Deterministic Automata for Unordered Trees

Automata for unordered unranked trees are relevant for defining schemas and queries for data trees in Json or Xml format. While the existing notions are well-investigated concerning expressiveness, they all lack a proper notion of determinism, which makes it difficult to distinguish subclasses of automata for which problems such as inclusion, equivalence, and minimization can be solved efficiently. In this paper, we propose and investigate different notions of "horizontal determinism", starting from automata for unranked trees in which the horizontal evaluation is performed by finite state automata. We show that a restriction to confluent horizontal evaluation leads to polynomial-time emptiness and universality, but still suffers from coNP-completeness of the emptiness of binary intersections. Finally, efficient algorithms can be obtained by imposing an order of horizontal evaluation globally for all automata in the class. Depending on the choice of the order, we obtain different classes of automata, each of which has the same expressiveness as CMso.Comment: In Proceedings GandALF 2014, arXiv:1408.556

{SAT} Solvers for Queries over Tree Automata with Constraints

International audienceTree automata turned out to be a very convenient framework for modeling and proving properties on infinite systems like communication protocols, Java programs and also in the context of XML programming. Unfortunately, these works are not always supported by efficient verification and validation tools. This paper investigates the use of two SAT solvers --- minisat and picosat--- to evaluate queries over tree automata with global equality and disequality constraints (TAGED s for short). Unlike general tree automata, TAGED s allow to express constraints useful for e.g., evaluating queries over XML documents, like "in the document, two nodes do not have the same key". These queries being based on the membership problem which is NP-complete for TAGEDs, we propose an efficient SAT encoding of the membership problem for TAGEDs and we show its correctness and soundness. The paper reports on the experimental results, and implementation details are given

From Linear Temporal Logic Properties to Rewrite Propositions

International audienceIn the regular model-checking framework, reachability analysis can be guided by temporal logic properties, for instance to achieve the counter example guided abstraction refinement (CEGAR) objectives. A way to perform this analysis is to translate a temporal logic formula expressed on maximal rewriting words into a "rewrite proposition" - a propositional formula whose atoms are language comparisons, and then to generate semi-decision procedures based on (approximations of) the rewrite proposition. This approach has recently been studied using a non-automatic translation method. The extent to which such a translation can be systematised needs to be investigated, as well as the applicability of approximated methods wherever no exact translation can be effected. This paper presents contributions to that effect: (1) we investigate suitable semantics for LTL on maximal rewriting words and their influence on the feasibility of a translation, and (2) we propose a general scheme providing exact results on a fragment of LTL corresponding mainly to safety formulæ, and approximations on a larger fragment

Automata for Unordered Trees

International audienceWe present a framework for defining automata for unordereddata trees that is parametrized by the way in which multisets of children nodes are described. Presburger tree automata and alternatingPresburger tree automata are particular instances. We establish the usual equivalence in expressiveness of tree automata and MSO for the automata defined inour framework.We then investigate subclasses of automata for unordered treesfor which testing language equivalence is in P-time. For this we start from automata in our framework that describe multisets of childrenby finite automata, and propose two approaches of how todo this deterministically. We show that a restriction to confluent horizontal evaluation leads to polynomial-time emptiness and universality, but still suffers fromcoNP-completeness of the emptiness of binary intersections. Finally, efficient algorithms can be obtained by imposing an order of horizontal evaluation globally for all automata in the class. Depending onthe choice of the order, we obtain different classes of automata, eachof which has the same expressiveness as Counting MSO

Toxoplasmosis in Rodents: Ecological Survey and First Evidences in Thailand.

International audienceDomestic and wild rodents known as the most abundant and diversified order of mammals have a key role in the ecological food chain and also in the transmission of parasites and pathogens to other animals. While foraging on the ground, they can get infected by Toxoplasma gondii, a protozoan parasite, which is the causative agent of toxoplasmosis. Therefore, they serve as intermediate hosts of T. gondii and can transmit it to their predators. To assess their role in the maintenance of T. gondii lifecycle in Thailand, we sampled rodents in a range of biotopes representative of the high biodiversity and conducted a serological survey with latex agglutination test to detect anti-T. gondii antibodies. Overall, 21 of 461 (4.6%) rodents had diagnostically significant antibody titers (cutoff, 1:64). Every species with at least 37 individuals captured tested positive, confirming the wide range of potential mammalian hosts of toxoplasmosis. None of the ecological traits (sex, maturity, morphology, season, or habitat) was found significant to predict the susceptibility to T. gondii both univariately and in a multivariate analysis. However, high prevalences were reported in either forested or anthropized areas. This survey constitutes the first confirmed serological investigation of T. gondii in rodents in Thailand. The rarity of both domestic and wild felids in Thailand emphasizes the importance of rodents in maintaining T. gondii, and questions the involvement of other carnivores in the life cycle

Random Generation of Positive TAGEDs wrt. the Emptiness Problem

Tree automata are a widely used formalism in Computer Science. Since their creation in the fifties, numerous more expressive extensions have been proposed. Unfortunately, the decision problems associated with these extensions are quite often undecidable or in prohibitive classes of algorithmic complexity (NP-complete or worse), and little work has gone into finding efficient heuristics for them. Beyond the inherent difficulty of those problems, a common hitch in this line of research is the experimental evaluation of new algorithms. As those extensions of tree automata have remained in chiefly theoretical spheres, there are no established testbeds from the "real world" against which to quantify the efficiency (or lack thereof) of new algorithms. Failing that, there is a need to generate suitable testbeds at random. Regrettably, there is little material in the literature regarding random generation of tree automata, and none at all regarding extensions such as Tree Automata with Global Equality and Disequality Constraints (TAGEDs). It should also be noted that what little material there is does not concern itself with the interest of the generated automata wrt. specific decision problems. In this report we present a scheme for random generation of positive TAGEDs, with a focus on making them interesting wrt. the Emptiness problem

Logics for Unordered Trees with Data Constraints on Siblings

International audienceWe study counting monadic second-order logics (CMso) for unordered data trees. Our objective is to enhance this logic with data constraints for comparing string data values attached to sibling edges of a data tree. We show that CMso satisfiability becomes undecidable when adding data constraints between siblings that can check the equality of factors of data values. For more restricted data constraints that can only check the equality of prefixes, we show that it becomes decidable, and propose a related automaton model with good complexities. This restricted logic is relevant to applications such as checking well-formedness properties of semi-structured databases and file trees. Our decidability results are obtained by compilation of CMso to automata for unordered trees, where both are enhanced with data constraints in a novel manner

Relationship of parasites and pathogens diversity to rodents in Thailand

International audienceRodents have proven to be of increasing importance in transmitting diseases to humans in recent decades, through the emergence of worldwide epidemics and, in Thailand, through the emergence of leptospirosis and scrub typhus. Investigations of parasites and pathogens in murine rodents have helped to describe the implication of the main species and understand the different ways of transmission. From wild to anthropized habitats, rodents can be reservoirs, hosts or vectors of infectious organisms. Related species can react very differently to the same pathogens, with pivotal implications for the understanding of their natural circulation. Scrub typhus is transmitted to humans through the bites of trombiculid mites that have previously fed on infected rodents, generally occurring in wild habitats. Leptospirosis can affect people without any direct contact with infected rodents, but by indirect spread in agricultural areas. Parasitic diseases, such as toxoplasmosis and trypanosomiasis benefit from the proximity of rodents to domesticated animals to jump from one vector to another before reaching humans. By occupying almost all biotopes and by rapidly adapting to environmental changes, rodents are fundamental in the maintenance and transmission of an impressive number of infectious organisms to humans

Genetic analysis of Thailand hantavirus in Bandicota indica trapped in Thailand

Sixty one tissue samples from several rodent species trapped in five provinces of Thailand were examined for the presence of hantaviral markers by enzyme-immunoassay and immunoblotting. Four samples, all from the great bandicoot rat Bandicota indica, were confirmed positive for the hantaviral N-antigen. Two of them were trapped in Nakhon Pathom province, the other two in Nakhon Ratchasima province, approximately 250 km from the other trapping site. When analysed by RT-nested PCR, all four rodents were found positive for the hantaviral S- and M-segment nucleotide sequences. Genetic analysis revealed that the four newly described wild-type strains belong to Thailand hantavirus. On the phylogenetic trees they formed a well-supported cluster within the group of Murinae-associated hantaviruses and shared a recent common ancestor with Seoul virus