A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks

Identifying significantly mutated genes in cancer is essential for understanding the mechanisms of tumor initiation and progression. This task is a key challenge since large-scale genomic studies have reported an endless number of genes mutated at a shallow frequency. Towards uncovering infrequently mutated genes, gene interaction networks combined with mutation data have been explored. This work proposes Discovering Significant Cancer Genes (DiSCaGe), a computational method for discovering significant genes for cancer. DiSCaGe computes a mutation score for the genes based on the type of mutations they have. The influence received for their neighbors in the network is also considered and obtained through an asymmetric spreading strength applied to a consensus gene network. DiSCaGe produces a ranking of prioritized possible cancer genes. An experimental evaluation with six types of cancer revealed the potential of DiSCaGe for discovering known and possible novel significant cancer genes.

Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India

Background: The COVID-19 pandemic is associated with high morbidity and mortality, with the emergence of numerous variants. The dynamics of SARS-CoV-2 with respect to clade distribution is uneven, unpredictable and fast changing. Aims: Retrieving the complete genomes of SARS-CoV-2 from India and subjecting them to analysis on phylogenetic clade diversity, Spike (S) protein mutations and their functional consequences such as immune escape features and impact on infectivity. Methods: Whole genome of SARS-CoV-2 isolates (n=4,326) deposited from India during the period from January 2020 to December 2020 is retrieved from GISAID and various analyses performed using in silico tools. Results: Notable clade dynamicity is observed indicating the emergence of diverse SARS-CoV-2 variants across the country. GR clade is predominant over the other clades and the distribution pattern of clades is uneven. D614G is the commonest and predominant mutation found among the S-protein followed by L54F. Mutation score prediction analyses reveal that there are several mutations in S-protein including the RBD and NTD regions that can influence the virulence of virus. Besides, mutations having immune escape features as well as impacting the immunogenicity and virulence through changes in the glycosylation patterns are identified. Conclusions: The study has revealed emergence of variants with shifting of clade dynamics within a year in India. It is shown uneven distribution of clades across the nation requiring timely deposition of SARS-CoV-2 sequences. Functional evaluation of mutations in S-protein reveals their significance in virulence, immune escape features and disease severity besides impacting therapeutics and prophylaxis.

Multiple-Searching Genetic Algorithm for Whole Test Suites

A test suite is a set of test cases that evaluate the quality of software. The aim of whole test suite generation is to create test cases with the highest coverage scores possible. This study investigated the efficiency of a multiple-searching genetic algorithm (MSGA) for whole test suite generation. In previous works, the MSGA has been effectively used in multicast routing of a network system and in the generation of test cases on individual coverage criteria for small- to medium-sized programs. The performance of the algorithms varies depending on the problem instances. In this experiment were generated whole test suites for complex programs. The MSGA was expanded in the EvoSuite test generation tool and compared with the available algorithms on EvoSuite in terms of the number of test cases, the number of statements, mutation score, and coverage score. All algorithms were evaluated on 14 problem instances with different corpus to satisfy multiple coverage criteria. The problem instances were Java open-source projects. Findings demonstrate that the MSGA generated test cases reached greater coverage scores and detected a larger number of faults in the test class when compared with the others.

Bridging the model-to-code abstraction gap with fuzzy logic in model-based regression test selection

Regression test selection (RTS) approaches reduce the cost of regression testing of evolving software systems. Existing RTS approaches based on UML models use behavioral diagrams or a combination of structural and behavioral diagrams. However, in practice, behavioral diagrams are incomplete or not used. In previous work, we proposed a fuzzy logic based RTS approach called FLiRTS that uses UML sequence and activity diagrams. In this work, we introduce FLiRTS 2, which drops the need for behavioral diagrams and relies on system models that only use UML class diagrams, which are the most widely used UML diagrams in practice. FLiRTS 2 addresses the unavailability of behavioral diagrams by classifying test cases using fuzzy logic after analyzing the information commonly provided in class diagrams. We evaluated FLiRTS 2 on UML class diagrams extracted from 3331 revisions of 13 open-source software systems, and compared the results with those of code-based dynamic (Ekstazi) and static (STARTS) RTS approaches. The average test suite reduction using FLiRTS 2 was 82.06%. The average safety violations of FLiRTS 2 with respect to Ekstazi and STARTS were 18.88% and 16.53%, respectively. FLiRTS 2 selected on average about 82% of the test cases that were selected by Ekstazi and STARTS. The average precision violations of FLiRTS 2 with respect to Ekstazi and STARTS were 13.27% and 9.01%, respectively. The average mutation score of the full test suites was 18.90%; the standard deviation of the reduced test suites from the average deviation of the mutation score for each subject was 1.78% for FLiRTS 2, 1.11% for Ekstazi, and 1.43% for STARTS. Our experiment demonstrated that the performance of FLiRTS 2 is close to the state-of-art tools for code-based RTS but requires less information and performs the selection in less time.

Better Prediction of Mutation Score

<div><div><div><p>Mutation score is widely accepted to be a reliable measurement for the effectiveness of software tests. Recent studies, however, show that mutation analysis is extremely costly and hard to use in practice. We present a novel direct prediction model of mutation score using neural networks. Relying solely on static code features that do not require generation of mutants or execution of the tests, we predict mutation score with an accuracy better than a quintile. When we include statement coverage as a feature, our accuracy rises to about a decile. Using a similar approach, we also improve the state-of-the-art results for binary test effectiveness prediction and introduce an intuitive, easy-to-calculate set of features superior to previously studied sets. We also publish the largest dataset of test-class level mutation score and static code features data to date, for future research. Finally, we discuss how our approach could be integrated into real-world systems, IDEs, CI tools, and testing frameworks.</p></div></div></div>

Better Prediction of Mutation Score

<div><div><div><p>Mutation score is widely accepted to be a reliable measurement for the effectiveness of software tests. Recent studies, however, show that mutation analysis is extremely costly and hard to use in practice. We present a novel direct prediction model of mutation score using neural networks. Relying solely on static code features that do not require generation of mutants or execution of the tests, we predict mutation score with an accuracy better than a quintile. When we include statement coverage as a feature, our accuracy rises to about a decile. Using a similar approach, we also improve the state-of-the-art results for binary test effectiveness prediction and introduce an intuitive, easy-to-calculate set of features superior to previously studied sets. We also publish the largest dataset of test-class level mutation score and static code features data to date, for future research. Finally, we discuss how our approach could be integrated into real-world systems, IDEs, CI tools, and testing frameworks.</p></div></div></div>

Diversifying Focused Testing for Unit Testing

Software changes constantly, because developers add new features or modifications. This directly affects the effectiveness of the test suite associated with that software, especially when these new modifications are in a specific area that no test case covers. This article tackles the problem of generating a high-quality test suite to cover repeatedly a given point in a program, with the ultimate goal of exposing faults possibly affecting the given program point. Both search-based software testing and constraint solving offer ready, but low-quality, solutions to this: Ideally, a maximally diverse covering test set is required, whereas search and constraint solving tend to generate test sets with biased distributions. Our approach, Diversified Focused Testing (DFT), uses a search strategy inspired by GödelTest. We artificially inject parameters into the code branching conditions and use a bi-objective search algorithm to find diverse inputs by perturbing the injected parameters, while keeping the path conditions still satisfiable. Our results demonstrate that our technique, DFT, is able to cover a desired point in the code at least 90% of the time. Moreover, adding diversity improves the bug detection and the mutation killing abilities of the test suites. We show that DFT achieves better results than focused testing, symbolic execution, and random testing by achieving from 3% to 70% improvement in mutation score and up to 100% improvement in fault detection across 105 software subjects.

An error-propagation aware method to reduce the software mutation cost using genetic algorithm

PurposeThe purpose of this study is to reduce the number of mutations and, consequently, reduce the cost of mutation test. The results of related studies indicate that about 40% of injected faults (mutants) in the source code are effect-less (equivalent). Equivalent mutants are one of the major costs of mutation testing and the identification of equivalent and effect-less mutants has been known as an undecidable problem.Design/methodology/approachIn a program with n branch instructions (if instruction) there are 2n execution paths (test paths) that the data and codes into each of these paths can be considered as a target of mutation. Given the role and impact of data in a program, some of data and codes propagates the injected mutants more likely to the output of the program. In this study, firstly the error-propagation rate of the program data is quantified using static analysis of the program control-flow graph. Then, the most error-propagating test paths are identified by the proposed heuristic algorithm (Genetic Algorithm [GA]). Data and codes with higher error-propagation rate are only considered as the strategic locations for the mutation testing.FindingsIn order to evaluate the proposed method, an extensive series of mutation testing experiments have been conducted on a set of traditional benchmark programs using MuJava tool set. The results depict that the proposed method reduces the number of mutants about 24%. Also, in the corresponding experiments, the mutation score is increased about 5.6%. The success rate of the GA in finding the most error-propagating paths of the input programs is 99%. On average, only 7.46% of generated mutants by the proposed method are equivalent. Indeed, 92.54% of generated mutants are non-equivalent.Originality/valueThe main contribution of this study is as follows: Proposing a set of equations to measure the error-propagation rate of each data, basic-block and execution path of a program. Proposing a genetic algorithm to identify a most error-propagating path of program as locations of mutations. Developing an efficient mutation-testing framework that mutates only the strategic locations of a program identified by the proposed genetic algorithms. Reducing the time and cost of mutation testing by reducing the equivalent mutants.

Search-based Test Data Generation for Mutation Testing: a tool for Python programs

Test data generation for mutation testing consists of identifying a set of inputs that maximizes the number of mutants killed. Mutation Testing is an excellent test criterion for detecting faults and measuring the effectiveness of test data sets. However, it is not widely used in practice due to the cost and complexity to perform some activities as generating test data. Although test suites can be produced and selected manually by a tester this practice is susceptible to errors and tools are needed to facilitate it. Several tools have been developed to automate mutation testing, but, only a few address the test data generation. The present paper proposes an automated test data generation tool based on weak mutation for Python programming language using the Hill Climbing algorithm. For evaluation, we performed an experiment concerning the effectiveness and cost computational of the tool in a database composed of 348 mutants and we compare it with random generation. Overall, the experiment achieved an average mutation score of 86% for our proposed tool and random testing 64% on average.