Renaming Global Variables in C Mechanically Proved Correct

Most integrated development environments are shipped with refactoring tools. However, their refactoring operations are often known to be unreliable. As a consequence, developers have to test their code after applying an automatic refactoring. In this article, we consider a refactoring operation (renaming of global variables in C), and we prove that its core implementation preserves the set of possible behaviors of transformed programs. That proof of correctness relies on the operational semantics of C provided by CompCert C in Coq.Comment: In Proceedings VPT 2016, arXiv:1607.0183

An Ontology Based Method to Solve Query Identifier Heterogeneity in Post-Genomic Clinical Trials

The increasing amount of information available for biomedical research has led to issues related to knowledge discovery in large collections of data. Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains—e.g. clinical and genetic data. One of the goals, among others, of the ACGT European is to provide seamless and homogeneous access to integrated databases. In this work, we describe an approach to overcome heterogeneities in identifiers inside queries. We present an ontology classifying the most common identifier semantic heterogeneities, and a service that makes use of it to cope with the problem using the described approach. Finally, we illustrate the solution by analysing a set of real queries

Interactive exploration of population scale pharmacoepidemiology datasets

Population-scale drug prescription data linked with adverse drug reaction (ADR) data supports the fitting of models large enough to detect drug use and ADR patterns that are not detectable using traditional methods on smaller datasets. However, detecting ADR patterns in large datasets requires tools for scalable data processing, machine learning for data analysis, and interactive visualization. To our knowledge no existing pharmacoepidemiology tool supports all three requirements. We have therefore created a tool for interactive exploration of patterns in prescription datasets with millions of samples. We use Spark to preprocess the data for machine learning and for analyses using SQL queries. We have implemented models in Keras and the scikit-learn framework. The model results are visualized and interpreted using live Python coding in Jupyter. We apply our tool to explore a 384 million prescription data set from the Norwegian Prescription Database combined with a 62 million prescriptions for elders that were hospitalized. We preprocess the data in two minutes, train models in seconds, and plot the results in milliseconds. Our results show the power of combining computational power, short computation times, and ease of use for analysis of population scale pharmacoepidemiology datasets. The code is open source and available at: https://github.com/uit-hdl/norpd_prescription_analyse

An overview of Mirjam and WeaveC

In this chapter, we elaborate on the design of an industrial-strength aspectoriented programming language and weaver for large-scale software development. First, we present an analysis on the requirements of a general purpose aspect-oriented language that can handle crosscutting concerns in ASML software. We also outline a strategy on working with aspects in large-scale software development processes. In our design, we both re-use existing aspect-oriented language abstractions and propose new ones to address the issues that we identified in our analysis. The quality of the code ensured by the realized language and weaver has a positive impact both on maintenance effort and lead-time in the first line software development process. As evidence, we present a short evaluation of the language and weaver as applied today in the software development process of ASML

Semantic Analysis of Macro Usage for Portability

C is an unsafe language. Researchers have been developing tools to port C to safer languages such as Rust, Checked C, or Go. Existing tools, however, resort to preprocessing the source file first, then porting the resulting code, leaving barely recognizable code that loses macro abstractions. To preserve macro usage, porting tools need analyses that understand macro behavior to port to equivalent constructs. But macro semantics differ from typical functions, precluding simple syntactic transformations to port them. We introduce the first comprehensive framework for analyzing the portability of macro usage. We decompose macro behavior into 26 fine-grained properties and implement a program analysis tool, called Maki, that identifies them in real-world code with 94% accuracy. We apply Maki to 21 programs containing a total of 86,199 macro definitions. We found that real-world macros are much more portable than previously known. More than a third (37%) are easy-to-port, and Maki provides hints for porting more complicated macros. We find, on average, 2x more easy-to-port macros and up to 7x more in the best case compared to prior work. Guided by Maki's output, we found and hand-ported macros in four real-world programs. We submitted patches to Linux maintainers that transform eleven macros, nine of which have been accepted.Comment: 12 pages. 4 figures. 2 tables. To appear in the 2024 IEEE/ACM 46th International Conference on Software Engineering (ICSE '24), April 14-20, 2024, Lisbon, Portugal. See https://zenodo.org/doi/10.5281/zenodo.7783131 for the latest version of the artifact associated with this pape