Automated metamorphic testing on the analyses of feature models

Copyright © 2010 Elsevier B.V. All rights reserved.Context: A feature model (FM) represents the valid combinations of features in a domain. The automated extraction of information from FMs is a complex task that involves numerous analysis operations, techniques and tools. Current testing methods in this context are manual and rely on the ability of the tester to decide whether the output of an analysis is correct. However, this is acknowledged to be time-consuming, error-prone and in most cases infeasible due to the combinatorial complexity of the analyses, this is known as the oracle problem.Objective: In this paper, we propose using metamorphic testing to automate the generation of test data for feature model analysis tools overcoming the oracle problem. An automated test data generator is presented and evaluated to show the feasibility of our approach.Method: We present a set of relations (so-called metamorphic relations) between input FMs and the set of products they represent. Based on these relations and given a FM and its known set of products, a set of neighbouring FMs together with their corresponding set of products are automatically generated and used for testing multiple analyses. Complex FMs representing millions of products can be efficiently created by applying this process iteratively.Results: Our evaluation results using mutation testing and real faults reveal that most faults can be automatically detected within a few seconds. Two defects were found in FaMa and another two in SPLOT, two real tools for the automated analysis of feature models. Also, we show how our generator outperforms a related manual suite for the automated analysis of feature models and how this suite can be used to guide the automated generation of test cases obtaining important gains in efficiency.Conclusion: Our results show that the application of metamorphic testing in the domain of automated analysis of feature models is efficient and effective in detecting most faults in a few seconds without the need for a human oracle.This work has been partially supported by the European Commission(FEDER)and Spanish Government under CICYT project SETI(TIN2009-07366)and the Andalusian Government project ISABEL(TIC-2533)

SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad-hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SMaSH, a benchmarking methodology for evaluating human genome variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes, and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on this benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single nucleotide polymorphism (SNP), indel, and structural variant calling algorithms. Availability: We provide free and open access online to the SMaSH toolkit, along with detailed documentation, at smash.cs.berkeley.edu

Robustness-Driven Resilience Evaluation of Self-Adaptive Software Systems

An increasingly important requirement for certain classes of software-intensive systems is the ability to self-adapt their structure and behavior at run-time when reacting to changes that may occur to the system, its environment, or its goals. A major challenge related to self-adaptive software systems is the ability to provide assurances of their resilience when facing changes. Since in these systems, the components that act as controllers of a target system incorporate highly complex software, there is the need to analyze the impact that controller failures might have on the services delivered by the system. In this paper, we present a novel approach for evaluating the resilience of self-adaptive software systems by applying robustness testing techniques to the controller to uncover failures that can affect system resilience. The approach for evaluating resilience, which is based on probabilistic model checking, quantifies the probability of satisfaction of system properties when the target system is subject to controller failures. The feasibility of the proposed approach is evaluated in the context of an industrial middleware system used to monitor and manage highly populated networks of devices, which was implemented using the Rainbow framework for architecture-based self-adaptation

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

You Cannot Fix What You Cannot Find! An Investigation of Fault Localization Bias in Benchmarking Automated Program Repair Systems

Properly benchmarking Automated Program Repair (APR) systems should contribute to the development and adoption of the research outputs by practitioners. To that end, the research community must ensure that it reaches significant milestones by reliably comparing state-of-the-art tools for a better understanding of their strengths and weaknesses. In this work, we identify and investigate a practical bias caused by the fault localization (FL) step in a repair pipeline. We propose to highlight the different fault localization configurations used in the literature, and their impact on APR systems when applied to the Defects4J benchmark. Then, we explore the performance variations that can be achieved by `tweaking' the FL step. Eventually, we expect to create a new momentum for (1) full disclosure of APR experimental procedures with respect to FL, (2) realistic expectations of repairing bugs in Defects4J, as well as (3) reliable performance comparison among the state-of-the-art APR systems, and against the baseline performance results of our thoroughly assessed kPAR repair tool. Our main findings include: (a) only a subset of Defects4J bugs can be currently localized by commonly-used FL techniques; (b) current practice of comparing state-of-the-art APR systems (i.e., counting the number of fixed bugs) is potentially misleading due to the bias of FL configurations; and (c) APR authors do not properly qualify their performance achievement with respect to the different tuning parameters implemented in APR systems.Comment: Accepted by ICST 201

Darwinian Data Structure Selection

Data structure selection and tuning is laborious but can vastly improve an application's performance and memory footprint. Some data structures share a common interface and enjoy multiple implementations. We call them Darwinian Data Structures (DDS), since we can subject their implementations to survival of the fittest. We introduce ARTEMIS a multi-objective, cloud-based search-based optimisation framework that automatically finds optimal, tuned DDS modulo a test suite, then changes an application to use that DDS. ARTEMIS achieves substantial performance improvements for \emph{every} project in $5$ Java projects from DaCapo benchmark, $8$ popular projects and $30$ uniformly sampled projects from GitHub. For execution time, CPU usage, and memory consumption, ARTEMIS finds at least one solution that improves \emph{all} measures for $86\%$ ($37/43$) of the projects. The median improvement across the best solutions is $4.8\%$, $10.1\%$, $5.1\%$ for runtime, memory and CPU usage. These aggregate results understate ARTEMIS's potential impact. Some of the benchmarks it improves are libraries or utility functions. Two examples are gson, a ubiquitous Java serialization framework, and xalan, Apache's XML transformation tool. ARTEMIS improves gson by $16.5$\%, $1\%$ and $2.2\%$ for memory, runtime, and CPU; ARTEMIS improves xalan's memory consumption by $23.5$\%. \emph{Every} client of these projects will benefit from these performance improvements.Comment: 11 page