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.

An essential step in understanding the function of sensory nervous systems is to characterize as accurately as possible the stimulus-response function (SRF) of the neurons that relay and process sensory information. One increasingly common experimental approach is to present a rapidly varying complex stimulus to the animal while recording the responses of one or more neurons, and then to directly estimate a functional transformation of the input that accounts for the neuronal firing. The estimation techniques usually employed, such as Wiener filtering or other correlation-based estimation of the Wiener or Volterra kernels, are equivalent to maximum likelihood estimation in a Gaussian-output-noise regression model. We explore the use of Bayesian evidence-optimization techniques to condition these estimates. We show that by learning hyperparameters that control the smoothness and sparsity of the transfer function it is possible to improve dramatically the quality of SRF estimates, as measured by their success in predicting responses to novel input.

We present a novel generative model for natural language tree structures in which semantic (lexical dependency) and syntactic (PCFG) structures are scored with separate models. This factorization provides conceptual simplicity, straightforward opportunities for separately improving the component models, and a level of performance comparable to similar, non-factored models. Most importantly, unlike other modern parsing models, the factored model admits an extremely effective A* parsing algorithm, which enables efficient, exact inference.

The distributional principle according to which morphemes that occur in identical contexts belong, in some sense, to the same category [1] has been advanced as a means for extracting syntactic structures from corpus data. We extend this principle by applying it recursively, and by using mutual information for estimating category coherence. The resulting model learns, in an unsupervised fashion, highly structured, distributed representations of syntactic knowledge from corpora. It also exhibits promising behavior in tasks usually thought to require representations anchored in a grammar, such as systematicity.

We explore the consequences of viewing semantic association as the result of attempting to predict the concepts likely to arise in a particular context. We argue that the success of existing accounts of semantic representation comes as a result of indirectly addressing this problem, and show that a closer correspondence to human data can be obtained by taking a probabilistic approach that explicitly models the generative structure of language.

In this paper we consider formulations of multi-class problems based on a generalized notion of a margin and using output coding. This includes, but is not restricted to, standard multi-class SVM formulations. Differently from many previous approaches we learn the code as well as the embedding function. We illustrate how this can lead to a formulation that allows for solving a wider range of problems with for instance many classes or even "missing classes". To keep our optimization problems tractable we propose an algorithm capable of solving them using twoclass classifiers, similar in spirit to Boosting.

We describe the RA scanner, a novel system for the examination of patients suffering from rheumatoid arthritis. The RA scanner is based on a novel laser-based imaging technique which is sensitive to the optical characteristics of finger joint tissue. Based on the laser images, finger joints are classified according to whether the inflammatory status has improved or worsened. To perform the classification task, various linear and kernel-based systems were implemented and their performances were compared. Special emphasis was put on measures to reliably perform parameter tuning and evaluation, since only a very small data set was available. Based on the results presented in this paper, it was concluded that the RA scanner permits a reliable classification of pathological finger joints, thus paving the way for a further development from prototype to product stage.

The problem of extracting the relevant aspects of data, in face of multiple conflicting structures, is inherent to modeling of complex data. Extracting structure in one random variable that is relevant for another variable has been principally addressed recently via the information bottleneck method [15]. However, such auxiliary variables often contain more information than is actually required due to structures that are irrelevant for the task. In many other cases it is in fact easier to specify what is irrelevant than what is, for the task at hand. Identifying the relevant structures, however, can thus be considerably improved by also minimizing the information about another, irrelevant, variable. In this paper we give a general formulation of this problem and derive its formal, as well as algorithmic, solution. Its operation is demonstrated in a synthetic example and in two real world problems in the context of text categorization and face images. While the original information bottleneck problem is related to rate distortion theory, with the distortion measure replaced by the relevant information, extracting relevant features while removing irrelevant ones is related to rate distortion with side information.

We introduce a new learning algorithm for decision lists to allow features that are constructed from the data and to allow a tradeoff between accuracy and complexity. We bound its generalization error in terms of the number of errors and the size of the classifier it finds on the training data. We also compare its performance on some natural data sets with the set covering machine and the support vector machine.

A key challenge for neural modeling is to explain how a continuous stream of multi-modal input from a rapidly changing environment can be processed by stereotypical recurrent circuits of integrate-and-fire neurons in real-time. We propose a new computational model that is based on principles of high dimensional dynamical systems in combination with statistical learning theory. It can be implemented on generic evolved or found recurrent circuitry.