Physics-informed machine learning (PIML) is emerging as a potentially transformative paradigm for modeling complex biomedical systems by integrating parameterized physical laws with data-driven methods. Here, we review three main classes of PIML frameworks: physics-informed neural networks (PINNs), neural ordinary differential equations (NODEs), and neural operators (NOs), highlighting their growing role in biomedical science and engineering. We begin with PINNs, which embed governing equations into deep learning models and have been successfully applied to biosolid and biofluid mechanics, mechanobiology, and medical imaging among other areas. We then review NODEs, which offer continuous-time modeling, especially suited to dynamic physiological systems, pharmacokinetics, and cell signaling. Finally, we discuss deep NOs as powerful tools for learning mappings between function spaces, enabling efficient simulations across multiscale and spatially heterogeneous biological domains. Throughout, we emphasize applications where physical interpretability, data scarcity, or system complexity make conventional black-box learning insufficient. We conclude by identifying open challenges and fu
Digital Engineering, the digital transformation of engineering to leverage digital technologies, is coming globally. This paper explores digital systems engineering, which aims at developing theory, methods, models, and tools to support the emerging digital engineering. A critical task is to digitalize engineering artifacts, thus enabling information sharing across platform, across life cycle, and across domains. We identify significant challenges and enabling digital technologies; analyze the transition from traditional engineering to digital engineering; define core concepts, including "digitalization", "unique identification", "digitalized artifacts", "digital augmentation", and others; present a big picture of digital systems engineering in four levels: vision, strategy, action, and foundation; briefly discuss each of main areas of research issues. Digitalization enables fast infusing and leveraging novel digital technologies; unique identification enables information traceability and accountability in engineering lifecycle; provenance enables tracing dependency relations among engineering artifacts; supporting model reproducibility and replicability; helping with trustworthine
By treating data and models as the source code, Foundation Models (FMs) become a new type of software. Mirroring the concept of software crisis, the increasing complexity of FMs making FM crisis a tangible concern in the coming decade, appealing for new theories and methodologies from the field of software engineering. In this paper, we outline our vision of introducing Foundation Model (FM) engineering, a strategic response to the anticipated FM crisis with principled engineering methodologies. FM engineering aims to mitigate potential issues in FM development and application through the introduction of declarative, automated, and unified programming interfaces for both data and model management, reducing the complexities involved in working with FMs by providing a more structured and intuitive process for developers. Through the establishment of FM engineering, we aim to provide a robust, automated, and extensible framework that addresses the imminent challenges, and discovering new research opportunities for the software engineering field.
The introduction of large language models (LLMs) has enhanced automation in software engineering tasks, including in Model Driven Engineering (MDE). However, using general-purpose LLMs for domain modeling has its limitations. One approach is to adopt fine-tuned models, but this requires significant computational resources and can lead to issues like catastrophic forgetting. This paper explores how hyperparameter tuning and prompt engineering can improve the accuracy of the Llama 3.1 model for generating domain models from textual descriptions. We use search-based methods to tune hyperparameters for a specific medical data model, resulting in a notable quality improvement over the baseline LLM. We then test the optimized hyperparameters across ten diverse application domains. While the solutions were not universally applicable, we demonstrate that combining hyperparameter tuning with prompt engineering can enhance results across nearly all examined domain models.
The aerospace industry operates at the frontier of technological innovation while maintaining high standards regarding safety and reliability. In this environment, with an enormous potential for re-use and adaptation of existing solutions and methods, Knowledge-Based Engineering (KBE) has been applied for decades. The objective of this study is to identify and examine state-of-the-art knowledge management practices in the field of aerospace engineering. Our contributions include: 1) A SWARM-SLR of over 1,000 articles with qualitative analysis of 164 selected articles, supported by two aerospace engineering domain expert surveys. 2) A knowledge graph of over 700 knowledge-based aerospace engineering processes, software, and data, formalized in the interoperable Web Ontology Language (OWL) and mapped to Wikidata entries where possible. The knowledge graph is represented on the Open Research Knowledge Graph (ORKG), and an aerospace Wikibase, for reuse and continuation of structuring aerospace engineering knowledge exchange. 3) Our resulting intermediate and final artifacts of the knowledge synthesis, available as a Zenodo dataset. This review sets a precedent for structured, semantic-
Developing complex, reliable advanced accelerators requires a coordinated, extensible, and comprehensive approach in modeling, from source to the end of beam lifetime. We present highlights in Exascale Computing to scale accelerator modeling software to the requirements set for contemporary science drivers. In particular, we present the first laser-plasma modeling on an exaflop supercomputer using the US DOE Exascale Computing Project WarpX. Leveraging developments for Exascale, the new DOE SCIDAC-5 Consortium for Advanced Modeling of Particle Accelerators (CAMPA) will advance numerical algorithms and accelerate community modeling codes in a cohesive manner: from beam source, over energy boost, transport, injection, storage, to application or interaction. Such start-to-end modeling will enable the exploration of hybrid accelerators, with conventional and advanced elements, as the next step for advanced accelerator modeling. Following open community standards, we seed an open ecosystem of codes that can be readily combined with each other and machine learning frameworks. These will cover ultrafast to ultraprecise modeling for future hybrid accelerator design, even enabling virtual t
The rapid emergence of generative AI models like Large Language Models (LLMs) has demonstrated its utility across various activities, including within Requirements Engineering (RE). Ensuring the quality and accuracy of LLM-generated output is critical, with prompt engineering serving as a key technique to guide model responses. However, existing literature provides limited guidance on how prompt engineering can be leveraged, specifically for RE activities. The objective of this study is to explore the applicability of existing prompt engineering guidelines for the effective usage of LLMs within RE. To achieve this goal, we began by conducting a systematic review of primary literature to compile a non-exhaustive list of prompt engineering guidelines. Then, we conducted interviews with RE experts to present the extracted guidelines and gain insights on the advantages and limitations of their application within RE. Our literature review indicates a shortage of prompt engineering guidelines for domain-specific activities, specifically for RE. Our proposed mapping contributes to addressing this shortage. We conclude our study by identifying an important future line of research within th
The prevailing net-centric environment demands and enables modeling and simulation to combine efforts from numerous disciplines. Software techniques and methodology, in particular service-oriented architecture, provide such an opportunity. Service-oriented simulation has been an emerging paradigm following on from object- and process-oriented methods. However, the ad-hoc frameworks proposed so far generally focus on specific domains or systems and each has its pros and cons. They are capable of addressing different issues within service-oriented simulation from different viewpoints. It is increasingly important to describe and evaluate the progress of numerous frameworks. In this paper, we propose a novel three-dimensional reference model for a service-oriented simulation paradigm. The model can be used as a guideline or an analytic means to find the potential and possible future directions of the current simulation frameworks. In particular, the model inspects the crossover between the disciplines of modeling and simulation, service-orientation, and software/systems engineering. Based on the model, we present a comprehensive survey on several classical service-oriented simulation
Context: The use of standards is considered a vital part of any engineering discipline. So one could expect that standards play an important role in Requirements Engineering (RE) as well. However, little is known about the actual knowledge and use of RE-related standards in industry. Objective: In this article, we investigate to which extent standards and related artifacts such as templates or guidelines are known and used by RE practitioners. Method: To this end, we have conducted a questionnaire-based online survey. We could analyze the replies from 90 RE practitioners using a combination of closed and open-text questions. Results: Our results indicate that the knowledge and use of standards and related artifacts in RE is less widespread than one might expect from an engineering perspective. For example, about 47% of the respondents working as requirements engineers or business analysts do not know the core standard in RE, ISO/IEC/IEEE 29148. Participants in our study mostly use standards by personal decision rather than being imposed by their respective company, customer, or regulator. Beyond insufficient knowledge, we also found cultural and organizational factors impeding the
Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other scientific disciplines, in software engineering, we are still struggling in adapting open science to the particularities of our discipline, rendering progress in our scientific community cumbersome. In this chapter, we reflect upon the essentials in open science for software engineering including what open science is, why we should engage in it, and how we should do it. We particularly draw from our experiences made as conference chairs implementing open science initiatives and as researchers actively engaging in open science to critically discuss challenges and pitfalls, and to address more advanced topics such as how and under which conditions to share preprints, what infrastructure and licence model to cover, or how do it within the limitations of different reviewing models, such as double-blind reviewing. Our hope is to help establishing a common ground and to contribute to make open science a norm also in software engineering.
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, or migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language to describe cellular dynamics must be able to naturally represent complex intra and extra-cellular spatial structures, and coupled mechanical, chemical and electrical processes. In order to be useful to domain experts, a modeling language should be based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated construct
Over twenty years ago, the Software Engineering (SE) research community have been involved with Evidence-Based Software Engineering (EBSE). EBSE aims to inform industrial practice with the best evidence from rigorous research, preferably from systematic literature reviews (SLRs). Since then, SE researchers have conducted many SLRs, perfected their SLR procedures, proposed alternative ways of presenting their results (such as Evidence Briefings), and profusely discussed how to conduct research that impacts practice. Nevertheless, there is still a feeling that SLRs' results are not reaching practitioners. Something is missing. In this vision paper, we introduce Evidence to Decision (EtD) frameworks from the health sciences, which propose gathering experts in panels to assess the existing best evidence about the impact of an intervention in all relevant outcomes and make structured recommendations based on them. The insight we can leverage from EtD frameworks is not their structure per se but all the relevant criteria for making recommendations to practitioners from SLRs. Furthermore, we provide a worked example based on an SE SLR. We also discuss the challenges the SE research and pr
Large-scale simulations play a central role in science and the industry. Several challenges occur when building simulation software, because simulations require complex software developed in a dynamic construction process. That is why simulation software engineering (SSE) is emerging lately as a research focus. The dichotomous trade-off between scalability and efficiency (SE) on the one hand and maintainability and portability (MP) on the other hand is one of the core challenges. We report on the SE/MP trade-off in the context of an ongoing systematic literature review (SLR). After characterizing the issue of the SE/MP trade-off using two examples from our own research, we (1) review the 33 identified articles that assess the trade-off, (2) summarize the proposed solutions for the trade-off, and (3) discuss the findings for SSE and future work. Overall, we see evidence for the SE/MP trade-off and first solution approaches. However, a strong empirical foundation has yet to be established; general quantitative metrics and methods supporting software developers in addressing the trade-off have to be developed. We foresee considerable future work in SSE across scientific communities.
The ability of Generative AI (GAI) technology to automatically check, synthesize and modify software engineering artifacts promises to revolutionize all aspects of software engineering. Using GAI for software engineering tasks is consequently one of the most rapidly expanding fields of software engineering research, with over a hundred LLM-based code models having been published since 2021. However, the overwhelming majority of existing code models share a major weakness - they are exclusively trained on the syntactic facet of software, significantly lowering their trustworthiness in tasks dependent on software semantics. To address this problem, a new class of "Morescient" GAI is needed that is "aware" of (i.e., trained on) both the semantic and static facets of software. This, in turn, will require a new generation of software observation platforms capable of generating large quantities of execution observations in a structured and readily analyzable way. In this paper, we present a vision and roadmap for how such "Morescient" GAI models can be engineered, evolved and disseminated according to the principles of open science.
Civic grassroots have proven their ability to create useful and scalable software that addresses pressing social needs. Although software engineering plays a fundamental role in the process of creating civic technology, academic literature that analyses the software development processes of civic tech grassroots is scarce. This paper aims to advance the understanding of how civic grassroots tackle the different activities in their software development processes. In this study, we followed the formation of two projects in a civic tech group (Code for Ireland) seeking to understand how their development processes evolved over time, and how the group carried out their work in creating new technology. Our preliminary findings show that such groups are capable of setting up systematic software engineering processes that address software specification, development, validation, and evolution. While they were able to deliver software according to self-specified quality standards, the group has challenges in requirements specification, stakeholder engagement, and reorienting from development to product delivery. Software engineering methods and tools can effectively support the future of ci
Web Engineering is the application of systematic, disciplined and quantifiable approaches to development, operation, and maintenance of Web-based applications. It is both a pro-active approach and a growing collection of theoretical and empirical research in Web application development. This paper gives an overview of Web Engineering by addressing the questions: a) why is it needed? b) what is its domain of operation? c) how does it help and what should it do to improve Web application development? and d) how should it be incorporated in education and training? The paper discusses the significant differences that exist between Web applications and conventional software, the taxonomy of Web applications, the progress made so far and the research issues and experience of creating a specialisation at the master's level. The paper reaches a conclusion that Web Engineering at this stage is a moving target since Web technologies are constantly evolving, making new types of applications possible, which in turn may require innovations in how they are built, deployed and maintained.
Requirements Engineering (RE) has established itself as a software engineering discipline during the past decades. While researchers have been investigating the RE discipline with a plethora of empirical studies, attempts to systematically derive an empirically-based theory in context of the RE discipline have just recently been started. However, such a theory is needed if we are to define and motivate guidance in performing high quality RE research and practice. We aim at providing an empirical and valid foundation for a theory of RE, which helps software engineers establish effective and efficient RE processes. We designed a survey instrument and theory that has now been replicated in 10 countries world-wide. We evaluate the propositions of the theory with bootstrapped confidence intervals and derive potential explanations for the propositions. We report on the underlying theory and the full results obtained from the replication studies with participants from 228 organisations. Our results represent a substantial step forward towards developing an empirically-based theory of RE giving insights into current practices with RE processes. The results reveal, for example, that there a
In this third decade of systems engineering in the twenty-first century, it is important to develop and demonstrate practical methods to exploit machine-readable models in the engineering of systems. Substantial investment has been made in languages and modelling tools for developing models. A key problem is that system architects and engineers work in a multidisciplinary environment in which models are not the product of any one individual. This paper provides preliminary results of a formal approach to specify models and structure preserving transformations between them that support model synchronization. This is an important area of research and practice in software engineering. However, it is limited to synchronization at the code level of systems. This paper leverages previous research of the authors to define a core fractal for interpretation of concepts into model specifications and transformation between models. This fractal is used to extend the concept of synchronization of models to the system level and is demonstrated through a practical engineering example for an advanced driver assistance system.
Realisation of significant advances in capabilities of sensors, computing, timing, and communication enabled by quantum technologies is dependent on engineering highly complex systems that integrate quantum devices into existing classical infrastructure. A systems engineering approach is considered to address the growing need for quantum-secure telecommunications that overcome the threat to encryption caused by maturing quantum computation. This work explores a range of existing and future quantum communication networks, specifically quantum key distribution network proposals, to model and demonstrate the evolution of quantum key distribution network architectures. Leveraging Orthogonal Variability Modelling and Systems Modelling Language as candidate modelling languages, the study creates traceable artefacts to promote modular architectures that are reusable for future studies. We propose a variability-driven framework for managing fast-evolving network architectures with respect to increasing stakeholder expectations. The result contributes to the systematic development of viable quantum key distribution networks and supports the investigation of similar integration challenges re
Context: Citations are a key measure of scientific performance in most fields, including software engineering. However, there is limited research that studies which characteristics of articles' metadata (title, abstract, keywords, and author list) are driving citations in this field. Objective: In this study, we propose a simple theoretical model for how citations come to be with respect to article metadata, we hypothesize theoretical linkages between metadata characteristics and citations of articles, and we empirically test these hypotheses. Method: We use multiple regression analyses to examine a data set comprising the titles, abstracts, keywords, and authors of 16,131 software engineering articles published between 1990 and 2020 in 20 highly influential software engineering venues. Results: We find that number of authors, number of keywords, number of question marks and dividers in the title, number of acronyms, abstract length, abstract propositional idea density, and corresponding authors in the core Anglosphere are significantly related to citations. Conclusion: Various characteristics of articles' metadata are linked to the frequency with which the corresponding articles a