We determine the asymptotic limit of the function computed by support vector machines (SVM) and related algorithms that minimize a regularized empirical convex loss function in the reproducing kernel Hilbert space of the Gaussian RBF kernel, in the situation where the number of examples tends to infinity, the bandwidth of the Gaussian kernel tends to 0, and the regularization parameter is held fixed.

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.

An increasing number of projects in neuroscience requires the statistical analysis of high dimensional data sets, as, for instance, in predicting behavior from neural firing or in operating artificial devices from brain recordings in brain-machine interfaces. Linear analysis techniques remain prevalent in such cases, but classical linear regression approaches are often numerically too fragile in high dimensions. In this paper, we address the question of whether EMG data collected from arm movements of monkeys can be faithfully reconstructed with linear approaches from neural activity in primary motor cortex (M1). To achieve robust data analysis, we develop a full Bayesian approach to linear regression that automatically detects and excludes irrelevant features in the data, regularizing against overfitting. In comparison with ordinary least squares, stepwise regression, partial least squares, LASSO regression and a brute force combinatorial search for the most predictive input features in the data, we demonstrate that the new Bayesian method offers a superior mixture of characteristics in terms of regularization against overfitting, computational efficiency and ease of use, demonstrating its potential as a drop-in replacement for other linear regression techniques. As neuroscientific results, our analyses demonstrate that EMG data can be well predicted from M1 neurons, further opening the path for possible real-time interfaces between brains and machines.

Active learning is the problem in supervised learning to design the locations of training input points so that the generalization error is minimized. Existing active learning methods often assume that the model used for learning is correctly specified, i.e., the learning target function can be expressed by the model at hand. In many practical situations, however, this assumption may not be fulfilled. In this paper, we first show that the existing active learning method can be theoretically justified under slightly weaker condition: the model does not have to be correctly specified, but slightly misspecified models are also allowed. However, it turns out that the weakened condition is still restrictive in practice. To cope with this problem, we propose an alternative active learning method which can be theoretically justified for a wider class of misspecified models. Thus, the proposed method has a broader range of applications than the existing method. Numerical studies show that the proposed active learning method is robust against the misspecification of models and is thus reliable.

While classical kernel-based learning algorithms are based on a single kernel, in practice it is often desirable to use multiple kernels. Lankriet et al. (2004) considered conic combinations of kernel matrices for classification, leading to a convex quadratically constraint quadratic program. We show that it can be rewritten as a semi-infinite linear program that can be efficiently solved by recycling the standard SVM implementations. Moreover, we generalize the formulation and our method to a larger class of problems, including regression and one-class classification. Experimental results show that the proposed algorithm helps for automatic model selection, improving the interpretability of the learning result and works for hundred thousands of examples or hundreds of kernels to be combined.

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 present a conditional temporal probabilistic framework for reconstructing 3D human motion in monocular video based on descriptors encoding image silhouette observations. For computational efficiency we restrict visual inference to low-dimensional kernel induced nonlinear state spaces. Our methodology (kBME) combines kernel PCA-based nonlinear dimensionality reduction (kPCA) and Conditional Bayesian Mixture of Experts (BME) in order to learn complex multivalued predictors between observations and model hidden states. This is necessary for accurate, inverse, visual perception inferences, where several probable, distant 3D solutions exist due to noise or the uncertainty of monocular perspective projection. Low-dimensional models are appropriate because many visual processes exhibit strong nonlinear correlations in both the image observations and the target, hidden state variables. The learned predictors are temporally combined within a conditional graphical model in order to allow a principled propagation of uncertainty. We study several predictors and empirically show that the proposed algorithm positively compares with techniques based on regression, Kernel Dependency Estimation (KDE) or PCA alone, and gives results competitive to those of high-dimensional mixture predictors at a fraction of their computational cost. We show that the method successfully reconstructs the complex 3D motion of humans in real monocular video sequences.

There has been a surge of interest in learning nonlinear manifold models to approximate high-dimensional data. Both for computational complexity reasons and for generalization capability, sparsity is a desired feature in such models. This usually means dimensionality reduction, which naturally implies estimating the intrinsic dimension, but it can also mean selecting a subset of the data to use as landmarks, which is especially important because many existing algorithms have quadratic complexity in the number of observations.

We propose an algorithm that uses Gaussian process regression to learn common hidden structure shared between corresponding sets of heterogenous observations. The observation spaces are linked via a single, reduced-dimensionality latent variable space. We present results from two datasets demonstrating the algorithms's ability to synthesize novel data from learned correspondences. We first show that the method can learn the nonlinear mapping between corresponding views of objects, filling in missing data as needed to synthesize novel views. We then show that the method can learn a mapping between human degrees of freedom and robotic degrees of freedom for a humanoid robot, allowing robotic imitation of human poses from motion capture data.

This makes Gaussian process regression too slow for large datasets. In this paper, we present a fast approximation method, based on kd-trees, that significantly reduces both the prediction and the training times of Gaussian process regression.