<p>Evolutionary dynamics can be notoriously complex and difficult to analyze. In this dissertation I describe a population genetic regime where the dynamics are simple enough to allow a relatively complete and elegant treatment. Consider a haploid, asexual population, where each possible genotype has been assigned a fitness. When mutations enter a population sufficiently rarely, we can model the evolution of this population as a Markov chain where the population jumps from one genotype to another at the birth of each new mutant destined for fixation. Furthermore, if the mutation rates are assigned in such a manner that the Markov chain is reversible when all genotypes are assigned the same fitness, then it is still reversible when genotypes are assigned differing fitnesses. </p><p>The key insight is that this Markov chain can be analyzed using the spectral theory of finite-state, reversible Markov chains. I describe the spectral decomposition of the transition matrix and use it to build a general framework with which I address a variety of both classical and novel topics. These topics include a method for creating low-dimensional visualizations of fitness landscapes; a measure of how easy it is for the evolutionary process to `find' a specific genotype or phenotype; the index of dispersion of the molecular clock and its generalizations; a definition for the neighborhood of a genotype based on evolutionary dynamics; and the expected fitness and number of substitutions that have occurred given that a population has been evolving on the fitness landscape for a given period of time. I apply these various analyses to both a simple one-codon fitness landscape and to a large neutral network derived from computational RNA secondary structure predictions.</p> / Dissertation

Mutation testing is a powerful, but resource intense technique for asserting software quality. This report investigates two claims about one of the mutation operators on procedural logic, the relation operator replacement (ROR). The constrained ROR mutant operator is a type of constrained mutation, which targets to lower the number of mutants as a “do smarter” approach, making mutation testing more suitable for industrial use. The findings in the report shows that the hypothesis on subsumption is rejected if mutants are to be detected on function return values. The second hypothesis stating that a test case can only detect a single top-level mutant in a subsumption graph is also rejected. The report presents a comprehensive overview on the domain of mutation testing, displays examples of the masking behaviour previously not described in the field of mutation testing, and discusses the importance of the granularity where the mutants should be detected under execution. The contribution is based on literature survey and experiment. The empirical findings as well as the implications are discussed in this master dissertation.

High-level language virtual machines (HLL VMs) have been playing a key role as a mechanism for implementing programming languages. Languages that run on these execution environments have many advantages over languages that are compiled to native code. These advantages have led HLL VMs to gain broad acceptance in both academy and industry. However, much of the research in this area has been devoted to boosting the performance of these execution environments. Few eorts have attempted to introduce features that automate or facilitate some software engineering activities, including software testing. This research argues that HLL VMs provide a reasonable basis for building an integrated software testing environment. To this end, two software testing features that build on the characteristics of a Java virtual machine (JVM) were devised. The purpose of the rst feature is to automate weak mutation. Augmented with mutation support, the chosen JVM achieved speedups of as much as 95% in comparison to a strong mutation tool. To support the testing of concurrent programs, the second feature is concerned with enabling the deterministic re-execution of Java programs and exploration of new scheduling sequences / Máquinas virtuais de linguagens de programação têm desempenhado um papel importante como mecanismo para a implementação de linguagens de programação. Linguagens voltadas para esses ambientes de execução possuem várias vantagens em relação às linguagens compiladas. Essas vantagens fizeram com que tais ambientes de execução se tornassem amplamente utilizados pela indústria e academia. Entretanto, a maioria dos estudos nessa area têm se dedicado a aprimorar o desempenho desses ambientes de execução e poucos têm enfocado o desenvolvimento de funcionalidades que automatizem ou facilitem a condução de atividades de engenharia de software, incluindo atividades de teste de software. Este trabalho apresenta indícios de que máquinas virtuais de linguagens de programação podem apoiar a criação de ambientes de teste de software integrado. Para tal, duas funcionalidades que tiram proveito das características de uma máquina virtual Java foram desenvolvidas. O propósito da primeira funcionalidade e automatizar a condução de atividades de mutação fraca. Após a implementação de tal funcionalidade na máquina virtual Java selecionada, observou-se um desempenho até 95% melhor em relação a uma ferramenta de mutação forte. Afim de apoiar o teste de programas concorrentes, a segunda funcionalidade permite reexecutá-los de forma determinística além de automatizar a exploração de que novas sequências de escalonamento

High-level language virtual machines (HLL VMs) have been playing a key role as a mechanism for implementing programming languages. Languages that run on these execution environments have many advantages over languages that are compiled to native code. These advantages have led HLL VMs to gain broad acceptance in both academy and industry. However, much of the research in this area has been devoted to boosting the performance of these execution environments. Few eorts have attempted to introduce features that automate or facilitate some software engineering activities, including software testing. This research argues that HLL VMs provide a reasonable basis for building an integrated software testing environment. To this end, two software testing features that build on the characteristics of a Java virtual machine (JVM) were devised. The purpose of the rst feature is to automate weak mutation. Augmented with mutation support, the chosen JVM achieved speedups of as much as 95% in comparison to a strong mutation tool. To support the testing of concurrent programs, the second feature is concerned with enabling the deterministic re-execution of Java programs and exploration of new scheduling sequences / Máquinas virtuais de linguagens de programação têm desempenhado um papel importante como mecanismo para a implementação de linguagens de programação. Linguagens voltadas para esses ambientes de execução possuem várias vantagens em relação às linguagens compiladas. Essas vantagens fizeram com que tais ambientes de execução se tornassem amplamente utilizados pela indústria e academia. Entretanto, a maioria dos estudos nessa area têm se dedicado a aprimorar o desempenho desses ambientes de execução e poucos têm enfocado o desenvolvimento de funcionalidades que automatizem ou facilitem a condução de atividades de engenharia de software, incluindo atividades de teste de software. Este trabalho apresenta indícios de que máquinas virtuais de linguagens de programação podem apoiar a criação de ambientes de teste de software integrado. Para tal, duas funcionalidades que tiram proveito das características de uma máquina virtual Java foram desenvolvidas. O propósito da primeira funcionalidade e automatizar a condução de atividades de mutação fraca. Após a implementação de tal funcionalidade na máquina virtual Java selecionada, observou-se um desempenho até 95% melhor em relação a uma ferramenta de mutação forte. Afim de apoiar o teste de programas concorrentes, a segunda funcionalidade permite reexecutá-los de forma determinística além de automatizar a exploração de que novas sequências de escalonamento