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

Digital Image Access & Retrieval

The 33th Annual Clinic on Library Applications of Data Processing, held at the University of Illinois at Urbana-Champaign in March of 1996, addressed the theme of "Digital Image Access & Retrieval." The papers from this conference cover a wide range of topics concerning digital imaging technology for visual resource collections. Papers covered three general areas: (1) systems, planning, and implementation; (2) automatic and semi-automatic indexing; and (3) preservation with the bulk of the conference focusing on indexing and retrieval.published or submitted for publicatio

Particular object retrieval with integral max-pooling of CNN activations

Recently, image representation built upon Convolutional Neural Network (CNN) has been shown to provide effective descriptors for image search, outperforming pre-CNN features as short-vector representations. Yet such models are not compatible with geometry-aware re-ranking methods and still outperformed, on some particular object retrieval benchmarks, by traditional image search systems relying on precise descriptor matching, geometric re-ranking, or query expansion. This work revisits both retrieval stages, namely initial search and re-ranking, by employing the same primitive information derived from the CNN. We build compact feature vectors that encode several image regions without the need to feed multiple inputs to the network. Furthermore, we extend integral images to handle max-pooling on convolutional layer activations, allowing us to efficiently localize matching objects. The resulting bounding box is finally used for image re-ranking. As a result, this paper significantly improves existing CNN-based recognition pipeline: We report for the first time results competing with traditional methods on the challenging Oxford5k and Paris6k datasets