Dynamically fighting bugs : prevention, detection and elimination

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 147-160).This dissertation presents three test-generation techniques that are used to improve software quality. Each of our techniques targets bugs that are found by different stake-holders: developers, testers, and maintainers. We implemented and evaluated our techniques on real code. We present the design of each tool and conduct experimental evaluation of the tools with available alternatives. Developers need to prevent regression errors when they create new functionality. This dissertation presents a technique that helps developers prevent regression errors in object-oriented programs by automatically generating unit-level regression tests. Our technique generates regressions tests by using models created dynamically from example executions. In our evaluation, our technique created effective regression tests, and achieved good coverage even for programs with constrained APIs. Testers need to detect bugs in programs. This dissertation presents a technique that helps testers detect and localize bugs in web applications. Our technique automatically creates tests that expose failures by combining dynamic test generation with explicit state model checking. In our evaluation, our technique discovered hundreds of faults in real applications. Maintainers have to reproduce failing executions in order to eliminate bugs found in deployed programs. This dissertation presents a technique that helps maintainers eliminate bugs by generating tests that reproduce failing executions. Our technique automatically generates tests that reproduce the failed executions by monitoring methods and storing optimized states of method arguments.(cont.) In our evaluation, our technique reproduced failures with low overhead in real programs Analyses need to avoid unnecessary computations in order to scale. This dissertation presents a technique that helps our other techniques to scale by inferring the mutability classification of arguments. Our technique classifies mutability by combining both static analyses and a novel dynamic mutability analysis. In our evaluation, our technique efficiently and correctly classified most of the arguments for programs with more than hundred thousand lines of code.by Shay Artzi.Ph.D

miRNAminer: A tool for homologous microRNA gene search

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experimental and computational methods were used to construct miRNA gene repositories agreeing with careful submission guidelines.</p> <p>Results</p> <p>An algorithm we developed – miRNAminer – is used for homologous conserved miRNA gene search in several animal species. Given a search query, candidate homologs from different species are tested for their known miRNA properties, such as secondary structure, energy and alignment and conservation, in order to asses their fidelity. When applying miRNAminer on seven mammalian species we identified several hundreds of high-confidence homologous miRNAs increasing the total collection of (miRbase) miRNAs, in these species, by more than 50%. miRNAminer uses stringent criteria and exhibits high sensitivity and specificity.</p> <p>Conclusion</p> <p>We present – miRNAminer – the first web-server for homologous miRNA gene search in animals. miRNAminer can be used to identify conserved homolog miRNA genes and can also be used prior to depositing miRNAs in public databases. miRNAminer is available at <url>http://pag.csail.mit.edu/mirnaminer</url>.</p

ReCrash: Making Crashes Reproducible

It is difficult to fix a problem without being able to reproduce it.However, reproducing a problem is often difficult and time-consuming.This paper proposes a novel algorithm, ReCrash, that generatesmultiple unit tests that reproduce a given program crash.ReCrash dynamically tracks method calls during every execution of the target program. If the program crashes, ReCrash saves information about the relevant method calls and uses the saved information to create unit tests reproducing the crash.We present reCrashJ an implementation of ReCrash for Java. reCrashJ reproducedreal crashes from javac, SVNKit, Eclipse JDT, and BST. reCrashJ is efficient, incurring 13%-64% performance overhead. If this overhead is unacceptable, then reCrashJ has another mode that has negligible overhead until a crash occurs and 0%-1.7% overhead until a second crash, at which point the test cases are generated

Object and Reference Immutability using Java Generics

A compiler-checked immutability guarantee provides useful documentation, facilitates reasoning, and enables optimizations. This paper presents Immutability Generic Java (IGJ), a novel language extension that expresses immutability without changing Javas syntax by building upon Javas generics and annotation mechanisms. In IGJ, each class has one additional generic parameter that is Immutable, Mutable, or ReadOnly. IGJ guarantees both reference immutability (only mutable references can mutate an object) and object immutability (an immutable reference points to an immutable object). IGJ is the first proposal for enforcing object immutability, and its reference immutability is more expressive than previous work. IGJ also permits covariant changes of generic arguments in a type-safe manner, e.g., a readonly list of integers is a subtype of a readonly list of numbers. IGJ extends Javas type system with a few simple rules. We formalize this type system and prove it sound. Our IGJ compiler works by type-erasure and generates byte-code that can be executed on any JVM without runtime penalty

Finding the needles in the haystack: Generating legal test inputs for object-oriented programs

A test input for an object-oriented program typically consists of asequence of method calls that use the API defined by the programunder test. Generating legal test inputs can be challenging because,for some programs, the set of legal method sequences is much smallerthan the set of all possible sequences; without a formalspecification of legal sequences, an input generator is bound toproduce mostly illegal sequences.We propose a scalable technique that combines dynamic analysis withrandom testing to help an input generator create legal test inputswithout a formal specification, even for programs in whichmost sequences are illegal. The technique uses an example executionof the program to infer a model of legal call sequences, and usesthe model to guide a random input generator towards legal butbehaviorally-diverse sequences.We have implemented our technique for Java, in a tool calledPalulu, and evaluated its effectiveness in creating legal inputsfor real programs. Our experimental results indicate that thetechnique is effective and scalable. Our preliminary evaluationindicates that the technique can quickly generate legal sequencesfor complex inputs: in a case study, Palulu created legal testinputs in seconds for a set of complex classes, for which it took anexpert thirty minutes to generate a single legal input

miRviewer: a multispecies microRNA homologous viewer

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression via binding to the 3' ends of mRNAs. MiRNAs have been associated with many cellular events ascertaining their central role in gene regulation. In order to better understand miRNAs of interest it is of utmost importance to learn about the genomic conservation of these genes.</p> <p>Findings</p> <p>The miRviewer web-server, presented here, encompasses all known miRNAs of currently fully annotated animal genomes in a visual 'birds-eye' view representation. miRviewer provides a graphical outlook of the current miRNA world together with sequence alignments and secondary structures of each miRNA. As a test case we experimentally examined the expression of several miRNAs in various animals.</p> <p>Conclusions</p> <p>miRviewer completes the homologous miRNA space with hundreds of unreported miRNAs and is available at: <url>http://people.csail.mit.edu/akiezun/miRviewer</url></p

Finding Bugs In Dynamic Web Applications

Web script crashes and malformed dynamically-generated web pages are common errors, and they seriously impact usability of web applications. Currenttools for web-page validation cannot handle the dynamically-generatedpages that are ubiquitous on today's Internet.In this work, we apply a dynamic test generation technique, based oncombined concrete and symbolic execution, to the domain of dynamic webapplications. The technique generates tests automatically andminimizes the bug-inducing inputs to reduce duplication and to makethe bug reports small and easy to understand and fix.We implemented the technique in Apollo, an automated tool thatfound dozens of bugs in real PHP applications. Apollo generatestest inputs for the web application, monitors the application forcrashes, and validates that the output conforms to the HTMLspecification. This paper presents Apollo's algorithms andimplementation, and an experimental evaluation that revealed a totalof 214 bugs in 4 open-source PHP web applications

Finding Bugs in Web Applications Using Dynamic Test Generation and Explicit State Model Checking

Web script crashes and malformed dynamically-generated web pages are common errors, and they seriously impact the usability of web applications. Current tools for web-page validation cannot handle the dynamically generated pages that are ubiquitous on today's Internet. We present a dynamic test generation technique for the domain of dynamic web applications. The technique utilizes both combined concrete and symbolic execution and explicit-state model checking. The technique generates tests automatically, runs the tests capturing logical constraints on inputs, and minimizes the conditions on the inputs to failing tests, so that the resulting bug reports are small and useful in finding and fixing the underlying faults. Our tool Apollo implements the technique for the PHP programming language. Apollo generates test inputs for a web application, monitors the application for crashes, and validates that the output conforms to the HTML specification. This paper presents Apollo's algorithms and implementation, and an experimental evaluation that revealed 302 faults in 6 PHP web applications

In vivo and in vitro tracking of erosion in biodegradable materials using non-invasive fluorescence imaging

Author Manuscript 2012 March 1.The design of erodible biomaterials relies on the ability to program the in vivo retention time, which necessitates real-time monitoring of erosion. However, in vivo performance cannot always be predicted by traditional determination of in vitro erosion[superscript 1, 2] , and standard methods sacrifice samples or animals[superscript 3], preventing sequential measures of the same specimen. We harnessed non-invasive fluorescence imaging to sequentially follow in vivo material-mass loss to model the degradation of materials hydrolytically (PEG:dextran hydrogel) and enzymatically (collagen). Hydrogel erosion rates in vivo and in vitro correlated, enabling the prediction of in vivo erosion of new material formulations from in vitro data. Collagen in vivo erosion was used to infer physiologic in vitro conditions that mimic erosive in vivo environments. This approach enables rapid in vitro screening of materials, and can be extended to simultaneously determine drug release and material erosion from a drug-eluting scaffold, or cell viability and material fate in tissue-engineering formulations.National Institutes of Health (U.S.) (GM/HL 49039)National Institutes of Health (U.S.) (UL1 RR 025758