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Recent work has shown that Large Language Models (LLMs) are not only a suitable tool for code generation but also capable of generating annotation-based code specifications. Scaling these methodologies may allow us to deduce provable…
Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…
Optimizing compilers have become a cornerstone for high-performance program generation in research and industry. Optimizations, including those implemented manually by a user and those target-specific and non-target-specific, are used to…
Support vector machines (SVMs) are a standard tool for binary classification, but their classical formulations are purely data-driven and offer no direct way to encode trusted benchmark models or structured preferences on selected subsets…
Scientists increasingly recognize the importance of providing rich, standards-adherent metadata to describe their experimental results. Despite the availability of sophisticated tools to assist in the process of data annotation,…
Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results:…
Large Language Models (LLMs) are rapidly becoming ubiquitous both as stand-alone tools and as components of current and future software systems. To enable usage of LLMs in the high-stake or safety-critical systems of 2030, they need to…
Validation is one of the software engineering disciplines that help build quality into software. The major objective of software validation process is to determine that the software performs its intended functions correctly and provide…
This survey aims at providing a comprehensive overview of the recent trends in the field of modeling and simulation (M&S) of interactions between users and recommender systems and applications of the M&S to the performance improvement of…
In this paper we will present SDeval, a software project that contains tools for creating and running benchmarks with a focus on problems in computer algebra. It is built on top of the Symbolic Data project, able to translate problems in…
The quality and correct functioning of software components embedded in electronic systems are of utmost concern especially for safety and mission-critical systems. Model-based testing and formal verification techniques can be employed to…
In the digital age, ensuring the correctness, safety, and reliability of software through formal verification is paramount, particularly as software increasingly underpins critical infrastructure. Formal verification, split into theorem…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
Rigorous software testing is crucial for developing and maintaining high-quality code, making automated test generation a promising avenue for both improving software quality and boosting the effectiveness of code generation methods.…
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed--the CEDAR Workbench--is a suite of Web-based tools and…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
Program analysis is on the brink of mainstream in embedded systems development. Formal verification of behavioural requirements, finding runtime errors and automated test case generation are some of the most common applications of automated…
Simulation has become an essential component of designing and developing scientific experiments. The conventional procedural approach to coding simulations of complex experiments is often error-prone, hard to interpret, and inflexible,…