5,927 research outputs found

    Algebraic view reconciliation

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    Embedded systems such as automotive systems are very complex to specify. Since it is difficult to capture all their requirements or their design in one single model, approaches working with several system views are adopted. The main problem there is to keep these views coherent; the issue is known as view reconciliation. This paper proposes an algebraic solution. It uses sets of integration constraints that link (families of) system features in one view to other (families of) features in the same or a different view. Both families and constraints are formalized using a feature algebra. Besides presenting a constraint relation and its mathematical properties, the paper shows in several examples the suitability of this approach for a wide class of integration constraint formulations

    Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies

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    The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by B{\'e}rard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. Following the approach pioneered by Sturmfels and Pachter, we describe how to modify the DeCo dynamic programming algorithm to identify classes of cost schemes that generates similar parsimonious evolutionary scenarios for gene adjacencies, as well as the robustness to changes to the cost scheme of evolutionary events of the presence or absence of specific ancestral gene adjacencies. We apply our method to six thousands mammalian gene families, and show that computing the robustness to changes to cost schemes provides new and interesting insights on the evolution of gene adjacencies and the DeCo model.Comment: Accepted, to appear in ISBRA - 11th International Symposium on Bioinformatics Research and Applications - 2015, Jun 2015, Norfolk, Virginia, United State

    Stochastic Einstein Locality Revisited

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    I discuss various formulations of stochastic Einstein locality (SEL), which is a version of the idea of relativistic causality, i.e. the idea that influences propagate at most as fast as light. SEL is similar to Reichenbach's Principle of the Common Cause (PCC), and Bell's Local Causality. My main aim is to discuss formulations of SEL for a fixed background spacetime. I previously argued that SEL is violated by the outcome dependence shown by Bell correlations, both in quantum mechanics and in quantum field theory. Here I re-assess those verdicts in the light of some recent literature which argues that outcome dependence does not violate the PCC. I argue that the verdicts about SEL still stand. Finally, I briefly discuss how to formulate relativistic causality if there is no fixed background spacetime.Comment: 59 pages latex, 3 figures. Forthcoming in The British Journal for the Philosophy of Scienc
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