In this paper we present a new algorithm suitable for matching discrete objects such as strings and trees in linear time, thus obviating dynarrtic programming with quadratic time complexity. Furthermore, prediction cost in many cases can be reduced to linear cost in the length of the sequence to be classified, regardless of the number of support vectors. This improvement on the currently available algorithms makes string kernels a viable alternative for the practitioner.

We introduce a general family of kernels based on weighted transducers or rational relations, rational kernels, that can be used for analysis of variable-length sequences or more generally weighted automata, in applications such as computational biology or speech recognition. We show that rational kernels can be computed efficiently using a general algorithm of composition of weighted transducers and a general single-source shortest-distance algorithm. We also describe several general families of positive definite symmetric rational kernels. These general kernels can be combined with Support Vector Machines to form efficient and powerful techniques for spoken-dialog classification: highly complex kernels become easy to design and implement and lead to substantial improvements in the classification accuracy. We also show that the string kernels considered in applications to computational biology are all specific instances of rational kernels.

We investigate the problem of learning a classification task for datasets which are described by matrices. Rows and columns of these matrices correspond to objects, where row and column objects may belong to different sets, and the entries in the matrix express the relationships between them. We interpret the matrix elements as being produced by an unknown kernel which operates on object pairs and we show that - under mild assumptions - these kernels correspond to dot products in some (unknown) feature space. Minimizing a bound for the generalization error of a linear classifier which has been obtained using covering numbers we derive an objective function for model selection according to the principle of structural risk minimization. The new objective function has the advantage that it allows the analysis of matrices which are not positive definite, and not even symmetric or square.

We present an algorithm to extract features from high-dimensional gene expression profiles, based on the knowledge of a graph which links together genes known to participate to successive reactions in metabolic pathways. Motivated by the intuition that biologically relevant features are likely to exhibit smoothness with respect to the graph topology, the algorithm involves encoding the graph and the set of expression profiles into kernel functions, and performing a generalized form of canonical correlation analysis in the corresponding reproducible kernel Hilbert spaces. Function prediction experiments for the genes of the yeast S. Cerevisiae validate this approach by showing a consistent increase in performance when a state-of-the-art classifier uses the vector of features instead of the original expression profile to predict the functional class of a gene.

We introduce a family of classifiers based on a physical analogy to an electrostatic system of charged conductors. The family, called Coulomb classifiers, includes the two best-known support-vector machines (SVMs), the ν-SVM and the C-SVM. In the electrostatics analogy, a training example corresponds to a charged conductor at a given location in space, the classification function corresponds to the electrostatic potential function, and the training objective function corresponds to the Coulomb energy. The electrostatic framework provides not only a novel interpretation of existing algorithms and their interrelationships, but it suggests a variety of new methods for SVMs including kernels that bridge the gap between polynomial and radial-basis functions, objective functions that do not require positive-definite kernels, regularization techniques that allow for the construction of an optimal classifier in Minkowski space. Based on the framework, we propose novel SVMs and perform simulation studies to show that they are comparable or superior to standard SVMs. The experiments include classification tasks on data which are represented in terms of their pairwise proximities, where a Coulomb Classifier outperformed standard SVMs.

We consider the problem of choosing a kernel suitable for estimation using a Gaussian Process estimator or a Support Vector Machine. A novel solution is presented which involves defining a Reproducing Kernel HilbertSpace on the space of kernels itself. By utilizing an analog of the classical representer theorem, the problem of choosing a kernel from a parameterized family of kernels (e.g. of varying width) is reduced to a statistical estimation problem akin to the problem of minimizing a regularized risk functional. Various classical settings for model or kernel selection are special cases of our framework.

We investigate the problem of learning a classification task for datasets which are described by matrices. Rows and columns of these matrices correspond to objects, where row and column objects may belong to different sets, and the entries in the matrix express the relationships between them. We interpret the matrix elements as being produced by an unknown kernel which operates on object pairs and we show that - under mild assumptions - these kernels correspond to dot products in some (unknown) feature space. Minimizing a bound for the generalization error of a linear classifier which has been obtained using covering numbers we derive an objective function for model selection according to the principle of structural risk minimization. The new objective function has the advantage that it allows the analysis of matrices which are not positive definite, and not even symmetric or square.

Spontaneous facial expressions differ substantially from posed expressions, similar to how continuous, spontaneous speech differs from isolated words produced on command. Previous methods for automatic facial expression recognition assumed images were collected in controlled environments in which the subjects deliberately facedthe camera. Since people often nod or turn their heads, automatic recognition of spontaneous facial behavior requires methods for handling out-of-image-plane head rotations. Here we explore an approach basedon 3-D warping of images into canonical views. We evaluated the performance of the approach as a front-end for a spontaneous expression recognition system using support vector machines and hidden Markov models. This system employed general purpose learning mechanisms thatcan be applied to recognition of any facial movement. The system was tested for recognition of a set of facial actions defined by the Facial Action Coding System (FACS). We showed that 3D tracking and warping followed by machine learning techniques directly applied to the warped images, is a viable and promising technology for automatic facial expression recognition. One exciting aspect of the approach presented hereis that information about movement dynamics emerged out of filters which were derived from the statistics of images.

We derive multiplicative updates for solving the nonnegative quadratic programming problem in support vector machines (SVMs). The updates have a simple closed form, and we prove that they converge monotonically tothe solution of the maximum margin hyperplane. The updates optimize the traditionally proposed objective function for SVMs. They do not involve any heuristics such as choosing a learning rate or deciding which variables to update at each iteration. They can be used to adjust all the quadratic programming variables in parallel with a guarantee of improvement ateach iteration. We analyze the asymptotic convergence of the updates and show that the coefficients of nonsupport vectors decay geometrically to zero at a rate that depends on their margins.

We introduce a family of classifiers based on a physical analogy to an electrostatic system of charged conductors. The family, called Coulomb classifiers, includes the two best-known support-vector machines (SVMs), the ν-SVM and the C-SVM. In the electrostatics analogy,a training example corresponds to a charged conductor at a given location in space, the classification function corresponds to the electrostatic potential function, and the training objective function corresponds to the Coulomb energy. The electrostatic framework provides not only a novel interpretation of existing algorithms andtheir interrelationships, but it suggests a variety of new methods for SVMs including kernels that bridge the gap between polynomial and radial-basis functions, objective functions that do not require positive-definite kernels, regularization techniques that allow for the construction of an optimal classifier in Minkowski space. Based on the framework, we propose novel SVMs and perform simulationstudies to show that they are comparable or superior tostandard SVMs. The experiments include classification tasks on data which are represented in terms of their pairwise proximities, wherea Coulomb Classifier outperformed standard SVMs.