Résultats de recherche pour « Kernel Methods »

Kernel methods in general, and support vector machines (SVMs) in particular, are increasingly used to solve various problems in computational biology.They offer versatile tools to process, analyze, and compare many types of data, and offer stateof-the-art performance in many cases.This self-contained introduction to positive definite kernels and kernel methods aims at providing the very basic knowledge and intuition that the reader might find useful in order to fully grasp the technical content of this book.

A detailed overview of current research in kernel methods and their application to computational biology. Modern machine learning techniques are proving to be extremely valuable for the analysis of data in computational biology problems. One branch of machine learning, kernel methods, lends itself particularly well to the difficult aspects of biological data, which include high dimensionality (as in microarray measurements), representation as discrete and structured data (as in DNA or amino acid sequences), and the need to combine heterogeneous sources of information. This book provides a detailed overview of current research in kernel methods and their applications to computational biology. Following three introductory chapters—an introduction to molecular and computational biology, a short review of kernel methods that focuses on intuitive concepts rather than technical details, and a detailed survey of recent applications of kernel methods in computational biology—the book is divided into three sections that reflect three general trends in current research. The first part presents different ideas for the design of kernel functions specifically adapted to various biological data; the second part covers different approaches to learning from heterogeneous data; and the third part offers examples of successful applications of support vector machine methods.

We present an application of kernel methods to extracting relations from unstructured natural language sources. We introduce kernels defined over shallow parse representations of text, and design efficient algorithms for computing the kernels. We use the devised kernels in conjunction with Support Vector Machine and Voted Perceptron learning algorithms for the task of extracting person-affiliation and organization-location relations from text. We experimentally evaluate the proposed methods and compare them with feature-based learning algorithms, with promising results.

We review machine learning methods employing positive definite kernels. These methods formulate learning and estimation problems in a reproducing kernel Hilbert space (RKHS) of functions defined on the data domain, expanded in terms of a kernel. Working in linear spaces of function has the benefit of facilitating the construction and analysis of learning algorithms while at the same time allowing large classes of functions. The latter include nonlinear functions as well as functions defined on nonvectorial data. We cover a wide range of methods, ranging from binary classifiers to sophisticated methods for estimation with structured data.

Random forests are ensemble methods which grow trees as base learners and combine their predictions by averaging. Random forests are known for their good practical performance, particularly in high-dimensional settings. On the theoretical side, several studies highlight the potentially fruitful connection between the random forests and the kernel methods. In this paper, we work out this connection in detail. In particular, we show that by slightly modifying their definition, random forests can be rewritten as kernel methods (called KeRF for kernel based on random forests) which are more interpretable and easier to analyze. Explicit expressions of KeRF estimates for some specific random forest models are given, together with upper bounds on their rate of consistency. We also show empirically that the KeRF estimates compare favourably to the random forest estimates.

Canonical correlation analysis is a technique to extract common features from a pair of multivariate data. In complex situations, however, it does not extract useful features because of its linearity. On the other hand, kernel method used in support vector machine is an efficient approach to improve such a linear method. In this paper, we investigate the effectiveness of applying kernel method to canonical correlation analysis.

We propose a framework for analyzing and comparing distributions, allowing us to design statistical tests to determine if two samples are drawn from different distributions. Our test statistic is the largest difference in expectations over functions in the unit ball of a reproducing kernel Hilbert space (RKHS). We present two tests based on large deviation bounds for the test statistic, while a third is based on the asymptotic distribution of this statistic. The test statistic can be computed in quadratic time, although efficient linear time approximations are available. Several classical metrics on distributions are recovered when the function space used to compute the difference in expectations is allowed to be more general (eg. a Banach space). We apply our two-sample tests to a variety of problems, including attribute matching for databases using the Hungarian marriage method, where they perform strongly. Excellent performance is also obtained when comparing distributions over graphs, for which these are the first such tests.

kernlab is an extensible package for kernel-based machine learning methods in R. It takes advantage of R's new S4 ob ject model and provides a framework for creating and using kernel-based algorithms. The package contains dot product primitives (kernels), implementations of support vector machines and the relevance vector machine, Gaussian processes, a ranking algorithm, kernel PCA, kernel CCA, and a spectral clustering algorithm. Moreover it provides a general purpose quadratic programming solver, and an incomplete Cholesky decomposition method.

Important information on the structure of complex systems can be obtained by measuring to what extent the individual components exchange information among each other. The linear Granger approach, to detect cause-effect relationships between time series, has emerged in recent years as a leading statistical technique to accomplish this task. Here we generalize Granger causality to the nonlinear case using the theory of reproducing kernel Hilbert spaces. Our method performs linear Granger causality in the feature space of suitable kernel functions, assuming arbitrary degree of nonlinearity. We develop a new strategy to cope with the problem of overfitting, based on the geometry of reproducing kernel Hilbert spaces. Applications to coupled chaotic maps and physiological data sets are presented.

In this paper, we develop an approach to exploiting kernel methods with manifold-valued data. In many computer vision problems, the data can be naturally represented as points on a Riemannian manifold. Due to the non-Euclidean geometry of Riemannian manifolds, usual Euclidean computer vision and machine learning algorithms yield inferior results on such data. In this paper, we define Gaussian radial basis function (RBF)-based positive definite kernels on manifolds that permit us to embed a given manifold with a corresponding metric in a high dimensional reproducing kernel Hilbert space. These kernels make it possible to utilize algorithms developed for linear spaces on nonlinear manifold-valued data. Since the Gaussian RBF defined with any given metric is not always positive definite, we present a unified framework for analyzing the positive definiteness of the Gaussian RBF on a generic metric space. We then use the proposed framework to identify positive definite kernels on two specific manifolds commonly encountered in computer vision: the Riemannian manifold of symmetric positive definite matrices and the Grassmann manifold, i.e., the Riemannian manifold of linear subspaces of a Euclidean space. We show that many popular algorithms designed for Euclidean spaces, such as support vector machines, discriminant analysis and principal component analysis can be generalized to Riemannian manifolds with the help of such positive definite Gaussian kernels.