Information-Theoretic Evaluation for Computational Biomedical Ontologies PDF Download
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Author: Wyatt Travis Clark
Publisher: Springer Science & Business Media
ISBN: 331904138X
Category : Computers
Languages : en
Pages : 50
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Book Description
The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, yet evaluating their performance is difficult due to problems caused by the structure of biomedical ontologies and incomplete annotations of genes. This work proposes an information-theoretic framework to evaluate the performance of computational protein function prediction. A Bayesian network is used, structured according to the underlying ontology, to model the prior probability of a protein's function. The concepts of misinformation and remaining uncertainty are then defined, that can be seen as analogs of precision and recall. Finally, semantic distance is proposed as a single statistic for ranking classification models. The approach is evaluated by analyzing three protein function predictors of gene ontology terms. The work addresses several weaknesses of current metrics, and provides valuable insights into the performance of protein function prediction tools.
Author: Wyatt Travis Clark
Publisher: Springer Science & Business Media
ISBN: 331904138X
Category : Computers
Languages : en
Pages : 50
Get Book Here
Book Description
The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, yet evaluating their performance is difficult due to problems caused by the structure of biomedical ontologies and incomplete annotations of genes. This work proposes an information-theoretic framework to evaluate the performance of computational protein function prediction. A Bayesian network is used, structured according to the underlying ontology, to model the prior probability of a protein's function. The concepts of misinformation and remaining uncertainty are then defined, that can be seen as analogs of precision and recall. Finally, semantic distance is proposed as a single statistic for ranking classification models. The approach is evaluated by analyzing three protein function predictors of gene ontology terms. The work addresses several weaknesses of current metrics, and provides valuable insights into the performance of protein function prediction tools.
Author: Information Resources Management Association
Publisher: IGI Global
ISBN: 146663605X
Category : Computers
Languages : en
Pages : 1826
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Book Description
"Bioinformatics: Concepts, Methodologies, Tools, and Applications highlights the area of bioinformatics and its impact over the medical community with its innovations that change how we recognize and care for illnesses"--Provided by publisher.
Author: John Hancock
Publisher: Frontiers Media SA
ISBN: 2889192776
Category : Biotechnology
Languages : en
Pages : 107
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Book Description
As the amount of biological information and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it. The Semantic Web is a new wave of web- based technologies that allows the linking of data between diverse data sets via standardised data formats (“big data”). Semantic Biology is the application of semantic web technology in the biological domain (including medical and health informatics). The Special Topic encompasses papers in this very broad area, including not only ontologies (development and applications), but also text mining, data integration and data analysis making use of the technologies of the Semantic Web. Ontologies are a critical requirement for such integration as they allow conclusions drawn about biological experiments, or descriptions of biological entities, to be understandable and integratable despite being contained in different databases and analysed by different software systems. Ontologies are the standard structures used in biology, and more broadly in computer science, to hold standardized terminologies for particular domains of knowledge. Ontologies consist of sets of standard terms, which are defined and may have synonyms for ease of searching and to accommodate different usages by different communities. These terms are linked by standard relationships, such as “is_a” (an eye “is_a” sense organ) or “part_of” (an eye is “part_of” a head). By linking terms in this way, more detailed, or granular, terms can be linked to broader terms, allowing computation to be carried out that takes these relationships into account.
Author: Yucong Duan
Publisher: Frontiers Media SA
ISBN: 2889741362
Category : Science
Languages : en
Pages : 247
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Book Description
Author: Zahir Tari
Publisher: Springer Science & Business Media
ISBN: 3540888721
Category : Computers
Languages : en
Pages : 673
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Book Description
This two-volume set LNCS 5331/5332 constitutes the refereed proceedings of the five confederated international conferences on Cooperative Information Systems (CoopIS 2008), Distributed Objects and Applications (DOA 2008), Grid computing, high performAnce and Distributed Applications (GADA 2008), Information Security (IS 2008), and Ontologies, Databases and Applications of Semantics (ODBASE 2008), held as OTM 2008 in Monterrey, Mexico, in November 2008. The 86 revised full and 9 revised short papers presented together with 5 invited papers and 4 keynote talks were carefully reviewed and selected from a total of 292 submissions. Corresponding to the five OTM 2008 main conferences CoopIS, DOA, GADA, IS, and ODBASE the papers are organized in topical sections on Web service, business process technology, E-service management, distributed process management, schema matching, business process tracing, workflow and business applications, designing distributed systems, context in distributed systems, high availability, adaptive distributed systems, scheduling allocation, databases in grids, grid applications, data management and storage, new tendencies and approaches, intrusion detection, information hiding, data and risk management, access control, evaluation and implementation, semantic matching and similarity measuring, semantic searching, ontology development, ontology maintanence and evaluation, ontology applications, and semantic query processing.
Author: Marcelo S. Reis
Publisher: Springer Nature
ISBN: 3031427157
Category : Science
Languages : en
Pages : 174
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Book Description
This book constitutes the proceedings of the 16th Brazilian Symposium on Bioinformatics on Advances in Bioinformatics and Computational Biology, BSB 2023, which took place in Curitiba, Brazil, in June 2023. The 11 full papers and 3 short papers presented in this volume were carefully reviewed and selected from 24 submissions. The papers focus on bioinformatics, computational biology, Biological Databases, Biological Networks, Cheminformatics, Evolutionary Genomics, Computational Proteomics, Systems Biology, Drug Design, Genomics, Machine Learning applications in Bioinformatics, Metagenomics, Molecular Docking and Modeling, Molecular Evolution and Phylogenetics, Protein Structure and Modeling, Proteomics, Transcriptomics, Single-Cell Analysis, Workflows in Bioinformatics.
Author: Sébastien Harispe
Publisher: Springer Nature
ISBN: 3031021568
Category : Computers
Languages : en
Pages : 245
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Book Description
Artificial Intelligence federates numerous scientific fields in the aim of developing machines able to assist human operators performing complex treatments---most of which demand high cognitive skills (e.g. learning or decision processes). Central to this quest is to give machines the ability to estimate the likeness or similarity between things in the way human beings estimate the similarity between stimuli. In this context, this book focuses on semantic measures: approaches designed for comparing semantic entities such as units of language, e.g. words, sentences, or concepts and instances defined into knowledge bases. The aim of these measures is to assess the similarity or relatedness of such semantic entities by taking into account their semantics, i.e. their meaning---intuitively, the words tea and coffee, which both refer to stimulating beverage, will be estimated to be more semantically similar than the words toffee (confection) and coffee, despite that the last pair has a higher syntactic similarity. The two state-of-the-art approaches for estimating and quantifying semantic similarities/relatedness of semantic entities are presented in detail: the first one relies on corpora analysis and is based on Natural Language Processing techniques and semantic models while the second is based on more or less formal, computer-readable and workable forms of knowledge such as semantic networks, thesauri or ontologies. Semantic measures are widely used today to compare units of language, concepts, instances or even resources indexed by them (e.g., documents, genes). They are central elements of a large variety of Natural Language Processing applications and knowledge-based treatments, and have therefore naturally been subject to intensive and interdisciplinary research efforts during last decades. Beyond a simple inventory and categorization of existing measures, the aim of this monograph is to convey novices as well as researchers of these domains toward a better understanding of semantic similarity estimation and more generally semantic measures. To this end, we propose an in-depth characterization of existing proposals by discussing their features, the assumptions on which they are based and empirical results regarding their performance in particular applications. By answering these questions and by providing a detailed discussion on the foundations of semantic measures, our aim is to give the reader key knowledge required to: (i) select the more relevant methods according to a particular usage context, (ii) understand the challenges offered to this field of study, (iii) distinguish room of improvements for state-of-the-art approaches and (iv) stimulate creativity toward the development of new approaches. In this aim, several definitions, theoretical and practical details, as well as concrete applications are presented.
Author: Jose C. Principe
Publisher: Springer Science & Business Media
ISBN: 1441915702
Category : Computers
Languages : en
Pages : 538
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Book Description
This book is the first cohesive treatment of ITL algorithms to adapt linear or nonlinear learning machines both in supervised and unsupervised paradigms. It compares the performance of ITL algorithms with the second order counterparts in many applications.
Author: Guillermo Navarro-Arribas
Publisher: Springer
ISBN: 3319098853
Category : Technology & Engineering
Languages : en
Pages : 453
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Book Description
This book provides an overview of the research work on data privacy and privacy enhancing technologies carried by the participants of the ARES project. ARES (Advanced Research in Privacy an Security, CSD2007-00004) has been one of the most important research projects funded by the Spanish Government in the fields of computer security and privacy. It is part of the now extinct CONSOLIDER INGENIO 2010 program, a highly competitive program which aimed to advance knowledge and open new research lines among top Spanish research groups. The project started in 2007 and will finish this 2014. Composed by 6 research groups from 6 different institutions, it has gathered an important number of researchers during its lifetime. Among the work produced by the ARES project, one specific work package has been related to privacy. This books gathers works produced by members of the project related to data privacy and privacy enhancing technologies. The presented works not only summarize important research carried in the project but also serve as an overview of the state of the art in current research on data privacy and privacy enhancing technologies.
Author: Xuemin Lin
Publisher: Springer
ISBN: 3642412300
Category : Computers
Languages : en
Pages : 550
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Book Description
This book constitutes the proceedings of the 14th International Conference on Web Information Systems Engineering, WISE 2013, held in Nanjing, China, in October 2013. The 48 full papers, 29 short papers, and 10 demo and 5 challenge papers, presented in the two-volume proceedings LNCS 8180 and 8181, were carefully reviewed and selected from 198 submissions. They are organized in topical sections named: Web mining; Web recommendation; Web services; data engineering and database; semi-structured data and modeling; Web data integration and hidden Web; challenge; social Web; information extraction and multilingual management; networks, graphs and Web-based business processes; event processing, Web monitoring and management; and innovative techniques and creations.
