29,268 research outputs found

    Graph theoretic methods for the analysis of structural relationships in biological macromolecules

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    Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and an efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Examples are provided of the use of graph theory to analyze proteins for which three-dimensional crystallographic or NMR structures are available, focusing on the use of the Bron-Kerbosch clique detection algorithm to identify common folding motifs and of the Ullmann subgraph isomorphism algorithm to identify patterns of amino acid residues. Our methods are also applicable to other types of biological macromolecule, such as carbohydrate and nucleic acid structures

    Entropy-scaling search of massive biological data

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    Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo

    Logic Programming as Constructivism

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    The features of logic programming that seem unconventional from the viewpoint of classical logic can be explained in terms of constructivistic logic. We motivate and propose a constructivistic proof theory of non-Horn logic programming. Then, we apply this formalization for establishing results of practical interest. First, we show that 'stratification can be motivated in a simple and intuitive way. Relying on similar motivations, we introduce the larger classes of 'loosely stratified' and 'constructively consistent' programs. Second, we give a formal basis for introducing quantifiers into queries and logic programs by defining 'constructively domain independent* formulas. Third, we extend the Generalized Magic Sets procedure to loosely stratified and constructively consistent programs, by relying on a 'conditional fixpoini procedure

    On the relation between Differential Privacy and Quantitative Information Flow

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    Differential privacy is a notion that has emerged in the community of statistical databases, as a response to the problem of protecting the privacy of the database's participants when performing statistical queries. The idea is that a randomized query satisfies differential privacy if the likelihood of obtaining a certain answer for a database xx is not too different from the likelihood of obtaining the same answer on adjacent databases, i.e. databases which differ from xx for only one individual. Information flow is an area of Security concerned with the problem of controlling the leakage of confidential information in programs and protocols. Nowadays, one of the most established approaches to quantify and to reason about leakage is based on the R\'enyi min entropy version of information theory. In this paper, we analyze critically the notion of differential privacy in light of the conceptual framework provided by the R\'enyi min information theory. We show that there is a close relation between differential privacy and leakage, due to the graph symmetries induced by the adjacency relation. Furthermore, we consider the utility of the randomized answer, which measures its expected degree of accuracy. We focus on certain kinds of utility functions called "binary", which have a close correspondence with the R\'enyi min mutual information. Again, it turns out that there can be a tight correspondence between differential privacy and utility, depending on the symmetries induced by the adjacency relation and by the query. Depending on these symmetries we can also build an optimal-utility randomization mechanism while preserving the required level of differential privacy. Our main contribution is a study of the kind of structures that can be induced by the adjacency relation and the query, and how to use them to derive bounds on the leakage and achieve the optimal utility

    Graph theoretic analysis of protein interaction networks of eukaryotes

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    Thanks to recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are universal across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and the yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interlogs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interlogs addition, for which we present a possible scenario through an in silico modeling.Comment: 7 pages, 6 figures, 2 table
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