An algebraic semantics for QVT-relations check-only transformations

Fundamenta Informaticae, 114 1, Juan de Lara, Esther Guerra, An algebraic semantics for QVT-relations check-only transformations, 73-101, Copyright 2012, with permission from IOS PressQVT is the standard for model transformation defined by the OMG in the context of the Model-Driven Architecture. It is made of several transformation languages. Among them, QVT-Relations is the one with the highest level of abstraction, as it permits developing bidirectional transformations in a declarative, relational style. Unfortunately, the standard only provides a semiformal description of its semantics, which hinders analysis and has given rise to ambiguities in existing tool implementations. In order to improve this situation, we propose a formal, algebraic semantics for QVT-Relations check-only transformations, defining a notion of satisfaction of QVT-Relations specifications by models.This work has been supported by the Spanish Ministry of Science and Innovation with projects METEORIC (TIN2008-02081) and Go Lite (TIN2011-24139), and by the R&D program of the Community of Madrid with project “e-Madrid” (S2009/TIC-1650)

Some Epistemic Extensions of G\"odel Fuzzy Logic

In this paper, we introduce some epistemic extensions of G\"odel fuzzy logic whose Kripke-based semantics have fuzzy values for both propositions and accessibility relations such that soundness and completeness hold. We adopt belief as our epistemic operator, then survey some fuzzy implications to justify our semantics for belief is appropriate. We give a fuzzy version of traditional muddy children problem and apply it to show that axioms of positive and negative introspections and Truth are not necessarily valid in our basic epistemic fuzzy models. In the sequel, we propose a derivation system $K_F$ as a fuzzy version of classical epistemic logic $K$. Next, we establish some other epistemic-fuzzy derivation systems $B_F, T_F, B_F^n$ and $T_F^n$ which are extensions of $K_F$, and prove that all of these derivation systems are sound and complete with respect to appropriate classes of Kripke-based models

Towards a Proof Theory of G\"odel Modal Logics

Analytic proof calculi are introduced for box and diamond fragments of basic modal fuzzy logics that combine the Kripke semantics of modal logic K with the many-valued semantics of G\"odel logic. The calculi are used to establish completeness and complexity results for these fragments

A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017