Speeding-Up Mutation Testing via Data Compression and State Infection

Mutation testing is widely considered as a high-end test criterion due to the vast number of mutants it generates. Although many efforts have been made to reduce the computational cost of mutation testing, its scalability issue remains in practice. In this paper, we introduce a novel method to speed up mutation testing based on state infection information. In addition to filtering out uninfected test executions, we further select a subset of mutants and a subset of test cases to run leveraging data-compression techniques. In particular, we adopt Formal Concept Analysis (FCA) to group similar mutants together and then select test cases to cover these mutants. To evaluate our method, we conducted an experimental study on six open source Java projects. We used EvoSuite to automatically generate test cases and to collect mutation data. The initial results show that our method can reduce the execution time by 83.93% with only 0.257% loss in precision

Learning in the Real World: Constraints on Cost, Space, and Privacy

The sheer demand for machine learning in fields as varied as: healthcare, web-search ranking, factory automation, collision prediction, spam filtering, and many others, frequently outpaces the intended use-case of machine learning models. In fact, a growing number of companies hire machine learning researchers to rectify this very problem: to tailor and/or design new state-of-the-art models to the setting at hand. However, we can generalize a large set of the machine learning problems encountered in practical settings into three categories: cost, space, and privacy. The first category (cost) considers problems that need to balance the accuracy of a machine learning model with the cost required to evaluate it. These include problems in web-search, where results need to be delivered to a user in under a second and be as accurate as possible. The second category (space) collects problems that require running machine learning algorithms on low-memory computing devices. For instance, in search-and-rescue operations we may opt to use many small unmanned aerial vehicles (UAVs) equipped with machine learning algorithms for object detection to find a desired search target. These algorithms should be small to fit within the physical memory limits of the UAV (and be energy efficient) while reliably detecting objects. The third category (privacy) considers problems where one wishes to run machine learning algorithms on sensitive data. It has been shown that seemingly innocuous analyses on such data can be exploited to reveal data individuals would prefer to keep private. Thus, nearly any algorithm that runs on patient or economic data falls under this set of problems. We devise solutions for each of these problem categories including (i) a fast tree-based model for explicitly trading off accuracy and model evaluation time, (ii) a compression method for the k-nearest neighbor classifier, and (iii) a private causal inference algorithm that protects sensitive data

Cardiac Arrhythmias

Cardiac arrhythmias are common triggers of emergency admission to cardiology or high-dependency departments. Most cases are easy to diagnose and treat, while others may present a challenge to healthcare professionals. A translational approach to arrhythmias links molecular and cellular scientific research with clinical diagnostics and therapeutic methods, which may include both pharmacological and non-pharmacologic treatments. This book presents a comprehensive overview of specific cardiac arrhythmias and discusses translational approaches to their diagnosis and treatment

Understanding host-microbe interactions in maize kernel and sweetpotato leaf metagenomic profiles.

Functional and quantitative metagenomic profiling remains challenging and limits our understanding of host-microbe interactions. This body of work aims to mediate these challenges by using a novel quantitative reduced representation sequencing strategy (OmeSeq-qRRS), development of a fully automated software for quantitative metagenomic/microbiome profiling (Qmatey: quantitative metagenomic alignment and taxonomic identification using exact-matching) and implementing these tools for understanding plant-microbe-pathogen interactions in maize and sweetpotato. The next generation sequencing-based OmeSeq-qRRS leverages the strengths of shotgun whole genome sequencing and costs lower that the more affordable amplicon sequencing method. The novel FASTQ data compression/indexing and enhanced-multithreading of the MegaBLAST in Qmatey allows for computational speeds several thousand-folds faster than typical runs. Regardless of sample number, the analytical pipeline can be completed within days for genome-wide sequence data and provides broad-spectrum taxonomic profiling (virus to eukaryotes). As a proof of concept, these protocols and novel analytical pipelines were implemented to characterize the viruses within the leaf microbiome of a sweetpotato population that represents the global genetic diversity and the kernel microbiomes of genetically modified (GMO) and nonGMO maize hybrids. The metagenome profiles and high-density SNP data were integrated to identify host genetic factors (disease resistance and intracellular transport candidate genes) that underpin sweetpotato-virus interactions Additionally, microbial community dynamics were observed in the presence of pathogens, leading to the identification of multipartite interactions that modulate disease severity through co-infection and species competition. This study highlights a low-cost, quantitative and strain/species-level metagenomic profiling approach, new tools that complement the assay’s novel features and provide fast computation, and the potential for advancing functional metagenomic studies

Inflammatory Bowel Disease

This book is an overview of invited contributions on recent data of inflammatory bowel diseases. The first part of the book covers topics related to the ethiopathogenesis of inflammatory bowel diseases including the environmental, genetic factors and immunological alternations. The next chapters deal with present day management of disease including radiological diagnosis and surgical treatment, which consider the advances of most up-to-date radiological methodology including MRI techniques and the role of surgical procedures in the therapy. The final part presents medical therapy and its future directions. These chapters discuss natural products exerting anti-inflammatory and anti-tumour effects, methods of colon targeting drug delivery systems including polysaccharides, peptides and nanoparticules; as well as the potential risks of nanotechnology based food materials

Evaluating Software Testing Techniques: A Systematic Mapping Study

Software testing techniques are crucial for detecting faults in software and reducing the risk of using it. As such, it is important that we have a good understanding of how to evaluate these techniques for their efficiency, scalability, applicability, and effectiveness at finding faults. This thesis enhances our understanding of testing technique evaluations by providing an overview of the state of the art in research. To accomplish this we utilize a systematic mapping study; structuring the field and identifying research gaps and publication trends. We then present a small case study demonstrating how our mapping study can be used to assist researchers in evaluating their own software testing techniques. We find that a majority of evaluations are empirical evaluations in the form of case studies and experiments, most of these evaluations are of low quality based on proper methodology guidelines, and that relatively few papers in the field discuss how testing techniques should be evaluated