. Unlike learning in SVMs, however, our framework requires no modification or extension for problems in multiway (as opposed to binary) classification.

We describe a hierarchy of motif-based kernels for multiple alignments of biological sequences, particularly suitable to process regulatory regions of genes. The kernels incorporate progressively more information, with the most complex kernel accounting for a multiple alignment of orthologous regions, the phylogenetic tree relating the species, and the prior knowledge that relevant sequence patterns occur in conserved motif blocks. These kernels can be used in the presence of a library of known transcription factor binding sites, or de novo by iterating over all k-mers of a given length. In the latter mode, a discriminative classifier built from such a kernel not only recognizes a given class of promoter regions, but as a side effect simultaneously identifies a collection of relevant, discriminative sequence motifs. We demonstrate the utility of the motif-based multiple alignment kernels by using a collection of aligned promoter regions from five yeast species to recognize classes of cell-cycle regulated genes.

The Perceptron algorithm, despite its simplicity, often performs well on online classification tasks. The Perceptron becomes especially effective when it is used in conjunction with kernels. However, a common difficulty encountered when implementing kernel-based online algorithms is the amount of memory required to store the online hypothesis, which may grow unboundedly. In this paper we present and analyze the Forgetron algorithm for kernel-based online learning on a fixed memory budget. To our knowledge, this is the first online learning algorithm which, on one hand, maintains a strict limit on the number of examples it stores while, on the other hand, entertains a relative mistake bound. In addition to the formal results, we also present experiments with real datasets which underscore the merits of our approach.

We present a new Gaussian process (GP) regression model whose covariance is parameterized by the the locations of M pseudo-input points, which we learn by a gradient based optimization.

We argue that when objects are characterized by many attributes, clustering them on the basis of a relatively small random subset of these attributes can capture information on the unobserved attributes as well. Moreover, we show that under mild technical conditions, clustering the objects on the basis of such a random subset performs almost as well as clustering with the full attribute set. We prove a finite sample generalization theorems for this novel learning scheme that extends analogous results from the supervised learning setting. The scheme is demonstrated for collaborative filtering of users with movies rating as attributes.