In this work, we study an information filtering model where the relevance labels associated to a sequence of feature vectors are realizations of an unknown probabilistic linear function. Building on the analysis of a restricted version of our model, we derive a general filtering rule based on the margin of a ridge regression estimator. While our rule may observe the label of a vector only by classfying the vector as relevant, experiments on a real-world document filtering problem show that the performance of our rule is close to that of the online classifier which is allowed to observe all labels. These empirical results are complemented by a theoretical analysis where we consider a randomized variant of our rule and prove that its expected number of mistakes is never much larger than that of the optimal filtering rule which knows the hidden linear model.

We describe the application of probabilistic model-based learning to the problem of automatically identifying classes of galaxies, based on both morphological and pixel intensity characteristics. The EM algorithm can be used to learn how to spatially orient a set of galaxies so that they are geometrically aligned. We augment this "ordering-model" with a mixture model on objects, and demonstrate how classes of galaxies can be learned in an unsupervised manner using a two-level EM algorithm. The resulting models provide highly accurate classi£cation of galaxies in cross-validation experiments.

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.

Most text categorization systems use simple models of documents and document collections. In this paper we describe a technique that improves a simple web page classifier's performance on pages from a new, unseen web site, by exploiting link structure within a site as well as page structure within hub pages. On real-world test cases, this technique significantly and substantially improves the accuracy of a bag-of-words classifier, reducing error rate by about half, on average. The system uses a variant of co-training to exploit unlabeled data from a new site. Pages are labeled using the base classifier; the results are used by a restricted wrapper-learner to propose potential "main-category anchor wrappers"; and finally, these wrappers are used as features by a third learner to find a categorization of the site that implies a simple hub structure, but which also largely agrees with the original bag-of-words classifier.

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 consider the general problem of utilizing both labeled and unlabeled data to improve classification accuracy. Under t he assumption that the data lie on a submanifold in a high dimensional space, we develop an algorithmic framework to classify a partially labeled data set in a principled manner. The central idea of our approach is that classification functions are naturally defined only on t he submanifold in question rather than the total ambient space. Using the Laplace Beltrami operator one produces a basis for a Hilbert space of square integrable functions on the submanifold. To recover such a basis, only unlabeled examples are required. Once a basis is obtained, training can be performed using the labeled data set. Our algorithm models the manifold using the adjacency graph for the data and approximates the Laplace Beltrami operator by the graph Laplacian. Practical applications to image and text classification are considered.

In this work, we study an information filtering model where the relevance labels associated to a sequence of feature vectors are realizations of an unknown probabilistic linear function. Building on the analysis of a restricted version of our model, we derive a general filtering rule based on the margin of a ridge regression estimator. While our rule may observe the label of a vector only by classfying the vector as relevant, experiments on a real-world document filtering problem show that the performance of our rule is close to that of the online classifier which is allowed to observe all labels. These empirical results are complemented by a theoretical analysis where we consider a randomized variant of our rule and prove that its expected number of mistakes is never much larger than that of the optimal filtering rule which knows the hidden linear model.

We develop and test new machine learning methods for the prediction oftopological representations of protein structures in the form of coarse-or fine-grained contact or distance maps that are translation androtation invariant. The methods are based on generalized input-output hidden Markov models (GIOHMMs) and generalized recursive neural networks (GRNNs). The methods are used to predict topologydirectly in the fine-grained case and, in the coarsegrained case,indirectly by first learning how to score candidate graphs and then using the scoring function to search the space of possible configurations. Computer simulations show that the predictors achievestate-of-the-art performance.

We consider the general problem of utilizing both labeled and unlabeled datato improve classification accuracy. Under t he assumption that the data lie on a submanifold in a high dimensional space, we develop an algorithmic framework to classify a partially labeled data set in a principled manner. The central idea of our approach is that classification functions are naturally defined only on t he submanifold inquestion rather than the total ambient space. Using the Laplace Beltrami operator one produces a basis for a Hilbert space of square integrable functions on the submanifold. To recover such a basis, only unlabeled examples are required. Once a basis is obtained, trainingcan be performed using the labeled data set.

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 tobe classified, regardless of the number of support vectors. This improvement on the currently available algorithms makes string kernels a viable alternative for the practitioner.