Effective algebraic geometry and normal forms of reversible mappings

We present a new method to compute normal forms, applied to the germs of reversible mappings. We translate the classification problem of these germs to the theory of ideals in the space of the coefficients of their jets. Integral factorization coupled with Gr¨obner basis construction is the key factor that makes the process efficient. We also show that a language with typed objects like AXIOM is very convenient to solve these kinds of problems.We present a new method to compute normal forms, applied to the germs of reversible mappings. We translate the classification problem of these germs to the theory of ideals in the space of the coefficients of their jets. Integral factorization coupled with Gr¨obner basis construction is the key factor that makes the process efficient. We also show that a language with typed objects like AXIOM is very convenient to solve these kinds of problems

Rewrite Closure and CF Hedge Automata

We introduce an extension of hedge automata called bidimensional context-free hedge automata. The class of unranked ordered tree languages they recognize is shown to be preserved by rewrite closure with inverse-monadic rules. We also extend the parameterized rewriting rules used for modeling the W3C XQuery Update Facility in previous works, by the possibility to insert a new parent node above a given node. We show that the rewrite closure of hedge automata languages with these extended rewriting systems are context-free hedge languages

Singular open book structures from real mappings

We prove extensions of Milnor's theorem for germs with nonisolated singularity and use them to find new classes of genuine real analytic mappings $\psi$ with positive dimensional singular locus \Sing \psi \subset \psi^{-1}(0), for which the Milnor fibration exists and yields an open book structure with singular binding.Comment: more remark

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

BACKGROUND: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. RESULTS: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. CONCLUSION: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL:

Decidability of the Monadic Shallow Linear First-Order Fragment with Straight Dismatching Constraints

The monadic shallow linear Horn fragment is well-known to be decidable and has many application, e.g., in security protocol analysis, tree automata, or abstraction refinement. It was a long standing open problem how to extend the fragment to the non-Horn case, preserving decidability, that would, e.g., enable to express non-determinism in protocols. We prove decidability of the non-Horn monadic shallow linear fragment via ordered resolution further extended with dismatching constraints and discuss some applications of the new decidable fragment.Comment: 29 pages, long version of CADE-26 pape

On the Expressivity and Applicability of Model Representation Formalisms

A number of first-order calculi employ an explicit model representation formalism for automated reasoning and for detecting satisfiability. Many of these formalisms can represent infinite Herbrand models. The first-order fragment of monadic, shallow, linear, Horn (MSLH) clauses, is such a formalism used in the approximation refinement calculus. Our first result is a finite model property for MSLH clause sets. Therefore, MSLH clause sets cannot represent models of clause sets with inherently infinite models. Through a translation to tree automata, we further show that this limitation also applies to the linear fragments of implicit generalizations, which is the formalism used in the model-evolution calculus, to atoms with disequality constraints, the formalisms used in the non-redundant clause learning calculus (NRCL), and to atoms with membership constraints, a formalism used for example in decision procedures for algebraic data types. Although these formalisms cannot represent models of clause sets with inherently infinite models, through an additional approximation step they can. This is our second main result. For clause sets including the definition of an equivalence relation with the help of an additional, novel approximation, called reflexive relation splitting, the approximation refinement calculus can automatically show satisfiability through the MSLH clause set formalism.Comment: 15 page