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<p> We study an alignment model for coding DNA sequences recently proposed by J. Hein in [4] that takes into account both DNA and protein information, and attempts to minimize the total amount of evolution at both DNA and protein levels[4,5,6]. Although there are two quadratic algorithms (i.e. Hua-Jiang algorithm[8] and PLH algorithm[9]) for Hein's model if the gap penalty function is affine, both of them are impractical because of the large constant factor embedded in the quadratic time complexity function. We therefore consider a mild simplification named Context-free Codon Alignment and present a much more efficient algorithm for the simplified model. The algorithms have been implemented and tested on both real and simulated sequences, and it is found that they produce almost identical alignments in most cases. Furthermore, we extend our model and design a heuristic algorithm to handle frame-shift errors and overlapping frames.</p> / Thesis / Master of Science (MSc)

This work discusses the effect of erasing rules to the generative power of regulated grammars, which is a big open problem in the theory of regulated rewriting. It studies the possibility of removal of erasing rules from regulated grammars by aggregation of current, up-to-date results concerning this elimination and by presentation of a new condition, called k-limited erasing, under which all erasing rules can be always removed from regularly controlled context-free grammars without affecting their generative power. This result partially solves the abovementioned problem. Moreover, a new algorithm for elimination of erasing rules from context-free grammars is presented. This algorithm does not require any predetermination of so called epsilon-nonterminals (in contrast to the standard algorithm used in textbooks). In the conclusion, a significance of these results concerning syntactical analysis is discussed.

The thesis aims to develop a method for extending the language platform Storm with a Java frontend.The project was conducted using an Action Research methodology and highlights triumphs andchallenges. Despite the significant overhead related to note generation and problem statementformulation, this methodology proved beneficial in identifying problems and providing the framework tosolve them. The first research question (RQ.1) evaluates to what extent the language platform Storm is suitable forimplementing the object oriented language Java. Using Storm, only a BNF and a specification for three-address code instructions are needed. Despite encountering difficulties during the implementation, theplatform offers tools that allow comprehensive customization of the new language's intended behaviorand functionality. The second research question (RQ.2) explores a suitable method for implementing a new language inStorm. It is suggested to first implement a foundational structure comprising of statements, blocks,scope handling and variable declarations. From this foundation, new functionalities can be graduallyintroduced and tested by connecting them to the appropriate location in the structure. When allfunctionality is added and tested a refactoring step can take place to modify the BNF if needed.

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The purpose of this dissertation is to develop a new generative grammar, based on the principles of intensional logic. More specifically, the goal is to create a psychologically real grammar model for use in natural language processing. The new grammar consists of a set of context-free rewrite rules tagged with intensional versions. Most generative grammars, such as transformational grammar, lexical functional-grammar and head-driven phrase structure grammar, extend traditional context-free grammars with a mechanism for dealing with contextual information, such as subcategorization of words and agreement between different phrasal elements. In these grammars there is not enough separation between the utterances of a language and the context in which they are uttered. Their models of language seem to assume that context is in some way encapsulated in the words of the language instead of the other way around. In intensional logic, the truth of a statement is considered in the context in which it is uttered, unlike traditional predicate logic in which truth is assigned in a vacuum, regardless of when or where it may have been stated. To date, the application of the principles of intensionality to natural languages has been confined to semantic theory. We remedy this by applying the ideas of intensional logic to syntactic context, resulting in intensional context-free grammar. Our grammar takes full advantage of the simplicity and elegance of context-free grammars while accounting for information that is beyond the sentence itself, in a realistic way. Sentence derivation is entirely encapsulated in the context of its utterance. In fact, for any particular context, the entire language of the grammar is encapsulated in that context. This is evidenced by our proof that the language of an intensional grammar is a set of context-free languages, indexed by context. To further support our claims we design and implement a small fragment of English using the grammar. The English grammar is capable of generating both passive and active sentences that include a subject, verb and up to two optional objects. Furthermore, we have implemented a partial French to English translation system that uses a single language dimension to initiate a translation. This allows us to include multiple languages in one grammar, unlike other systems which must separate the grammars of each language. This result has led this author to believe that we have created a grammar that is a viable candidate for a true Universal Grammar, far exceeding our initial goals. / Graduate / 0984 / 0800 / 0290 / rlittle@uvic.ca

Languages occasionally have syntactic constructions that are difficult, if not impossible, to describe using a context-free grammar. One such construction is a crossing dependency. Crossing dependencies have been well studied for Dutch and Swiss German (Huybregts, 1976; Shieber, 1985), and recently for Tagalog (Maclachlan and Rambow, 2003). In this paper I propose that Persian exhibits crossing dependencies. In this SOV language, a light verb construction in the future tense becomes interrupted by a future auxiliary verb, which agrees with its subject in person and number. The future auxiliary also splits passive constructions in a similar manner. These forms present interesting challenges for computational models of language. I will discuss implications of this phenomenon within current formal and linguistic theories.

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Approved for public release, distribution is unlimited / The focus of this thesis is to use and leverage the strengths of dynamic computer program analysis methodologies in software engineering testing and debugging such as program behavior modeling and event grammars to automate the building and analysis of combat simulations. An original high level language METALS (Meta-Language for Combat Simulations) and its associated parser and C++ code generator were designed to reduce the amount of time and developmental efforts needed to build sophisticated real world combat simulations. A C++ simulation of the Navy's current mine avoidance problem in littoral waters was generated using high level METALS description in the thesis as a demonstration. The software tools that were developed will allow users to focus their attention and efforts in the problem domain while sparing them to a considerable extent the rigors of detailed implementation. / Major, Republic of Singapore Navy