搜索结果：Bioprocess and biosystems engineering

This paper explores how generative AI can help automate and improve key steps in systems engineering. It examines AI's ability to analyze system requirements based on INCOSE's "good requirement" criteria, identifying well-formed and poorly written requirements. The AI does not just classify requirements but also explains why some do not meet the standards. By comparing AI assessments with those of experienced engineers, the study evaluates the accuracy and reliability of AI in identifying quality issues. Additionally, it explores AI's ability to classify functional and non-functional requirements and generate test specifications based on these classifications. Through both quantitative and qualitative analysis, the research aims to assess AI's potential to streamline engineering processes and improve learning outcomes. It also highlights the challenges and limitations of AI, ensuring its safe and ethical use in professional and academic settings.

Empirical research in reverse engineering and software protection is crucial for evaluating the efficacy of methods designed to protect software against unauthorized access and tampering. However, conducting such studies with professional reverse engineers presents significant challenges, including access to professionals and affordability. This paper explores the use of students as participants in empirical reverse engineering experiments, examining their suitability and the necessary training; the design of appropriate challenges; strategies for ensuring the rigor and validity of the research and its results; ways to maintain students' privacy, motivation, and voluntary participation; and data collection methods. We present a systematic literature review of existing reverse engineering experiments and user studies, a discussion of related work from the broader domain of software engineering that applies to reverse engineering experiments, an extensive discussion of our own experience running experiments ourselves in the context of a master-level software hacking and protection course, and recommendations based on this experience. Our findings aim to guide future empirical studies

Software Engineering (SE) faces simultaneous pressure from AI automation (reducing code production costs) and hardware-energy constraints (amplifying failure costs). We position that SE must redefine itself around human discernment-intent articulation, architectural control, and verification-rather than code construction. This shift introduces accountability collapse as a central risk and requires fundamental changes to research priorities, educational curricula, and industrial practices. We argue that Software Engineering, as traditionally defined around code construction and process management, is no longer sufficient. Instead, the discipline must be redefined around intent articulation, architectural control, and systematic verification. This redefinition shifts Software Engineering from a production-oriented field to one centered on human judgment under automation, with profound implications for research, practice, and education.

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

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-

Research in software engineering is essential for improving development practices, leading to reliable and secure software. Leveraging the principles of quantum physics, quantum computing has emerged as a new computational paradigm that offers significant advantages over classical computing. As quantum computing progresses rapidly, its potential applications across various fields are becoming apparent. In software engineering, many tasks involve complex computations where quantum computers can greatly speed up the development process, leading to faster and more efficient solutions. With the growing use of quantum-based applications in different fields, quantum software engineering (QSE) has emerged as a discipline focused on designing, developing, and optimizing quantum software for diverse applications. This paper aims to review the role of quantum computing in software engineering research and the latest developments in QSE. To our knowledge, this is the first comprehensive review on this topic. We begin by introducing quantum computing, exploring its fundamental concepts, and discussing its potential applications in software engineering. We also examine various QSE techniques th

Efficient and robust bioprocess control is essential for maximizing performance and adaptability in advanced biotechnological systems. In this work, we present a reinforcement-learning framework for multi-setpoint and multi-trajectory tracking. Tracking multiple setpoints and time-varying trajectories in reinforcement learning is challenging due to the complexity of balancing multiple objectives, a difficulty further exacerbated by system uncertainties such as uncertain initial conditions and stochastic dynamics. This challenge is relevant, e.g., in bioprocesses involving microbial consortia, where precise control over population compositions is required. We introduce a novel return function based on multiplicative reciprocal saturation functions, which explicitly couples reward gains to the simultaneous satisfaction of multiple references. Through a case study involving light-mediated cybergenetic growth control in microbial consortia, we demonstrate via computational experiments that our approach achieves faster convergence, improved stability, and superior control compliance compared to conventional quadratic-cost-based return functions. Moreover, our method enables tuning of th

Bioprocesses are central to modern biotechnology, enabling sustainable production in pharmaceuticals, specialty chemicals, cosmetics, and food. However, developing high-performing processes is costly and complex, requiring iterative, multi-scale experimentation from microtiter plates to pilot reactors. Conventional Design of Experiments (DoE) approaches often struggle to address process scale-up and the joint optimization of reaction conditions and biocatalyst selection. We propose a multi-fidelity batch Bayesian optimization framework to accelerate bioprocess development and reduce experimental costs. The method integrates Gaussian Processes tailored for multi-fidelity modeling and mixed-variable optimization, guiding experiment selection across scales and biocatalysts. A custom simulation of a Chinese Hamster Ovary bioprocess, capturing non-linear and coupled scale-up dynamics, is used for benchmarking against multiple simulated industrial DoE baselines. Multiple case studies show how the proposed workflow can achieve a reduction in experimental costs and increased yield. This work provides a data-efficient strategy for bioprocess optimization and highlights future opportunities

Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small datasets, and provide adaptive suggestions for sequential experimentation. While still in its infancy, Bayesian optimization has recently gained traction in bioprocess engineering. However, experimentation with biological systems is highly complex and the resulting experimental uncertainty requires specific extensions to classical Bayesian optimization. Moreover, current literature often targets readers with a strong statistical background, limiting its accessibility for practitioners. In light of these developments, this review has two aims: first, to provide an intuitive and practical introduction to Bayesian optimization; and second, to outline promising application areas and open algorithmic challenges, thereby highlighting opportunities for future research in machine learning.

Agile software development relies on self-organized teams, underlining the importance of individual responsibility. How developers take responsibility and build ownership are influenced by external factors such as architecture and development methods. This paper examines the existing literature on ownership in software engineering and in psychology, and argues that a more comprehensive view of ownership in software engineering has a great potential in improving software team's work. Initial positions on the issue are offered for discussion and to lay foundations for further research.

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

For decades, much software engineering research has been dedicated to devising automated solutions aimed at enhancing developer productivity and elevating software quality. The past two decades have witnessed an unparalleled surge in the development of intelligent solutions tailored for software engineering tasks. This momentum established the Artificial Intelligence for Software Engineering (AI4SE) area, which has swiftly become one of the most active and popular areas within the software engineering field. This Future of Software Engineering (FoSE) paper navigates through several focal points. It commences with a succinct introduction and history of AI4SE. Thereafter, it underscores the core challenges inherent to AI4SE, particularly highlighting the need to realize trustworthy and synergistic AI4SE. Progressing, the paper paints a vision for the potential leaps achievable if AI4SE's key challenges are surmounted, suggesting a transition towards Software Engineering 2.0. Two strategic roadmaps are then laid out: one centered on realizing trustworthy AI4SE, and the other on fostering synergistic AI4SE. While this paper may not serve as a conclusive guide, its intent is to catalyze

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.

Machine learning (ML) is becoming increasingly crucial in many fields of engineering but has not yet played out its full potential in bioprocess engineering. While experimentation has been accelerated by increasing levels of lab automation, experimental planning and data modeling are still largerly depend on human intervention. ML can be seen as a set of tools that contribute to the automation of the whole experimental cycle, including model building and practical planning, thus allowing human experts to focus on the more demanding and overarching cognitive tasks. First, probabilistic programming is used for the autonomous building of predictive models. Second, machine learning automatically assesses alternative decisions by planning experiments to test hypotheses and conducting investigations to gather informative data that focus on model selection based on the uncertainty of model predictions. This review provides a comprehensive overview of ML-based automation in bioprocess development. On the one hand, the biotech and bioengineering community should be aware of the potential and, most importantly, the limitation of existing ML solutions for their application in biotechnology an

Software engineering researchers repeatedly argue that the impact of their research on industrial practice, while desired and intended, is rarely achieved. We believe that a possible explanation of this phenomenon is the opposition of "caring about" and "caring for", based on the ethics of care. Indeed, while software engineering is collaborative and hence builds on interpersonal relations, researchers tend to care about "industrial impact" and "practitioners" in abstract terms, but rarely care for specific individuals working in specific contexts facing specific challenges. In this position paper, we advocate for the adoption of ethics of care in software engineering and discuss the implications of this adoption for researchers and conference organizers.

The software engineering researchers from countries with smaller economies, particularly non-English speaking ones, represent valuable minorities within the software engineering community. As researchers from Poland, we represent such a country. We analyzed the ICSE FOSE (Future of Software Engineering) community survey through reflexive thematic analysis to show our viewpoint on key software community issues. We believe that the main problem is the growing research-industry gap, which particularly impacts smaller communities and small local companies. Based on this analysis and our experiences, we present a set of recommendations for improvements that would enhance software engineering research and industrial collaborations in smaller economies.

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

Peer review is the main mechanism by which the software engineering community assesses the quality of scientific results. However, the rapid growth of paper submissions in software engineering venues has outpaced the availability of qualified reviewers, creating a growing imbalance that risks constraining and negatively impacting the long-term growth of the Software Engineering (SE) research community. Our vision of the Future of the SE research landscape involves a more scalable, inclusive, and resilient peer review process that incorporates additional mechanisms for: 1) attracting and training newcomers to serve as high-quality reviewers, 2) incentivizing more community members to serve as peer reviewers, and 3) cautiously integrating AI tools to support a high-quality review process.

The discussion around AI-Engineering, that is, Software Engineering (SE) for AI-enabled Systems, cannot ignore a crucial class of software systems that are increasingly becoming AI-enhanced: Those used to enable or support the SE process, such as Computer-Aided SE (CASE) tools and Integrated Development Environments (IDEs). In this paper, we study the energy efficiency of these systems. As AI becomes seamlessly available in these tools and, in many cases, is active by default, we are entering a new era with significant implications for energy consumption patterns throughout the Software Development Lifecycle (SDLC). We focus on advanced Machine Learning (ML) capabilities provided by Large Language Models (LLMs). Our proposed approach combines Retrieval-Augmented Generation (RAG) with Prompt Engineering Techniques (PETs) to enhance both the quality and energy efficiency of LLM-based code generation. We present a comprehensive framework that measures real-time energy consumption and inference time across diverse model architectures ranging from 125M to 7B parameters, including GPT-2, CodeLlama, Qwen 2.5, and DeepSeek Coder. These LLMs, chosen for practical reasons, are sufficient to