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

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

Learning a Complete Image Indexing Pipeline

To work at scale, a complete image indexing system comprises two components: An inverted file index to restrict the actual search to only a subset that should contain most of the items relevant to the query; An approximate distance computation mechanism to rapidly scan these lists. While supervised deep learning has recently enabled improvements to the latter, the former continues to be based on unsupervised clustering in the literature. In this work, we propose a first system that learns both components within a unifying neural framework of structured binary encoding

Learning a Complete Image Indexing Pipeline

To work at scale, a complete image indexing system comprises two components: An inverted file index to restrict the actual search to only a subset that should contain most of the items relevant to the query; An approximate distance computation mechanism to rapidly scan these lists. While supervised deep learning has recently enabled improvements to the latter, the former continues to be based on unsupervised clustering in the literature. In this work, we propose a first system that learns both components within a unifying neural framework of structured binary encoding

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

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