Describing and Organizing Semantic Web and Machine Learning Systems in the SWeMLS-KG

In line with the general trend in artificial intelligence research to create intelligent systems that combine learning and symbolic components, a new sub-area has emerged that focuses on combining machine learning (ML) components with techniques developed by the Semantic Web (SW) community - Semantic Web Machine Learning (SWeML for short). Due to its rapid growth and impact on several communities in the last two decades, there is a need to better understand the space of these SWeML Systems, their characteristics, and trends. Yet, surveys that adopt principled and unbiased approaches are missing. To fill this gap, we performed a systematic study and analyzed nearly 500 papers published in the last decade in this area, where we focused on evaluating architectural, and application-specific features. Our analysis identified a rapidly growing interest in SWeML Systems, with a high impact on several application domains and tasks. Catalysts for this rapid growth are the increased application of deep learning and knowledge graph technologies. By leveraging the in-depth understanding of this area acquired through this study, a further key contribution of this paper is a classification system for SWeML Systems which we publish as ontology.Comment: Preprint of a paper in the resource track of the 20th Extended Semantic Web Conference (ESWC'23

Using the ResearchEHR platform to facilitate the practical application of the EHR standards

Possibly the most important requirement to support co-operative work among health professionals and institutions is the ability of sharing EHRs in a meaningful way, and it is widely acknowledged that standardization of data and concepts is a prerequisite to achieve semantic interoperability in any domain. Different international organizations are working on the definition of EHR architectures but the lack of tools that implement them hinders their broad adoption. In this paper we present ResearchEHR, a software platform whose objective is to facilitate the practical application of EHR standards as a way of reaching the desired semantic interoperability. This platform is not only suitable for developing new systems but also for increasing the standardization of existing ones. The work reported here describes how the platform allows for the edition, validation, and search of archetypes, converts legacy data into normalized, archetypes extracts, is able to generate applications from archetypes and finally, transforms archetypes and data extracts into other EHR standards. We also include in this paper how ResearchEHR has made possible the application of the CEN/ISO 13606 standard in a real environment and the lessons learnt with this experience. © 2011 Elsevier Inc..This work has been partially supported by the Spanish Ministry of Science and Innovation under Grants TIN2010-21388-C02-01 and TIN2010-21388-C02-02, and by the Health Institute Carlos in through the RETICS Combiomed, RD07/0067/2001. Our most sincere thanks to the Hospital of Fuenlabrada in Madrid, including its Medical Director Pablo Serrano together with Marta Terron and Luis Lechuga for their support and work during the development of the medications reconciliation project.Maldonado Segura, JA.; Martínez Costa, C.; Moner Cano, D.; Menárguez-Tortosa, M.; Boscá Tomás, D.; Miñarro Giménez, JA.; Fernández-Breis, JT.... (2012). Using the ResearchEHR platform to facilitate the practical application of the EHR standards. Journal of Biomedical Informatics. 45(4):746-762. doi:10.1016/j.jbi.2011.11.004S74676245

Technologies and Applications for Big Data Value

This open access book explores cutting-edge solutions and best practices for big data and data-driven AI applications for the data-driven economy. It provides the reader with a basis for understanding how technical issues can be overcome to offer real-world solutions to major industrial areas. The book starts with an introductory chapter that provides an overview of the book by positioning the following chapters in terms of their contributions to technology frameworks which are key elements of the Big Data Value Public-Private Partnership and the upcoming Partnership on AI, Data and Robotics. The remainder of the book is then arranged in two parts. The first part “Technologies and Methods” contains horizontal contributions of technologies and methods that enable data value chains to be applied in any sector. The second part “Processes and Applications” details experience reports and lessons from using big data and data-driven approaches in processes and applications. Its chapters are co-authored with industry experts and cover domains including health, law, finance, retail, manufacturing, mobility, and smart cities. Contributions emanate from the Big Data Value Public-Private Partnership and the Big Data Value Association, which have acted as the European data community's nucleus to bring together businesses with leading researchers to harness the value of data to benefit society, business, science, and industry. The book is of interest to two primary audiences, first, undergraduate and postgraduate students and researchers in various fields, including big data, data science, data engineering, and machine learning and AI. Second, practitioners and industry experts engaged in data-driven systems, software design and deployment projects who are interested in employing these advanced methods to address real-world problems

Incorporation of ontologies in data warehouse/business intelligence systems - A systematic literature review

Semantic Web (SW) techniques, such as ontologies, are used in Information Systems (IS) to cope with the growing need for sharing and reusing data and knowledge in various research areas. Despite the increasing emphasis on unstructured data analysis in IS, structured data and its analysis remain critical for organizational performance management. This systematic literature review aims at analyzing the incorporation and impact of ontologies in Data Warehouse/Business Intelligence (DW/BI) systems, contributing to the current literature by providing a classification of works based on the field of each case study, SW techniques used, and the authors’ motivations for using them, with a focus on DW/BI design, development and exploration tasks. A search strategy was developed, including the definition of keywords, inclusion and exclusion criteria, and the selection of search engines. Ontologies are mainly defined using the Ontology Web Language standard to support multiple DW/BI tasks, such as Dimensional Modeling, Requirement Analysis, Extract-Transform-Load, and BI Application Design. Reviewed authors present a variety of motivations for ontology-driven solutions in DW/BI, such as eliminating or solving data heterogeneity/semantics problems, increasing interoperability, facilitating integration, or providing semantic content for requirements and data analysis. Further, implications for practice and research agenda are indicated.info:eu-repo/semantics/publishedVersio

Artificial Intelligence for Drug Discovery: Are We There Yet?

Drug discovery is adapting to novel technologies such as data science, informatics, and artificial intelligence (AI) to accelerate effective treatment development while reducing costs and animal experiments. AI is transforming drug discovery, as indicated by increasing interest from investors, industrial and academic scientists, and legislators. Successful drug discovery requires optimizing properties related to pharmacodynamics, pharmacokinetics, and clinical outcomes. This review discusses the use of AI in the three pillars of drug discovery: diseases, targets, and therapeutic modalities, with a focus on small molecule drugs. AI technologies, such as generative chemistry, machine learning, and multi-property optimization, have enabled several compounds to enter clinical trials. The scientific community must carefully vet known information to address the reproducibility crisis. The full potential of AI in drug discovery can only be realized with sufficient ground truth and appropriate human intervention at later pipeline stages.Comment: 30 pages, 4 figures, 184 reference

Understanding and Managing Medical Data and Knowledge Dynamics

For several decades, Artificial Intelligence is concerned with the definition of the concept of knowledge in order to exploit it for various purposes such as information retrieval, decision support or semantic interoperability. This is mainly done thanks to knowledge representation models such as ontologies aiming at representing and organising the concepts of a given domain. However, the evolution of these models and its impact on depending artefacts remain open research problems.The biomedical domain is specific in a sense that its associated knowledge is complex and constantly evolving as underlined by the ever increasing number of published scientific communications. This is why I have focus on this domain and its specificities have been the various lines I have followed during my research work.Three main thematics have focused my efforts over the past years:1- Biomedical knowledge representation2- The management of the evolution of biomedical knowledge representation models 3- The validation of biomedical knowledge representation models These topics are more largely detailed in this manuscriptDepuis plusieurs décennies, le domaine de l’Intelligence Artificielle s’intéresse à définir la notion de connaissance afin de l’exploiter à des fins diverses dans plusieurs cadres d’application tels que la recherche d’information, l’aide à la décision ou encore l’interopérabilité sémantique. Ceci est en partie réalisé grâce à l’utilisation de modèles de représentation des connaissances tels que les ontologies permettant la spécification d’une conceptualisation. Cependant, les aspects liés à l'évolution des connaissances et des modèles qui leur sont associés restent largement inexplorés et demeurent des problèmes de recherche ouverts.Le domaine biomédical est un domaine très riche dans la mesure où les connaissances qu’il intègre sont complexes et en perpétuelle évolution comme le démontre le nombre sans cesse croissant de communications scientifiques publiées au quotidien. C’est pour ces raisons qu’il a suscité mon intérêt et ses spécificités ont constitué la ligne directrice de mes activités de recherche.Trois grandes thématiques ont focalisé mes efforts au cours de ces dernières années et ont concentré la majeure partie de mes contributions scientifiques et collaborations dans ce domaine particulier.1- La représentation des connaissances en santé.2- La gestion de l'évolution des modèles de représentation des connaissances biomédicales.3- La validation des modèles de représentation des connaissances biomédicales.Mes travaux autour de ces trois thématiques sont détaillés dans ce manuscrit

Data Spaces

This open access book aims to educate data space designers to understand what is required to create a successful data space. It explores cutting-edge theory, technologies, methodologies, and best practices for data spaces for both industrial and personal data and provides the reader with a basis for understanding the design, deployment, and future directions of data spaces. The book captures the early lessons and experience in creating data spaces. It arranges these contributions into three parts covering design, deployment, and future directions respectively. The first part explores the design space of data spaces. The single chapters detail the organisational design for data spaces, data platforms, data governance federated learning, personal data sharing, data marketplaces, and hybrid artificial intelligence for data spaces. The second part describes the use of data spaces within real-world deployments. Its chapters are co-authored with industry experts and include case studies of data spaces in sectors including industry 4.0, food safety, FinTech, health care, and energy. The third and final part details future directions for data spaces, including challenges and opportunities for common European data spaces and privacy-preserving techniques for trustworthy data sharing. The book is of interest to two primary audiences: first, researchers interested in data management and data sharing, and second, practitioners and industry experts engaged in data-driven systems where the sharing and exchange of data within an ecosystem are critical