Context-free grammars are the most suitable and most widely used method for describing the syntax of programming languages. They can be used to generate parsers, which transform a piece of source code into a tree-shaped representation of the code's syntactic structure. These parse trees can then be used for further processing or analysis of the source text. In this sense, grammars form the basis of many engineering and reverse engineering applications, like compilers, interpreters and tools for software analysis and transformation. Unfortunately, context-free grammars have the undesirable property that they can be ambiguous, which can seriously hamper their applicability. A grammar is ambiguous if at least one sentence in its language has more than one valid parse tree. Since the parse tree of a sentence is often used to infer its semantics, an ambiguous sentence can have multiple meanings. For programming languages this is almost always unintended. Ambiguity can therefore be seen as a grammar bug. A specific category of context-free grammars that is particularly sensitive to ambiguity are character-level grammars, which are used to generate scannerless parsers. Unlike traditional token-based grammars, character-level grammars include the full lexical definition of their language. This has the advantage that a language can be specified in a single formalism, and that no separate lexer or scanner phase is necessary in the parser. However, the absence of a scanner does require some additional lexical disambiguation. Character-level grammars can therefore be annotated with special disambiguation declarations to specify which parse trees to discard in case of ambiguity. Unfortunately, it is very hard to determine whether all ambiguities have been covered. The task of searching for ambiguities in a grammar is very complex and time consuming, and is therefore best automated. Since the invention of context-free grammars, several ambiguity detection methods have been developed to this end. However, the ambiguity problem for context-free grammars is undecidable in general, so the perfect detection method cannot exist. This implies a trade-off between accuracy and termination. Methods that apply exhaustive searching are able to correctly find all ambiguities, but they might never terminate. On the other hand, approximative search techniques do always produce an ambiguity report, but these might contain false positives or false negatives. Nevertheless, the fact that every method has flaws does not mean that ambiguity detection cannot be useful in practice. This thesis investigates ambiguity detection with the aim of checking grammars for programming languages. The challenge is to improve upon the state-of-the-art, by finding accurate enough methods that scale to realistic grammars. First we evaluate existing methods with a set of criteria for practical usability. Then we present various improvements to ambiguity detection in the areas of accuracy, performance and report quality. The main contributions of this thesis are two novel techniques. The first is an ambi- guity detection method that applies both exhaustive and approximative searching, called AMBIDEXTER. The key ingredient of AMBIDEXTER is a grammar filtering technique that can remove harmless production rules from a grammar. A production rule is harmless if it does not contribute to any ambiguity in the grammar. Any found harmless rules can therefore safely be removed. This results in a smaller grammar that still contains the same ambiguities as the original one. However, it can now be searched with exhaustive techniques in less time. The grammar filtering technique is formally proven correct, and experimentally validated. A prototype implementation is applied to a series of programming language grammars, and the performance of exhaustive detection methods are measured before and after filtering. The results show that a small investment in filtering time can substantially reduce the run-time of exhaustive searching, sometimes with several orders of magnitude. After this evaluation on token-based grammars, the grammar filtering technique is extended for use with character-level grammars. The extensions deal with the increased complexity of these grammars, as well as their disambiguation declarations. This enables the detection of productions that are harmless due to disambiguation. The extentions are experimentally validated on another set of programming language grammars from practice, with similar results as before. Measurements show that, even though character-level grammars are more expensive to filter, the investment is still very worthwhile. Exhaustive search times were again reduced substantially. The second main contribution of this thesis is DR. AMBIGUITY, an expert system to help grammar developers to understand and solve found ambiguities. If applied to an ambiguous sentence, DR. AMBIGUITY analyzes the causes of the ambiguity and proposes a number of applicable solutions. A prototype implementation is presented and evaluated with a mature Java grammar. After removing disambiguation declarations from the grammar we analyze sentences that have become ambiguous by this removal. The results show that in all cases the removed filter is proposed by DR. AMBIGUITY as a possible cure for the ambiguity. Concluding, this thesis improves ambiguity detection with two novel methods. The first is the ambiguity detection method AMBIDEXTER that applies grammar filtering to substantially speed up exhaustive searching. The second is the expert system DR. AMBIGUITY that automatically analyzes found ambiguities and proposes applicable cures. The results obtained with both methods show that automatic ambiguity detection is now ready for realistic programming language grammars.

CertiCrypt est une bibliothèque qui permet de vérifier la sécurité exacte de primitives cryptographiques dans l'assistant à la preuve Coq. CertiCrypt instrumente l'approche des preuves par jeux, et repose sur de nombreux domaines comme les probabilités, la complexité, l'algèbre, la sémantique des langages de programmation, et les optimisations de programmes. Dans cette thèse, nous présentons deux exemples d'utilisation d'EasyCrypt: le schéma d'encryption Hashed ElGamal, et les protocoles à connaissance nulle. Ces exemples, ainsi que les travaux antérieurs sur CertiCrypt, démontrent qu'il est possible de formaliser des preuves complexes; toutefois, l'utilisation de CertiCrypt demande une bonne expertise en Coq, et demeure laborieuse. Afin de faciliter l'adoption des preuves formelles par la communauté cryptographique, nous avons développé EasyCrypt, un outil semi-automatique capable de reconstruire des preuves formelles de sécurité à partir d'une ébauche formelle de preuve. EasyCrypt utilise des outils de preuves automatiques pour vérifier les ébauches de preuves, puis les compiles vers des preuves vérifiables avec CertiCrypt. Nous validons EasyCrypt en prouvant à nouveau Hashed ElGamal, et comparons cette nouvelle preuve avec celle en CertiCrypt. Nous prouvons également le schéma d'encryption Cramer-Shoup. Enfin, nous expliquerons comment étendre le langage de CertiCrypt à des classes de complexité implicite, permettant de modéliser la notion de fonctions en temps polynomial.

Vues de sécurité xml : requêtes, mises à jour, et schémas. Les évolutions technologiques ont consacré l'émergence des services web et du stockage des données en ligne, en complément des bases de données traditionnelles. Ces évolutions facilitent l'accès aux données, mais en contrepartie soulèvent de nouvelles problématiques de sécurité. La mise en œuvre de politiques de contrôle d'accès appropriées est une des approches permettant de réduire ces risques.Nous étudions ici les politiques de contrôle d'accès au niveau d'un document XML, politiques que nous modélisons par des vues de sécurité XML (non matérialisées) à l'instar de Fan et al. Ces vues peuvent être représentées facilement par des alignements d'arbres grâce à l'absence d'opérateurs arithmétiques ou de restructuration. Notre objectif est par conséquent d'examiner comment manipuler efficacement ce type de vues, à l'aide des méthodes formelles, et plus particulièrement des techniques de réécriture de requêtes et la théorie des automates d'arbres. Trois directions principales ont orienté nos recherches: nous avons tout d'abord élaboré des algorithmes pour évaluer l'expressivité d'une vue, en fonction des requêtes qui peuvent être exprimées à travers cette vue. Il s'avère que l'on ne peut décider en général si une vue permet d'exprimer une requête particulière, mais cela devient possible lorsque la vue satisfait des hypothèses générales. En second lieu, nous avons considéré les problèmes soulevés par la mises à jour du document à travers une vue. Enfin, nous proposons des solutions pour construire automatiquement un schéma de la vue. En particulier, nous présentons différentes techniques pour représenter de façon approchée l'ensemble des documents au moyen d'une DTD.

Lipids are the main component of semipermeable cell membranes and linked to several important physiological processes. Shotgun lipidomics relies on the direct infusion of total lipid extracts from cells, tissues or organisms into the mass spectrometer and is a powerful tool to elucidate their molecular composition. Despite the technical advances in modern mass spectrometry the currently available software underperforms in several aspects of the lipidomics pipeline. This thesis addresses these issues by presenting a new concept for lipid identification using a customized query language for mass spectra in combination with efficient spectra alignment algorithms which are implemented in the open source kit “LipidXplorer”.

La vérification automatique est aujourd'hui devenue un domaine central de recherche en informatique. Depuis plus de 25 ans, une riche théorie a été développée menant à de nombreux outils, à la fois académiques et industriels, permettant la vérification de propriétés booléennes -- celles qui peuvent être soit vraies soit fausses. Les besoins actuels évoluent vers une analyse plus fine, c'est-à-dire plus quantitative. L'extension des techniques de vérification aux domaines quantitatifs a débuté depuis 15 ans avec les systèmes probabilistes. Cependant, de nombreuses autres propriétés quantitatives existent, telles que la durée de vie d'un équipement, la consommation énergétique d'une application, la fiabilité d'un programme, ou le nombre de résultats d'une requête dans une base de données. Exprimer ces propriétés requiert de nouveaux langages de spécification, ainsi que des algorithmes vérifiant ces propriétés sur une structure donnée. Cette thèse a pour objectif l'étude de plusieurs formalismes permettant de spécifier de telles propriétés, qu'ils soient dénotationnels -- expressions régulières, logiques monadiques ou logiques temporelles -- ou davantage opérationnels, comme des automates pondérés, éventuellement étendus avec des jetons. Un premier objectif de ce manuscript est l'étude de résultats d'expressivité comparant ces formalismes. En particulier, on donne des traductions efficaces des formalismes dénotationnels vers celui opérationnel. Ces objets, ainsi que les résultats associés, sont présentés dans un cadre unifié de structures de graphes. Ils peuvent, entre autres, s'appliquer aux mots et arbres finis, aux mots emboîtés (nested words), aux images ou aux traces de Mazurkiewicz. Par conséquent, la vérification de propriétés quantitatives de traces de programmes (potentiellement récursifs, ou concurrents), les requêtes sur des documents XML (modélisant par exemple des bases de données), ou le traitement des langues naturelles sont des applications possibles. On s'intéresse ensuite aux questions algorithmiques que soulèvent naturellement ces résultats, tels que l'évaluation, la satisfaction et le model checking. En particulier, on étudie la décidabilité et la complexité de certains de ces problèmes, en fonction du semi-anneau sous-jacent et des structures considérées (mots, arbres...). Finalement, on considère des restrictions intéressantes des formalismes précédents. Certaines permettent d'étendre l'ensemble des semi-anneau sur lesquels on peut spécifier des propriétés quantitatives. Une autre est dédiée à l'étude du cas spécial de spécifications probabilistes : on étudie en particulier des fragments syntaxiques de nos formalismes génériques de spécification générant uniquement des comportements probabilistes.

Tree automata, and their applications to verification from the common thread of this thesis In the first part, we definie a complete model-cheking framework.[...] The second part focus on an important aspect of the automata involved: constraints.[...] Finaly, we also study the very different variety of tree-walking automata which have tight connections with navigational languages on semi-structured documents.

This thesis investigates a method for tackling the verification of parametric systems, systems whose behaviour may depend on the value of one or more parameters. The range of allowable values for such parameters may, in general, be large or unknown. This results in a large number of instances of a system that require verification, one instance for each allowable combination of parameter values. When one or more parameters are unbounded, the family of systems that require verification becomes infinite. Computer protocols are one example of such parametric systems. They may have parameters such as the maximum sequence number or the maximum number of retransmissions. Traditional protocol verification approaches usually only analyse and verify properties of a parametric system for a small range of parameter values. It is impossible to verify in this way every concrete instance of an infinite family of systems. Also, the number of reachable states tends to increase dramatically with increasing parameter values, and thus the well known state explosion phenomenon also limits the range of parameters for which the system can be analysed. In this thesis, we concentrate on the parametric verification of the Stop-and-Wait Protocol (SWP), an elementary flow control protocol. We have used Coloured Petri Nets (CPNs) to model the SWP, operating over an in-order but lossy medium, with two unbounded parameters: the maximum sequence number; and the maximum number of retransmissions. A novel method has been used for symbolically representing the parametric reachability graph of our parametric SWP CPN model. This parametric reachability graph captures exactly the infinite family of reachability graphs resulting from the infinite family of SWP CPNs. The parametric reachability graph is represented symbolically as a set of closed-form algebraic expressions for the nodes and arcs of the reachability graph, expressed in terms of the two parameters. By analysing the reachability graphs of the SWP CPN model for small parameter values, structural regularities in the reachability graphs were identified and exploited to develop the appropriate algebraic expressions for the parametric reachability graph. These expressions can be analysed and manipulated directly, thus the properties that are verified from these expressions are verified for all instances of the system. Several properties of the SWP that are able to be verified directly from the parametric reachability graph have been identified. These include a proof of the size of the parametric reachability graph in terms of both parameters, absence of deadlocks (undesired terminal states), absence of livelocks (undesirable cycles of behaviour from which the protocol cannot escape), absence of dead transitions (actions that can never occur) and the upper bounds on the content of the underlying communication channel. These are verified from the algebraic expressions and thus hold for all parameter values. Significantly, language analysis is also carried out on the parametric SWP. The parametric reachability graph is translated into a parametric Finite State Automaton (FSA), capturing symbolically the infinite set of protocol languages (i.e. sequences of user observable events) by means of similar algebraic expressions to those of the parametric reachability graph. Standard FSA reduction techniques were applied in a symbolic fashion directly to the parametric FSA, firstly to obtain a deterministic representation of the parametric FSA, then to obtain an equivalent minimised FSA. It was found that the determinisation procedure removed the effect of the maximum number of retransmissions parameter, and the minimisation procedure removed the effect of the maximum sequence number parameter. Conformance of all instances of the SWP over both parameters to its desired service language is proved. The development of algebraic expressions to represent the infinite class of Stop-and-Wait Protocols, and the verification of properties (including language analysis) directly from these algebraic expressions, has demonstrated the potential of this method for the verification of more general parametric systems. This thesis provides a significant contribution toward the development of a general parametric verification methodology.

Thesis (MSc (Mathematical Sciences))--University of Stellenbosch, 2008. / Context-free grammars are well-studied and well-behaved in terms of decidability, but many real-world problems cannot be described with context-free grammars. Grammars with regulated rewriting are grammars with mechanisms to regulate the applications of rules, so that certain derivations are avoided. Thus, with context-free rules and regulated rewriting mechanisms, one can often generate languages that are not context-free. In this thesis we study grammars with regulated rewriting mechanisms. We consider problems in which context-free grammars are insufficient and in which more descriptive grammars are required. We compare bag context grammars with other well-known classes of grammars with regulated rewriting mechanisms. We also discuss the relation between bag context grammars and recognizing devices such as counter automata and Petri net automata. We show that regular bag context grammars can generate any recursively enumerable language. We reformulate the pumping lemma for random permitting context languages with context-free rules, as introduced by Ewert and Van der Walt, by using the concept of a string homomorphism. We conclude the thesis with decidability and complexity properties of grammars with regulated rewriting.

A inferência gramatical lida com o problema de aprender um classificador capaz de reconhecer determinada construção ou característica em um conjunto qualquer de exemplos. Neste trabalho, um modelo de inferência gramatical baseado em uma variante de Programação Genética é proposto. A representação de cada indivíduo é baseada em uma lista ligada de árvores representando o conjunto de produções da gramática. A atuação dos operadores genéticos é feita de forma heurística. Além disto, dois novos operadores genéticos são apresentados. O primeiro, denominado Aprendizagem Incremental, é capaz de reconhecer, com base em exemplos, quais regras de produção estão faltando. O segundo, denominado Expansão, é capaz de prover a diversidade necessária. Em experimentos efetuados, o modelo proposto inferiu com sucesso seis gramáticas regulares e duas gramáticas livres de contexto: parênteses e palíndromos de quatro letras, tanto o comum quanto o disjunto, sendo superior a abordagens recentes. Atualmente, modelos de inferência gramatical têm sido aplicados a problemas de reconhecimento de sequências biológicas de DNA. Neste trabalho, dois problemas de identificação de padrão foram abordados: reconhecimento de promotores e splice-junction. Para o primeiro, o modelo proposto obteve resultado superior a outras abordagens. Para o segundo, o modelo proposto apresentou bons resultados. O modelo foi estendido para o uso de gramáticas fuzzy, mais especificamente, as gramáticas fuzzy fracionárias. Para tal, um método de estimação adequado dos valores da função de pertinência das produções da gramática é proposto. Os resultados obtidos na identificação de splice-junctions comprovam a utilidade do modelo de inferência gramatical fuzzy proposto. / Grammatical inference deals with the task of learning a classifier that can recognize a particular pattern in a set of examples. In this work, a new grammatical inference model based on a variant of Genetic Programming is proposed. In this approach, an individual is a list of structured trees representing their productions. Ordinary genetic operators are modified so as to bias the search and two new operators are proposed. The first one, called Incremental Learning, is able to recognize, based on examples, which productions are missing. The second, called Expansion is able to provide the diversity necessary to achieve convergence. In a suite of experiments performed, the proposed model successfully inferred six regular grammars and two context-free grammars: parentheses and palindromes with four letters, including the disjunct one. Results achieved were better than those obtained by recently published algorithms. Nowadays, grammatical inference has been applied to problems of recognition of biological sequences of DNA. In this work, two problems of this class were addressed: recognition of promoters and splice junction detection. In the former, the proposed model obtained results better than other published approaches. In the latter, the proposed model showed promising results. The model was extended to support fuzzy grammars, namely the fuzzy fractional grammars. Furthermore, an appropriate method of estimation of the values of the production's membership function is also proposed. Results obtained in the identification of splice junctions shows the utility of the fuzzy inference model proposed.

At safety-critical, mission-critical and business-critical systems the high cost of failure makes required the use of methods and techniques to ensure application reliability. In this context, formal languages, as Circus or specific languages versions like Safety-Critical Java, were created to facilitate the verification and validation of applications so consequently assisting to increase the overall reliability. Despite of the reliability increase, the modeled systems in formal languages can not be executed subsequently has to be implemented in a traditional programming language. It is in this process of free translation where occur most mistakes that end up not ensuring that the generated code conforms to the specification. Based on that premise, this paper propose to expound a strategy of translation from models written in Circus language to executable programs in SCJ language. Among the main objectives and contributions include the creation of EBNFs of the two languages and the detailed description of the translation of all elements between the two languages. / Em sistemas críticos de segurança, missão ou negócios o alto custo das falhas faz com que sejam necessários o uso de métodos e técnicas para garantir a confiabilidade da aplicação. É neste contexto que foram criadas linguagens formais como o Circus ou versões específicas de linguagens como o Safety-Critical Java para facilitar a verificação e validação das aplicações criadas e aumentar consequentemente a confiabilidade geral da aplicação. Apesar de aumentar a confiabilidade, os sistemas modelados em linguagens formais não podem ser executados e então precisam ser implementados em uma linguagem de programação tradicional. É nesse processo de livre tradução do sistema especificado onde ocorrem a maioria dos erros que acabam por não garantir que o código gerado esteja de acordo com a especificação. Baseando-se nessa premissa o presente trabalho propõem-se a apresentar uma estratégia de tradução de modelos escritos na linguagem Circus para programas executáveis na linguagem SCJ. Entre os principais objetivos e contribuições do trabalho estão a criação das EBNFs das duas linguagens e a descrição detalhada da tradução de todos os elementos entre as duas linguagens.