Formal Methods for the Analysis of Biomedical Ontologies

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Publisher : Springer Nature
ISBN 13 : 3031121317
Total Pages : 258 pages
Book Rating : 4.0/5 (311 download)

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Book Synopsis Formal Methods for the Analysis of Biomedical Ontologies by : Guo-Qiang Zhang

Download or read book Formal Methods for the Analysis of Biomedical Ontologies written by Guo-Qiang Zhang and published by Springer Nature. This book was released on 2022-11-08 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book synthesizes research on the analysis of biomedical ontologies using formal concept analysis, including through auditing, curation, and enhancement. As the evolution of biomedical ontologies almost inevitably involves manual work, formal methods are a particularly useful tool for ontological engineering and practice, particularly in uncovering unexpected "bugs" and content materials. The book first introduces simple but formalized strategies for discovering undesired and incoherent patterns in ontologies before exploring the application of formal concept analysis for semantic completeness. The book then turns to formal concept analysis, a classical approach used in the mathematical treatment of orders and lattices, as an ontological engineering principle, focusing on the structural property of ontologies with respect to its conformation to lattice or not (non-lattice). The book helpfully covers the development of more efficient algorithms for non-lattice detection and extraction required by exhaustive lattice/non-lattice analysis. The book goes on to highlight the power and utility of uncovering non-lattice structure for debugging ontologies and describes methods that leverage the linguistic information in concept names (labels) for ontological analysis. It also addresses visualization and performance evaluation issues before closing with an overview and forward-looking perspectives on the field. This book is intended for graduate students and researchers interested in biomedical ontologies and their applications. It can be a useful supplement for courses on knowledge representation and engineering and also provide readers with a reference for related scientific publications and literature to assist in identifying potential research topics. All mathematical concepts and notations used in this book can be found in standard discrete mathematics textbooks, and the appendix at the end of the book provides a list of key ontological resources, as well as annotated non-lattice and lattice examples that were discovered using the authors' methods, demonstrating how "bugs are fixed" by converting non-lattices to lattices with minimal edit changes.

Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications

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Publisher : Springer
ISBN 13 : 3662452316
Total Pages : 661 pages
Book Rating : 4.6/5 (624 download)

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Book Synopsis Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications by : Tiziana Margaria

Download or read book Leveraging Applications of Formal Methods, Verification and Validation. Specialized Techniques and Applications written by Tiziana Margaria and published by Springer. This book was released on 2014-09-26 with total page 661 pages. Available in PDF, EPUB and Kindle. Book excerpt: The two-volume set LNCS 8802 and LNCS 8803 constitutes the refereed proceedings of the 6th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, ISoLA 2014, held in Imperial, Corfu, Greece, in October 2014. The total of 67 full papers was carefully reviewed and selected for inclusion in the proceedings. Featuring a track introduction to each section, the papers are organized in topical sections named: evolving critical systems; rigorous engineering of autonomic ensembles; automata learning; formal methods and analysis in software product line engineering; model-based code generators and compilers; engineering virtualized systems; statistical model checking; risk-based testing; medical cyber-physical systems; scientific workflows; evaluation and reproducibility of program analysis; processes and data integration in the networked healthcare; semantic heterogeneity in the formal development of complex systems. In addition, part I contains a tutorial on automata learning in practice; as well as the preliminary manifesto to the LNCS Transactions on the Foundations for Mastering Change with several position papers. Part II contains information on the industrial track and the doctoral symposium and poster session.

Implicit and Explicit Semantics Integration in Proof-Based Developments of Discrete Systems

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Publisher : Springer Nature
ISBN 13 : 9811550549
Total Pages : 345 pages
Book Rating : 4.8/5 (115 download)

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Book Synopsis Implicit and Explicit Semantics Integration in Proof-Based Developments of Discrete Systems by : Yamine Ait-Ameur

Download or read book Implicit and Explicit Semantics Integration in Proof-Based Developments of Discrete Systems written by Yamine Ait-Ameur and published by Springer Nature. This book was released on 2020-07-27 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses mechanisms for reducing model heterogeneity induced by the absence of explicit semantics expression in the formal techniques used to specify design models. More precisely, it highlights the advances in handling both implicit and explicit semantics in formal system developments, and discusses different contributions expressing different views and perceptions on the implicit and explicit semantics. The book is based on the discussions at the Shonan meeting on this topic held in 2016, and includes contributions from the participants summarising their perspectives on the problem and offering solutions. Divided into 5 parts: domain modelling, knowledge-based modelling, proof-based modelling, assurance cases, and refinement-based modelling, and offers inspiration for researchers and practitioners in the fields of formal methods, system and software engineering, domain knowledge modelling, requirement analysis, and explicit and implicit semantics of modelling languages.

Leveraging Applications of Formal Methods, Verification and Validation. Technologies for Mastering Change

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Author :
Publisher : Springer
ISBN 13 : 3662452340
Total Pages : 564 pages
Book Rating : 4.6/5 (624 download)

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Book Synopsis Leveraging Applications of Formal Methods, Verification and Validation. Technologies for Mastering Change by : Tiziana Margaria

Download or read book Leveraging Applications of Formal Methods, Verification and Validation. Technologies for Mastering Change written by Tiziana Margaria and published by Springer. This book was released on 2014-09-26 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: The two-volume set LNCS 8802 and LNCS 8803 constitutes the refereed proceedings of the 6th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, ISoLA 2014, held in Imperial, Corfu, Greece, in October 2014. The total of 67 full papers was carefully reviewed and selected for inclusion in the proceedings. Featuring a track introduction to each section, the papers are organized in topical sections named: evolving critical systems; rigorous engineering of autonomic ensembles; automata learning; formal methods and analysis in software product line engineering; model-based code generators and compilers; engineering virtualized systems; statistical model checking; risk-based testing; medical cyber-physical systems; scientific workflows; evaluation and reproducibility of program analysis; processes and data integration in the networked healthcare; semantic heterogeneity in the formal development of complex systems. In addition, part I contains a tutorial on automata learning in practice; as well as the preliminary manifesto to the LNCS Transactions on the Foundations for Mastering Change with several position papers. Part II contains information on the industrial track and the doctoral symposium and poster session.

Formal Ontology in Information Systems

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Author :
Publisher : IOS Press
ISBN 13 : 1586039237
Total Pages : 340 pages
Book Rating : 4.5/5 (86 download)

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Book Synopsis Formal Ontology in Information Systems by : Carola Eschenbach

Download or read book Formal Ontology in Information Systems written by Carola Eschenbach and published by IOS Press. This book was released on 2008 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Since its start ten years ago, the International Conference in Formal Ontology on Information Systems (FOIS) has explored the multiple perspectives on the notion of ontology that have arisen from such diverse research communities as philosophy, logic, computer science, cognitive science, linguistics, and various scientific domains. As ontologies have been applied in new and exciting domains such as the World Wide Web, bioinformatics, and geographical information systems, it has become evident that there is a need for ontologies that have been developed with solid theoretical foundations based on philosophical, linguistic and logical analysis. Similarly, there is also a need for theoretical research that is driven by the issues that have been raised by recent work in the more applied domains. FOIS is intended to be a forum in which to explore this interplay between the theoretical insights of formal ontology and their application to information systems and emerging semantic technologies. Themes emerging from this volume give a snapshot of current issues within the fields of formal ontology and ontological engineering, as well providing a glimpse of future research directions."--BOOK JACKET.

Formal Concept Analysis

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Publisher : Springer Science & Business Media
ISBN 13 : 3642018149
Total Pages : 350 pages
Book Rating : 4.6/5 (42 download)

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Book Synopsis Formal Concept Analysis by : Sébastien Ferré

Download or read book Formal Concept Analysis written by Sébastien Ferré and published by Springer Science & Business Media. This book was released on 2009-05-12 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 7th International Conference on Formal Concept Analysis, ICFCA 2009, held in Darmstadt, Germany, in May 2009. The 15 revised full papers presented were carefully reviewed and selected from 29 submissions for inclusion in the book. The papers comprise state of the art research and present new results in Formal Concept Analysis and related fields. These results range from theoretical novelties to advances in FCA-related algorithmic issues, as well as application domains of FCA such as data visualization, information retrieval, machine learning, data analysis and knowledge management.

Formal Ontologies Meet Industry

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Author :
Publisher : IOS Press
ISBN 13 : 1607504588
Total Pages : 144 pages
Book Rating : 4.6/5 (75 download)

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Book Synopsis Formal Ontologies Meet Industry by : R. Ferrario

Download or read book Formal Ontologies Meet Industry written by R. Ferrario and published by IOS Press. This book was released on 2009-08-21 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a collection of papers addressing the multi-shaped character of knowledge, new studies and applications in the field of ontology and semantic technology. The semantic dimension of information plays an increasingly central role in a networked, knowledge-centred economy and the need to encode information into computer systems has led to a bias towards Knowledge Engineering (KE) solutions as opposed to Knowledge Management (KM). Although the intersection between KE and KM has led to a general improvement of information systems, the overlap between these two fields has tended to eclipse interest in genuine knowledge processes. For this reason, the fourth FOMI workshop was held to coincide with the 10th European Conference of Knowledge Management (ECKM), with the explicit aim of bringing together KR and KM (sub)-communities, providing a platform for discussion of these topics. Subjects covered include: the evolution of ontologies in accordance with the evolution of the domain they are designed for; the study of the notions of functional composition and decomposition; modular ontologies for architecture; ontology infrastructure for electromagnetics; ontology of beliefs; enterprise modelling; the application of ontology-based methodologies and techniques to knowledge management issues; ontologies for standards and domain ontologies for biomedicine. The double focus on methodological and applicative issues represents the main feature of these FOMI 2009 articles. This comprehensive perspective will advance progress towards new frontiers in information systems and knowledge management, where research and development in formal ontology will play a leading role.

Building Ontologies with Basic Formal Ontology

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Publisher : MIT Press
ISBN 13 : 0262527812
Total Pages : 245 pages
Book Rating : 4.2/5 (625 download)

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Book Synopsis Building Ontologies with Basic Formal Ontology by : Robert Arp

Download or read book Building Ontologies with Basic Formal Ontology written by Robert Arp and published by MIT Press. This book was released on 2015-07-31 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the field of applied ontology with examples derived particularly from biomedicine, covering theoretical components, design practices, and practical applications. In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

Formal Ontology in Information Systems

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Publisher : IOS Press
ISBN 13 : 1607505347
Total Pages : 444 pages
Book Rating : 4.6/5 (75 download)

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Book Synopsis Formal Ontology in Information Systems by : Antony Galton

Download or read book Formal Ontology in Information Systems written by Antony Galton and published by IOS Press. This book was released on 2010 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ontology began life in ancient times as a fundamental part of philosophical enquiry concerned with the analysis and categorisation of what exists. In recent years, the subject has taken a practical turn with the advent of complex computerised information systems which are reliant on robust and coherent representations of their subject matter. The systematisation and elaboration of such representations and their associated reasoning techniques constitute the modern discipline of formal ontology, which is now being applied to such diverse domains as artificial intelligence, computational linguistics, bioinformatics, GIS, knowledge engineering, information retrieval and the Semantic Web. Researchers in all these areas are becoming increasingly aware of the need for serious engagement with ontology, understood as a general theory of the types of entities and relations making up their respective domains of enquiry, to provide a solid foundation for their work. The conference series Formal Ontology in Information Systems (FOIS) provides a meeting point for researchers from these and other disciplines with an interest in formal ontology, where both theoretical issues and concrete applications can be explored in a spirit of genuine interdisciplinarity. This volume contains the proceedings of the sixth FOIS conference, held in Toronto, Canada, during 11-14 May 2010, including invited talks by Francis Jeffry Pelletier, John Bateman, and Alan Rector and the 28 peer-reviewed submissions selected for presentation at the conference, ranging from foundational issues to more application-oriented topics. IOS Press is an international science, technical and medical publisher of high-quality books for academics, scientists, and professionals in all fields. Some of the areas we publish in: -Biomedicine -Oncology -Artificial intelligence -Databases and information systems -Maritime engineering -Nanotechnology -Geoengineering -All aspects of physics -E-governance -E-commerce -The knowledge economy -Urban studies -Arms control -Understanding and responding to terrorism -Medical informatics -Computer Sciences

Formal Ontology in Information Systems

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Publisher : IOS Press
ISBN 13 : 1614996601
Total Pages : 392 pages
Book Rating : 4.6/5 (149 download)

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Book Synopsis Formal Ontology in Information Systems by : R. Ferrario

Download or read book Formal Ontology in Information Systems written by R. Ferrario and published by IOS Press. This book was released on 2016-07-06 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ontology, originally a fundamental part of philosophical enquiry, is concerned with the analysis and categorization of what exists. The advent of complex information systems which rely on robust and coherent formal representations of their subject matter has led to a renewed focus on ontological enquiry, and the systematic study of such representations are at the center of the modern discipline of formal ontology. This is now a research focus in domains as diverse as conceptual modeling, database design, software engineering, artificial intelligence, computational linguistics, the life sciences, bioinformatics, geographic information science, knowledge engineering, information retrieval and the semantic web. This book presents the proceedings of the 9th edition of the Formal Ontology in Information Systems conference (FOIS 2016) held in Annecy, France, in July 2016. It contains the 25 full papers delivered at the conference (an acceptance rate of 30.9% for the main track), as well as the abstracts of the 3 keynotes by Gilberto Câmara, Stephen Mumford and Friederike Moltmann. The remainder of the book is divided into the sections: Foundations; Space, Time and Change; Cognition, Language and Semantics; Empiricism and Measurement; Ontology for Engineering; Biomedical Ontologies; and Ontology of Social Reality. The domains addressed by the papers include geography, biomedicine, economics, social reality and engineering, and the book will be of interest to all those working in these fields, as well as to anybody with an interest in formal ontology.

Computation, Information, Cognition

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Publisher : Cambridge Scholars Publishing
ISBN 13 : 1443809322
Total Pages : 380 pages
Book Rating : 4.4/5 (438 download)

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Book Synopsis Computation, Information, Cognition by : Gordana Dodig Crnkovic

Download or read book Computation, Information, Cognition written by Gordana Dodig Crnkovic and published by Cambridge Scholars Publishing. This book was released on 2009-03-26 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book draws together a number of important strands in contemporary approaches to the philosophical and scientific questions that emerge when dealing with the issues of computing, information, cognition and the conceptual issues that arise at their intersections. It discovers and develops the connections at the borders and in the interstices of disciplines and debates, and presents a range of essays that deal with the currently vigorous concerns of the philosophy of information, ontology creation and control, bioinformation and biosemiotics, computational and post- computational ap- proaches to the philosophy of cognitive science, computational linguistics, ethics, and education.

Formal Verification of Tree Ensembles in Safety-Critical Applications

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Author :
Publisher : Linköping University Electronic Press
ISBN 13 : 917929748X
Total Pages : 22 pages
Book Rating : 4.1/5 (792 download)

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Book Synopsis Formal Verification of Tree Ensembles in Safety-Critical Applications by : John Törnblom

Download or read book Formal Verification of Tree Ensembles in Safety-Critical Applications written by John Törnblom and published by Linköping University Electronic Press. This book was released on 2020-10-28 with total page 22 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the presence of data and computational resources, machine learning can be used to synthesize software automatically. For example, machines are now capable of learning complicated pattern recognition tasks and sophisticated decision policies, two key capabilities in autonomous cyber-physical systems. Unfortunately, humans find software synthesized by machine learning algorithms difficult to interpret, which currently limits their use in safety-critical applications such as medical diagnosis and avionic systems. In particular, successful deployments of safety-critical systems mandate the execution of rigorous verification activities, which often rely on human insights, e.g., to identify scenarios in which the system shall be tested. A natural pathway towards a viable verification strategy for such systems is to leverage formal verification techniques, which, in the presence of a formal specification, can provide definitive guarantees with little human intervention. However, formal verification suffers from scalability issues with respect to system complexity. In this thesis, we investigate the limits of current formal verification techniques when applied to a class of machine learning models called tree ensembles, and identify model-specific characteristics that can be exploited to improve the performance of verification algorithms when applied specifically to tree ensembles. To this end, we develop two formal verification techniques specifically for tree ensembles, one fast and conservative technique, and one exact but more computationally demanding. We then combine these two techniques into an abstraction-refinement approach, that we implement in a tool called VoTE (Verifier of Tree Ensembles). Using a couple of case studies, we recognize that sets of inputs that lead to the same system behavior can be captured precisely as hyperrectangles, which enables tractable enumeration of input-output mappings when the input dimension is low. Tree ensembles with a high-dimensional input domain, however, seems generally difficult to verify. In some cases though, conservative approximations of input-output mappings can greatly improve performance. This is demonstrated in a digit recognition case study, where we assess the robustness of classifiers when confronted with additive noise.

Formal Ontology in Information Systems

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Publisher : IOS Press
ISBN 13 : 1607502119
Total Pages : 388 pages
Book Rating : 4.6/5 (75 download)

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Book Synopsis Formal Ontology in Information Systems by : B. Bennett

Download or read book Formal Ontology in Information Systems written by B. Bennett and published by IOS Press. This book was released on 2006-10-26 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researchers in areas such as artificial intelligence, formal and computational linguistics, biomedical informatics, conceptual modeling, knowledge engineering and information retrieval have come to realise that a solid foundation for their research calls for serious work in ontology, understood as a general theory of the types of entities and relations that make up their respective domains of inquiry. In all these areas, attention is now being focused on the content of information rather than on just the formats and languages used to represent information. The clearest example of this development is provided by the many initiatives growing up around the project of the Semantic Web. And, as the need for integrating research in these different fields arises, so does the realisation that strong principles for building well-founded ontologies might provide significant advantages over ad hoc, case-based solutions. The tools of formal ontology address precisely these needs, but a real effort is required in order to apply such philosophical tools to the domain of information systems. Reciprocally, research in the information sciences raises specific ontological questions which call for further philosophical investigations. The purpose of FOIS is to provide a forum for genuine interdisciplinary exchange in the spirit of a unified effort towards solving the problems of ontology, with an eye to both theoretical issues and concrete applications. This book contains a wide range of areas, all of which are important to the development of formal ontologies.

MEDINFO 2019: Health and Wellbeing e-Networks for All

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Publisher : IOS Press
ISBN 13 : 164368003X
Total Pages : 2078 pages
Book Rating : 4.6/5 (436 download)

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Book Synopsis MEDINFO 2019: Health and Wellbeing e-Networks for All by : L. Ohno-Machado

Download or read book MEDINFO 2019: Health and Wellbeing e-Networks for All written by L. Ohno-Machado and published by IOS Press. This book was released on 2019-11-12 with total page 2078 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combining and integrating cross-institutional data remains a challenge for both researchers and those involved in patient care. Patient-generated data can contribute precious information to healthcare professionals by enabling monitoring under normal life conditions and also helping patients play a more active role in their own care. This book presents the proceedings of MEDINFO 2019, the 17th World Congress on Medical and Health Informatics, held in Lyon, France, from 25 to 30 August 2019. The theme of this year’s conference was ‘Health and Wellbeing: E-Networks for All’, stressing the increasing importance of networks in healthcare on the one hand, and the patient-centered perspective on the other. Over 1100 manuscripts were submitted to the conference and, after a thorough review process by at least three reviewers and assessment by a scientific program committee member, 285 papers and 296 posters were accepted, together with 47 podium abstracts, 7 demonstrations, 45 panels, 21 workshops and 9 tutorials. All accepted paper and poster contributions are included in these proceedings. The papers are grouped under four thematic tracks: interpreting health and biomedical data, supporting care delivery, enabling precision medicine and public health, and the human element in medical informatics. The posters are divided into the same four groups. The book presents an overview of state-of-the-art informatics projects from multiple regions of the world; it will be of interest to anyone working in the field of medical informatics.

Biomedical Data and Applications

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Publisher : Springer Science & Business Media
ISBN 13 : 3642021921
Total Pages : 344 pages
Book Rating : 4.6/5 (42 download)

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Book Synopsis Biomedical Data and Applications by : Amandeep S. Sidhu

Download or read book Biomedical Data and Applications written by Amandeep S. Sidhu and published by Springer Science & Business Media. This book was released on 2009-06-16 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Compared with data from general application domains, modern biological data has many unique characteristics. The goal of this book is to cover data and applications identifying new issues and directions for future research in biomedical domain.

Theory and Applications of Ontology: Computer Applications

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Publisher : Springer Science & Business Media
ISBN 13 : 9048188474
Total Pages : 582 pages
Book Rating : 4.0/5 (481 download)

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Book Synopsis Theory and Applications of Ontology: Computer Applications by : Roberto Poli

Download or read book Theory and Applications of Ontology: Computer Applications written by Roberto Poli and published by Springer Science & Business Media. This book was released on 2010-09-02 with total page 582 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ontology was once understood to be the philosophical inquiry into the structure of reality: the analysis and categorization of ‘what there is’. Recently, however, a field called ‘ontology’ has become part of the rapidly growing research industry in information technology. The two fields have more in common than just their name. Theory and Applications of Ontology is a two-volume anthology that aims to further an informed discussion about the relationship between ontology in philosophy and ontology in information technology. It fills an important lacuna in cutting-edge research on ontology in both fields, supplying stage-setting overview articles on history and method, presenting directions of current research in either field, and highlighting areas of productive interdisciplinary contact. Theory and Applications of Ontology: Computer Applications presents ontology in ways that philosophers are not likely to find elsewhere. The volume offers an overview of current research in ontology, distinguishing basic conceptual issues, domain applications, general frameworks, and mathematical formalisms. It introduces the reader to current research on frameworks and applications in information technology in ways that are sure to invite reflection and constructive responses from ontologists in philosophy.

Advanced Machine Learning Technologies and Applications

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Publisher : Springer Nature
ISBN 13 : 9811533830
Total Pages : 737 pages
Book Rating : 4.8/5 (115 download)

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Book Synopsis Advanced Machine Learning Technologies and Applications by : Aboul Ella Hassanien

Download or read book Advanced Machine Learning Technologies and Applications written by Aboul Ella Hassanien and published by Springer Nature. This book was released on 2020-05-25 with total page 737 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the refereed proceedings of the 5th International Conference on Advanced Machine Learning Technologies and Applications (AMLTA 2020), held at Manipal University Jaipur, India, on February 13 – 15, 2020, and organized in collaboration with the Scientific Research Group in Egypt (SRGE). The papers cover current research in machine learning, big data, Internet of Things, biomedical engineering, fuzzy logic and security, as well as intelligence swarms and optimization.