Leveraging Static Analysis for Bug Repair

We propose a method combining machine learning with a static analysis tool (i.e. Infer) to automatically repair source code. Machine Learning methods perform well for producing idiomatic source code. However, their output is sometimes difficult to trust as language models can output incorrect code with high confidence. Static analysis tools are trustable, but also less flexible and produce non-idiomatic code. In this paper, we propose to fix resource leak bugs in IR space, and to use a sequence-to-sequence model to propose fix in source code space. We also study several decoding strategies, and use Infer to filter the output of the model. On a dataset of CodeNet submissions with potential resource leak bugs, our method is able to find a function with the same semantics that does not raise a warning with around 97% precision and 66% recall.Comment: 13 pages. DL4C 202

Comprehensive needs analysis for the development of construction safety education tools in immersive reality

Construction industry remains one of the most hazardous industries to work in, despite numerous efforts by researchers and practitioners to improve levels of Health & Safety (H&S) and reduce the number of accidents which occur on the construction sites. A potential method to reduce the number accidents is to educate construction workers in hazard identification and to raise their awareness of the risks they face at the construction site through the use of emerging technologies such as Virtual Reality (VR) and Augmented Reality (AR). This paper presents the first intellectual output of an Erasmus+ project titled Construction Safety with Education and Training using Immersive Reality (CSETIR), whose goal is to examine and apply such VR and AR tools to improve the levels of H&S. Through the literature review and discussions with relevant stakeholders, most appropriate training methods were identified for the development of safety educational tools in the following project phases. VR and AR technologies have the potential to train construction workers in H&S, especially those who have little experience in construction safety, workers with literacy limitations and workers that do not speak the local language. Visual training tools, especially immersive ones, also provide better retention of acquired knowledge and skills. An immersive reality safety education tool, therefore, has the potential to increase the levels of construction H&S and to reduce the number of accidents at construction sites

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Achieving QVTO & ATL Interoperability: An Experience Report on the Realization of a QVTO to ATL Computer

With the emergence of a number of model transformation languages the need for interoperability among them increases. The degree at which this interoperability can be achieved between two given languages depends heavily on their paradigms (declarative vs imperative). Previous studies have indicated that the QVT and ATL languages are compatible. In this paper we study the possibility to compile QVT Operational to the ATL virtual machine. We describe our experience of developing such a compiler. The resulting compiled QVT transformations can run on top of existing ATL tools. Thereby we achieve not only QVT/ATL interoperability but also QVT conformance for the ATL tools as defined in the QVT specification

Recent trends related to the use of formal methods in software engineering

An account is given of some recent developments and trends related to the development and use of formal methods in software engineering. Ongoing activities in Europe are focussed on, since there seems to be a notable difference in attitude towards industrial usage of formal methods in Europe and in the U.S. A more detailed account is given of the currently most widespread formal method in Europe: the Vienna Development Method. Finally, the use of Ada is discussed in relation to the application of formal methods, and the potential for constructing Ada-specific tools based on that method is considered

Towards a General Framework for Formal Reasoning about Java Bytecode Transformation

Program transformation has gained a wide interest since it is used for several purposes: altering semantics of a program, adding features to a program or performing optimizations. In this paper we focus on program transformations at the bytecode level. Because these transformations may introduce errors, our goal is to provide a formal way to verify the update and establish its correctness. The formal framework presented includes a definition of a formal semantics of updates which is the base of a static verification and a scheme based on Hoare triples and weakest precondition calculus to reason about behavioral aspects in bytecode transformationComment: In Proceedings SCSS 2012, arXiv:1307.802

Verification of Timed Automata Using Rewrite Rules and Strategies

ELAN is a powerful language and environment for specifying and prototyping deduction systems in a language based on rewrite rules controlled by strategies. Timed automata is a class of continuous real-time models of reactive systems for which efficient model-checking algorithms have been devised. In this paper, we show that these algorithms can very easily be prototyped in the ELAN system. This paper argues through this example that rewriting based systems relying on rules and strategies are a good framework to prototype, study and test rather efficiently symbolic model-checking algorithms, i.e. algorithms which involve combination of graph exploration rules, deduction rules, constraint solving techniques and decision procedures

Pluggable AOP: Designing Aspect Mechanisms for Third-party Composition

Studies of Aspect-Oriented Programming (AOP) usually focus on a language in which a specific aspect extension is integrated with a base language. Languages specified in this manner have a fixed, non-extensible AOP functionality. In this paper we consider the more general case of integrating a base language with a set of domain specific third-party aspect extensions for that language. We present a general mixin-based method for implementing aspect extensions in such a way that multiple, independently developed, dynamic aspect extensions can be subject to third-party composition and work collaboratively