Repeated patterns in tree genetic programming

We extend our analysis of repetitive patterns found in genetic programming genomes to tree based GP. As in linear GP, repetitive patterns are present in large numbers. Size fair crossover limits bloat in automatic programming, preventing the evolution of recurring motifs. We examine these complex properties in detail: e.g. using depth v. size Catalan binary tree shape plots, subgraph and subtree matching, information entropy, syntactic and semantic fitness correlations and diffuse introns. We relate this emergent phenomenon to considerations about building blocks in GP and how GP works

Understanding The Impact of Solver Choice in Model-Based Test Generation

Background: In model-based test generation, SMT solvers explore the state-space of the model in search of violations of specified properties. If the solver finds that a predicate can be violated, it produces a partial test specification demonstrating the violation.Aims: The choice of solvers is important, as each may produce differing counterexamples. We aim to understand how solver choice impacts the effectiveness of generated test suites at finding faults.Method: We have performed experiments examining the impact of solver choice across multiple dimensions, examining the ability to attain goal satisfaction and fault detection when satisfaction is achieved---varying the source of test goals, data types of model input, and test oracle.Results: The results of our experiment show that solvers vary in their ability to produce counterexamples, and---for models where all solvers achieve goal satisfaction---in the resulting fault detection of the generated test suites. The choice of solver has an impact on the resulting test suite, regardless of the oracle, model structure, or source of testing goals.Conclusions: The results of this study identify factors that impact fault-detection effectiveness, and advice that could improve future approaches to model-based test generation

Mutation testing in the wild: findings from GitHub

Mutation testing exploits artificial faults to measure the adequacy of test suites and guide their improvement. It has become an extremely popular testing technique as evidenced by the vast literature, numerous tools, and research events on the topic. Previous survey papers have successfully compiled the state of research, its evolution, problems, and challenges. However, the use of mutation testing in practice is still largely unexplored. In this paper, we report the results of a thorough study on the use of mutation testing in GitHub projects. Specifically, we first performed a search for mutation testing tools, 127 in total, and we automatically searched the GitHub repositories including evidence of their use. Then, we focused on the top ten most widely used tools, based on the previous results, and manually revised and classified over 3.5K GitHub active repositories importing them. Among other findings, we observed a recent upturn in interest and activity, with Infection (PHP), PIT (Java) and Humbug (PHP) being the most widely used mutation tools in recent years. The predominant use of mutation testing is development, followed by teaching and learning, and research projects, although with significant differences among mutation tools found in the literature—less adopted and largely used in teaching and research—and those found in GitHub only—more popular and more widely used in development. Our work provides a new and encouraging perspective on the state of practice of mutation testing.Junta de Andalucía US-1264651 (APOLO)Junta de Andalucía P18-FR-2895 (EKIPMENT-PLUS)Ministerio de Ciencia, Innovación y Universidades RTI2018-101204-B-C21 (HORATIO)Ministerio de Ciencia, Innovación y Universidades RTI2018-093608-BC33 (FAME

High-throughput Binding Affinity Calculations at Extreme Scales

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or evolutionarily selected during treatment. Key to overcoming this challenge is an understanding of the molecular determinants of drug binding. Using multi-stage pipelines of molecular simulations we can gain insights into the binding free energy and the residence time of a ligand, which can inform both stratified and personal treatment regimes and drug development. To support the scalable, adaptive and automated calculation of the binding free energy on high-performance computing resources, we introduce the High- throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block approach in order to attain both workflow flexibility and performance. We demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage binding affinity calculation pipelines. This permits a rapid time-to-solution that is essentially invariant of the calculation protocol, size of candidate ligands and number of ensemble simulations. As such, HTBAC advances the state of the art of binding affinity calculations and protocols

The Effect of Program and Model Structure on the Effectiveness of MC/DC Test Adequacy Coverage

Test adequacy metrics defined over the structure of a program, such as Modified Condition and Decision Coverage (MC/DC), are used to assess testing efforts. However, MC/DC can be “cheated” by restructuring a program to make it easier to achieve the desired coverage. This is concerning, given the importance of MC/DC in assessing the adequacy of test suites for critical systems domains. In this work, we have explored the impact of implementation structure on the efficacy of test suites satisfying the MC/DC criterion using four real-world avionics systems. Our results demonstrate that test suites achieving MC/DC over implementations with structurally complex Boolean expressions are generally larger and more effective than test suites achieving MC/DC over functionally equivalent, but structurally simpler, implementations. Additionally, we found that test suites generated over simpler implementations achieve significantly lower MC/DC and fault-finding effectiveness when applied to complex implementations, whereas test suites generated over the complex implementation still achieve high MC/DC and attain high fault finding over the simpler implementation. By measuring MC/DC over simple implementations, we can significantly reduce the cost of testing, but in doing so, we also reduce the effectiveness of the testing process. Thus, developers have an economic incentive to “cheat” the MC/DC criterion, but this cheating leads to negative consequences. Accordingly, we recommend that organizations require MC/DC over a structurally complex implementation for testing purposes to avoid these consequences.</jats:p

Major genes and QTL influencing wool production and quality: a review

The opportunity exists to utilise our knowledge of major genes that influence the economically important traits in wool sheep. Genes with Mendelian inheritance have been identified for many important traits in wool sheep. Of particular importance are genes influencing pigmentation, wool quality and the keratin proteins, the latter of which are important for the morphology of the wool fibre. Gene mapping studies have identified some chromosomal regions associated with variation in wool quality and production traits. The challenge now is to build on this knowledge base in a cost-effective way to deliver molecular tools that facilitate enhanced genetic improvement programs for wool sheep