Medicine, including fields in healthcare and life sciences, has seen a flurry of quantum-related activities and experiments in the last few years (although biology and quantum theory have arguably been entangled ever since Schrödinger's cat). The initial focus was on biochemical and computational biology problems; recently, however, clinical and medical quantum solutions have drawn increasing interest. The rapid emergence of quantum computing in health and medicine necessitates a mapping of the landscape. In this review, clinical and medical proof-of-concept quantum computing applications are outlined and put into perspective. These consist of over 40 experimental and theoretical studies. The use case areas span genomics, clinical research and discovery, diagnostics, and treatments and interventions. Quantum machine learning (QML) in particular has rapidly evolved and shown to be competitive with classical benchmarks in recent medical research. Near-term QML algorithms have been trained with diverse clinical and real-world data sets. This includes studies in generating new molecular entities as drug candidates, diagnosing based on medical image classification, predicting patient pe
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
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
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
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
Model Medicine is the science of understanding, diagnosing, treating, and preventing disorders in AI models, grounded in the principle that AI models -- like biological organisms -- have internal structures, dynamic processes, heritable traits, observable symptoms, classifiable conditions, and treatable states. This paper introduces Model Medicine as a research program, bridging the gap between current AI interpretability research (anatomical observation) and the systematic clinical practice that complex AI systems increasingly require. We present five contributions: (1) a discipline taxonomy organizing 15 subdisciplines across four divisions -- Basic Model Sciences, Clinical Model Sciences, Model Public Health, and Model Architectural Medicine; (2) the Four Shell Model (v3.3), a behavioral genetics framework empirically grounded in 720 agents and 24,923 decisions from the Agora-12 program, explaining how model behavior emerges from Core--Shell interaction; (3) Neural MRI (Model Resonance Imaging), a working open-source diagnostic tool mapping five medical neuroimaging modalities to AI interpretability techniques, validated through four clinical cases demonstrating imaging, compari
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.
Hydro-Science and Engineering (Hydro-SE) is a critical and irreplaceable domain that secures human water supply, generates clean hydropower energy, and mitigates flood and drought disasters. Featuring multiple engineering objectives, Hydro-SE is an inherently interdisciplinary domain that integrates scientific knowledge with engineering expertise. This integration necessitates extensive expert collaboration in decision-making, which poses difficulties for intelligence. With the rapid advancement of large language models (LLMs), their potential application in the Hydro-SE domain is being increasingly explored. However, the knowledge and application abilities of LLMs in Hydro-SE have not been sufficiently evaluated. To address this issue, we propose the Hydro-SE LLM evaluation benchmark (Hydro-SE Bench), which contains 4,000 multiple-choice questions. Hydro-SE Bench covers nine subfields and enables evaluation of LLMs in aspects of basic conceptual knowledge, engineering application ability, and reasoning and calculation ability. The evaluation results on Hydro-SE Bench show that the accuracy values vary among 0.74 to 0.80 for commercial LLMs, and among 0.41 to 0.68 for small-paramet
Labeling or classifying time series is a persistent challenge in the physical sciences, where expert annotations are scarce, costly, and often inconsistent. Yet robust labeling is essential to enable machine learning models for understanding, prediction, and forecasting. We present the \textit{Clustering and Indexation Pipeline with Human Evaluation for Recognition} (CIPHER), a framework designed to accelerate large-scale labeling of complex time series in physics. CIPHER integrates \textit{indexable Symbolic Aggregate approXimation} (iSAX) for interpretable compression and indexing, density-based clustering (HDBSCAN) to group recurring phenomena, and a human-in-the-loop step for efficient expert validation. Representative samples are labeled by domain scientists, and these annotations are propagated across clusters to yield systematic, scalable classifications. We evaluate CIPHER on the task of classifying solar wind phenomena in OMNI data, a central challenge in space weather research, showing that the framework recovers meaningful phenomena such as coronal mass ejections and stream interaction regions. Beyond this case study, CIPHER highlights a general strategy for combining sy
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
With the increasing interest in deploying Artificial Intelligence in medicine, we previously introduced HAIM (Holistic AI in Medicine), a framework that fuses multimodal data to solve downstream clinical tasks. However, HAIM uses data in a task-agnostic manner and lacks explainability. To address these limitations, we introduce xHAIM (Explainable HAIM), a novel framework leveraging Generative AI to enhance both prediction and explainability through four structured steps: (1) automatically identifying task-relevant patient data across modalities, (2) generating comprehensive patient summaries, (3) using these summaries for improved predictive modeling, and (4) providing clinical explanations by linking predictions to patient-specific medical knowledge. Evaluated on the HAIM-MIMIC-MM dataset, xHAIM improves average AUC from 79.9% to 90.3% across chest pathology and operative tasks. Importantly, xHAIM transforms AI from a black-box predictor into an explainable decision support system, enabling clinicians to interactively trace predictions back to relevant patient data, bridging AI advancements with clinical utility.
Various research initiatives try to utilize the operational principles of organisms and brains to develop alternative, biologically inspired computing paradigms and artificial cognitive systems. This paper reviews key features of the standard method applied to complexity in the cognitive and brain sciences, i.e. decompositional analysis or reverse engineering. The indisputable complexity of brain and mind raise the issue of whether they can be understood by applying the standard method. Actually, recent findings in the experimental and theoretical fields, question central assumptions and hypotheses made for reverse engineering. Using the modeling relation as analyzed by Robert Rosen, the scientific analysis method itself is made a subject of discussion. It is concluded that the fundamental assumption of cognitive science, i.e. complex cognitive systems can be analyzed, understood and duplicated by reverse engineering, must be abandoned. Implications for investigations of organisms and behavior as well as for engineering artificial cognitive systems are discussed.
Background: Harnessing advanced computing for scientific discovery and technological innovation demands scientists and engineers well-versed in both domain science and computational science and engineering (CSE). However, few universities provide access to both integrated domain science/CSE cross-training and Top-500 High-Performance Computing (HPC) facilities. National laboratories offer internship opportunities capable of developing these skills. Purpose: This student presents an evaluation of federally-funded postgraduate internship outcomes at a national laboratory. This study seeks to answer three questions: 1) What computational skills, research skills, and professional skills do students improve through internships at the selected national laboratory. 2) Do students gain knowledge in domain science topics through their internships. 3) Do students' career interests change after these internships? Design/Method: We developed a survey and collected responses from past participants of five federally-funded internship programs and compare participant ratings of their prior experience to their internship experience. Findings: Our results indicate that participants improve CSE skil
Publication selection bias undermines the systematic accumulation of evidence. To assess the extent of this problem, we survey over 68,000 meta-analyses containing over 700,000 effect size estimates from medicine (67,386/597,699), environmental sciences (199/12,707), psychology (605/23,563), and economics (327/91,421). Our results indicate that meta-analyses in economics are the most severely contaminated by publication selection bias, closely followed by meta-analyses in environmental sciences and psychology, whereas meta-analyses in medicine are contaminated the least. After adjusting for publication selection bias, the median probability of the presence of an effect decreased from 99.9% to 29.7% in economics, from 98.9% to 55.7% in psychology, from 99.8% to 70.7% in environmental sciences, and from 38.0% to 29.7% in medicine. The median absolute effect sizes (in terms of standardized mean differences) decreased from d = 0.20 to d = 0.07 in economics, from d = 0.37 to d = 0.26 in psychology, from d = 0.62 to d = 0.43 in environmental sciences, and from d = 0.24 to d = 0.13 in medicine.
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.
Machine learning is rapidly making its pathway across all of the natural sciences, including physical sciences. The rate at which ML is impacting non-scientific disciplines is incomparable to that in the physical sciences. This is partly due to the uninterpretable nature of deep neural networks. Symbolic machine learning stands as an equal and complementary partner to numerical machine learning in speeding up scientific discovery in physics. This perspective discusses the main differences between the ML and scientific approaches. It stresses the need to develop and apply symbolic machine learning to physics problems equally, in parallel to numerical machine learning, because of the dual nature of physics research.
Background: Despite a long history, numerous laws and regulations, ethics remains an unnatural topic for many software engineering researchers. Poor research ethics may lead to mistrust of research results, lost funding and retraction of publications. A core principle for research ethics is confidentiality, and anonymization is a standard approach to guarantee it. Many guidelines for qualitative software engineering research, and for qualitative research in general, exist, but these do not penetrate how and why to anonymize interview data. Aims: In this paper we aim to identify ethical guidelines for software engineering interview studies involving industrial practitioners. Method: By learning from previous experiences and listening to the authority of existing guidelines in the more mature field of medicine as well as in software engineering, a comprehensive set of checklists for interview studies was distilled. Results: The elements of an interview study were identified and ethical considerations and recommendations for each step were produced, in particular with respect to anonymization. Important ethical principles are: consent, beneficence, confidentiality, scientific value, r
Symbolic regression (SR) has emerged as a powerful method for uncovering interpretable mathematical relationships from data, offering a novel route to both scientific discovery and efficient empirical modelling. This article introduces the Special Issue on Symbolic Regression for the Physical Sciences, motivated by the Royal Society discussion meeting held in April 2025. The contributions collected here span applications from automated equation discovery and emergent-phenomena modelling to the construction of compact emulators for computationally expensive simulations. The introductory review outlines the conceptual foundations of SR, contrasts it with conventional regression approaches, and surveys its main use cases in the physical sciences, including the derivation of effective theories, empirical functional forms and surrogate models. We summarise methodological considerations such as search-space design, operator selection, complexity control, feature selection, and integration with modern AI approaches. We also highlight ongoing challenges, including scalability, robustness to noise, overfitting and computational complexity. Finally we emphasise emerging directions, particula
Large Language Models (LLMs) are increasingly integrated into software applications, giving rise to a broad class of prompt-enabled systems, in which prompts serve as the primary 'programming' interface for guiding system behavior. Building on this trend, a new software paradigm, promptware, has emerged, which treats natural language prompts as first-class software artifacts for interacting with LLMs. Unlike traditional software, which relies on formal programming languages and deterministic runtime environments, promptware is based on ambiguous, unstructured, and context-dependent natural language and operates on LLMs as runtime environments, which are probabilistic and non-deterministic. These fundamental differences introduce unique challenges in prompt development. In practice, prompt development remains largely ad hoc and relies heavily on time-consuming trial-and-error, a challenge we term the promptware crisis. To address this, we propose promptware engineering, a new methodology that adapts established Software Engineering (SE) principles to prompt development. Drawing on decades of success in traditional SE, we envision a systematic framework encompassing prompt requiremen