Search algorithms for regression test case prioritization

Regression testing is an expensive, but important, process. Unfortunately, there may be insufficient resources to allow for the re-execution of all test cases during regression testing. In this situation, test case prioritisation techniques aim to improve the effectiveness of regression testing, by ordering the test cases so that the most beneficial are executed first. Previous work on regression test case prioritisation has focused on Greedy Algorithms. However, it is known that these algorithms may produce sub-optimal results, because they may construct results that denote only local minima within the search space. By contrast, meta-heuristic and evolutionary search algorithms aim to avoid such problems. This paper presents results from an empirical study of the application of several greedy, meta-heuristic and evolutionary search algorithms to six programs, ranging from 374 to 11,148 lines of code for 3 choices of fitness metric. The paper addresses the problems of choice of fitness metric, characterisation of landscape modality and determination of the most suitable search technique to apply. The empirical results replicate previous results concerning Greedy Algorithms. They shed light on the nature of the regression testing search space, indicating that it is multi-modal. The results also show that Genetic Algorithms perform well, although Greedy approaches are surprisingly effective, given the multi-modal nature of the landscape

Estimating Effects and Making Predictions from Genome-Wide Marker Data

In genome-wide association studies (GWAS), hundreds of thousands of genetic markers (SNPs) are tested for association with a trait or phenotype. Reported effects tend to be larger in magnitude than the true effects of these markers, the so-called ``winner's curse.'' We argue that the classical definition of unbiasedness is not useful in this context and propose to use a different definition of unbiasedness that is a property of the estimator we advocate. We suggest an integrated approach to the estimation of the SNP effects and to the prediction of trait values, treating SNP effects as random instead of fixed effects. Statistical methods traditionally used in the prediction of trait values in the genetics of livestock, which predates the availability of SNP data, can be applied to analysis of GWAS, giving better estimates of the SNP effects and predictions of phenotypic and genetic values in individuals.Comment: Published in at http://dx.doi.org/10.1214/09-STS306 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization

<p>Abstract</p> <p>Background</p> <p>High-throughput molecular interaction data have been used effectively to prioritize candidate genes that are linked to a disease, based on the observation that the products of genes associated with similar diseases are likely to interact with each other heavily in a network of protein-protein interactions (PPIs). An important challenge for these applications, however, is the incomplete and noisy nature of PPI data. Information flow based methods alleviate these problems to a certain extent, by considering indirect interactions and multiplicity of paths.</p> <p>Results</p> <p>We demonstrate that existing methods are likely to favor highly connected genes, making prioritization sensitive to the skewed degree distribution of PPI networks, as well as ascertainment bias in available interaction and disease association data. Motivated by this observation, we propose several statistical adjustment methods to account for the degree distribution of known disease and candidate genes, using a PPI network with associated confidence scores for interactions. We show that the proposed methods can detect loosely connected disease genes that are missed by existing approaches, however, this improvement might come at the price of more false negatives for highly connected genes. Consequently, we develop a suite called D<smcaps>A</smcaps>D<smcaps>A</smcaps>, which includes different uniform prioritization methods that effectively integrate existing approaches with the proposed statistical adjustment strategies. Comprehensive experimental results on the Online Mendelian Inheritance in Man (OMIM) database show that D<smcaps>A</smcaps>D<smcaps>A</smcaps> outperforms existing methods in prioritizing candidate disease genes.</p> <p>Conclusions</p> <p>These results demonstrate the importance of employing accurate statistical models and associated adjustment methods in network-based disease gene prioritization, as well as other network-based functional inference applications. D<smcaps>A</smcaps>D<smcaps>A</smcaps> is implemented in Matlab and is freely available at <url>http://compbio.case.edu/dada/</url>.</p

Improvements to Test Case Prioritisation considering Efficiency and Effectiveness on Real Faults

Despite the best efforts of programmers and component manufacturers, software does not always work perfectly. In order to guard against this, developers write test suites that execute parts of the code and compare the expected result with the actual result. Over time, test suites become expensive to run for every change, which has led to optimisation techniques such as test case prioritisation. Test case prioritisation reorders test cases within the test suite with the goal of revealing faults as soon as possible. Test case prioritisation has received a lot of research that has indicated that prioritised test suites can reveal faults faster, but due to a lack of real fault repositories available for research, prior evaluations have often been conducted on artificial faults. This thesis aims to investigate whether the use of artificial faults represents a threat to the validity of previous studies, and proposes new strategies for test case prioritisation that increase the effectiveness of test case prioritisation on real faults. This thesis conducts an empirical evaluation of existing test case prioritisation strategies on real and artificial faults, which establishes that artificial faults provide unreliable results for real faults. The study found that there are four occasions on which a strategy for test case prioritisation would be considered no better than the baseline when using one fault type, but would be considered a significant improvement over the baseline when using the other. Moreover, this evaluation reveals that existing test case prioritisation strategies perform poorly on real faults, with no strategies significantly outperforming the baseline. Given the need to improve test case prioritisation strategies for real faults, this thesis proceeds to consider other techniques that have been shown to be effective on real faults. One such technique is defect prediction, a technique that provides estimates that a class contains a fault. This thesis proposes a test case prioritisation strategy, called G-Clef, that leverages defect prediction estimates to reorder test suites. While the evaluation of G-Clef indicates that it outperforms existing test case prioritisation strategies, the average predicted location of a faulty class is 13% of all classes in a system, which shows potential for improvement. Finally, this thesis conducts an investigative study as to whether sentiments expressed in commit messages could be used to improve the defect prediction element of G-Clef. Throughout the course of this PhD, I have created a tool called Kanonizo, an open-source tool for performing test case prioritisation on Java programs. All of the experiments and strategies used in this thesis were implemented into Kanonizo

How to understand the cell by breaking it: network analysis of gene perturbation screens

Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental perturbations on a genome-wide scale. This review surveys the current state-of-the-art in analyzing perturbation screens from a network point of view. We describe approaches to make the step from the parts list to the wiring diagram by using phenotypes for network inference and integrating them with complementary data sources. The first part of the review describes methods to analyze one- or low-dimensional phenotypes like viability or reporter activity; the second part concentrates on high-dimensional phenotypes showing global changes in cell morphology, transcriptome or proteome.Comment: Review based on ISMB 2009 tutorial; after two rounds of revisio

FACILITATING AQUATIC INVASIVE SPECIES MANAGEMENT USING SATELLITE REMOTE SENSING AND MACHINE LEARNING FRAMEWORKS

The urgent decision-making needs of invasive species managers can be better met by the integration of biodiversity big data with large-domain models and environmental data products in the form of new workflows and tools that facilitate data utilization across platforms. Timely risk assessments allow for the spatial prioritization of monitoring that could streamline invasive species management paradigms and invasive species’ ability to prevent irreversible damage, such that decision makers can focus surveillance and intervention efforts where they are likely to be most effective under budgetary and resource constraints. I present a workflow that generates rapid spatial risk assessments on aquatic invasive species by combining occurrence data, spatially explicit environmental data, and an ensemble approach to species distribution modeling using five machine learning algorithms. For proof of concept and validation, I tested this workflow using extensive spatial and temporal occurrence data from Rainbow Trout (RBT; Oncorhynchus mykiss) invasion in the upper Flathead River system in northwestern Montana, USA. Due to this workflow’s high performance against cross-validated datasets (87% accuracy) and congruence with known drivers of RBT invasion, I developed a tool that generates agile risk assessments based on the above workflow and suggest that it can be generalized to broader spatial and taxonomic scales in order to provide data-driven management information for early detection of potential invaders. I then use this tool as technical input for a management framework that provides guidance for users to incorporate and synthesize the component features of the workflow and toolkit to derive actionable insight in an efficient manner

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues