13,300 research outputs found

    Identification of functionally related enzymes by learning-to-rank methods

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    Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes

    Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data

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    In domains like bioinformatics, information retrieval and social network analysis, one can find learning tasks where the goal consists of inferring a ranking of objects, conditioned on a particular target object. We present a general kernel framework for learning conditional rankings from various types of relational data, where rankings can be conditioned on unseen data objects. We propose efficient algorithms for conditional ranking by optimizing squared regression and ranking loss functions. We show theoretically, that learning with the ranking loss is likely to generalize better than with the regression loss. Further, we prove that symmetry or reciprocity properties of relations can be efficiently enforced in the learned models. Experiments on synthetic and real-world data illustrate that the proposed methods deliver state-of-the-art performance in terms of predictive power and computational efficiency. Moreover, we also show empirically that incorporating symmetry or reciprocity properties can improve the generalization performance

    Advances in Hyperspectral Image Classification: Earth monitoring with statistical learning methods

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    Hyperspectral images show similar statistical properties to natural grayscale or color photographic images. However, the classification of hyperspectral images is more challenging because of the very high dimensionality of the pixels and the small number of labeled examples typically available for learning. These peculiarities lead to particular signal processing problems, mainly characterized by indetermination and complex manifolds. The framework of statistical learning has gained popularity in the last decade. New methods have been presented to account for the spatial homogeneity of images, to include user's interaction via active learning, to take advantage of the manifold structure with semisupervised learning, to extract and encode invariances, or to adapt classifiers and image representations to unseen yet similar scenes. This tutuorial reviews the main advances for hyperspectral remote sensing image classification through illustrative examples.Comment: IEEE Signal Processing Magazine, 201
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