A Unified Framework for Parallel Anisotropic Mesh Adaptation

Finite-element methods are a critical component of the design and analysis procedures of many (bio-)engineering applications. Mesh adaptation is one of the most crucial components since it discretizes the physics of the application at a relatively low cost to the solver. Highly scalable parallel mesh adaptation methods for High-Performance Computing (HPC) are essential to meet the ever-growing demand for higher fidelity simulations. Moreover, the continuous growth of the complexity of the HPC systems requires a systematic approach to exploit their full potential. Anisotropic mesh adaptation captures features of the solution at multiple scales while, minimizing the required number of elements. However, it also introduces new challenges on top of mesh generation. Also, the increased complexity of the targeted cases requires departing from traditional surface-constrained approaches to utilizing CAD (Computer-Aided Design) kernels. Alongside the functionality requirements, is the need of taking advantage of the ubiquitous multi-core machines. More importantly, the parallel implementation needs to handle the ever-increasing complexity of the mesh adaptation code. In this work, we develop a parallel mesh adaptation method that utilizes a metric-based approach for generating anisotropic meshes. Moreover, we enhance our method by interfacing with a CAD kernel, thus enabling its use on complex geometries. We evaluate our method both with fixed-resolution benchmarks and within a simulation pipeline, where the resolution of the discretization increases incrementally. With the Telescopic Approach for scalable mesh generation as a guide, we propose a parallel method at the node (multi-core) for mesh adaptation that is expected to scale up efficiently to the upcoming exascale machines. To facilitate an effective implementation, we introduce an abstract layer between the application and the runtime system that enables the use of task-based parallelism for concurrent mesh operations. Our evaluation indicates results comparable to state-of-the-art methods for fixed-resolution meshes both in terms of performance and quality. The integration with an adaptive pipeline offers promising results for the capability of the proposed method to function as part of an adaptive simulation. Moreover, our abstract tasking layer allows the separation of different aspects of the implementation without any impact on the functionality of the method

Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Pattern Recognition

A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition

MAPPING BPEL PROCESSES TO DIAGNOSTIC MODELS

Web services are loosely-coupled, self-contained, and self-describing software modules that perform a predetermined task. These services can be linked together to develop an appli­ cation that spans multiple organizations. This linking is referred to as a composition of web services. These compositions potentially can help businesses respond more quickly and more cost-effectively to changing market conditions. Compositions can be specified using a high- level workflow process language. A fault or problem is a defect in a software or software component. A system is said to have a failure if the service it delivers to the user deviates from compliance with the system specification for a specified period of time. A problem causes a failure. Failures are often referred to as symptoms of a problem. A problem can occur on one component but a failure is detected on another component. This suggests a need to be able to determine a problem based on failures. This is referred to as fault diagnosis. This thesis focuses on the design, implementation and evaluation of a diagnostic module that performs automated mapping of a high-level specification of a web services composition to a diagnostics model. A diagnosis model expresses the relationship between problems and potential symptoms. This mapping can be done by a third party service that is not part of the application resulting from the composition of the web services. Automation will allow a third party to do diagnosis for a large number of compositions and should be less error-prone

Visual approaches to knowledge organization and contextual exploration

This thesis explores possible visual approaches for the representation of semantic structures, such as zz-structures. Some holistic visual representations of complex domains have been investigated through the proposal of new views - the so-called zz-views - that allow both to make visible the interconnections between elements and to support a contextual and multilevel exploration of knowledge. The potential of this approach has been examined in the context of two case studies that have led to the creation of two Web applications. The \ufb01rst domain of study regarded the visual representation, analysis and management of scienti\ufb01c bibliographies. In this context, we modeled a Web application, we called VisualBib, to support researchers in building, re\ufb01ning, analyzing and sharing bibliographies. We adopted a multi-faceted approach integrating features that are typical of three di\ufb00erent classes of tools: bibliography visual analysis systems, bibliographic citation indexes and personal research assistants. The evaluation studies carried out on a \ufb01rst prototype highlighted the positive impact of our visual model and encouraged us to improve it and develop further visual analysis features we incorporated in the version 3.0 of the application. The second case study concerned the modeling and development of a multimedia catalog of Web and mobile applications. The objective was to provide an overview of a significant number of tools that can help teachers in the implementation of active learning approaches supported by technology and in the design of Teaching and Learning Activities (TLAs). We analyzed and documented 281 applications, preparing for each of them a detailed multilingual card and a video-presentation, organizing all the material in an original purpose-based taxonomy, visually represented through a browsable holistic view. The catalog, we called AppInventory, provides contextual exploration mechanisms based on zz-structures, collects user contributions and evaluations about the apps and o\ufb00ers visual analysis tools for the comparison of the applications data and user evaluations. The results of two user studies carried out on groups of teachers and students shown a very positive impact of our proposal in term of graphical layout, semantic structure, navigation mechanisms and usability, also in comparison with two similar catalogs

LIDeB Tools: A Latin American resource of freely available, open-source cheminformatics apps

Cheminformatics is the chemical field that deals with the storage, retrieval, analysis and manipulation of an increasing volume of available chemical data, and it plays a fundamental role in the fields of drug discovery, biology, chemistry, and biochemistry. Open source and freely available cheminformatics tools not only contribute to the generation of public knowledge, but also to reduce the technological gap between high- and low- to middle-income countries. Here, we describe a series of in-house cheminformatics applications developed by our academic drug discovery team, which are freely available on our website (https://lideb.biol.unlp.edu.ar/) as Web Apps and stand-alone versions. These apps include tools for clustering small molecules, decoy generation, druggability assessment, classificatory model evaluation, and data standardization and visualization.Fil: Prada Gori, Denis Nihuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencas Exactas. Laboratorio de Investigación y Desarrollo de Bioactivos; ArgentinaFil: Alberca, Lucas Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencas Exactas. Laboratorio de Investigación y Desarrollo de Bioactivos; ArgentinaFil: Rodríguez, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; Argentina. Universidad Nacional de La Plata. Facultad de Ciencas Exactas. Laboratorio de Investigación y Desarrollo de Bioactivos; ArgentinaFil: Alice, Juan Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencas Exactas. Laboratorio de Investigación y Desarrollo de Bioactivos; ArgentinaFil: Llanos, Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencas Exactas. Laboratorio de Investigación y Desarrollo de Bioactivos; ArgentinaFil: Bellera, Carolina Leticia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencas Exactas. Laboratorio de Investigación y Desarrollo de Bioactivos; ArgentinaFil: Talevi, Alan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencas Exactas. Laboratorio de Investigación y Desarrollo de Bioactivos; Argentin

Search improvement within the geospatial web in the context of spatial data infrastructures

El trabajo desarrollado en esta tesis doctoral demuestra que es posible mejorar la búsqueda en el contexto de las Infraestructuras de Datos Espaciales mediante la aplicación de técnicas y buenas prácticas de otras comunidades científicas, especialmente de las comunidades de la Web y de la Web Semántica (por ejemplo, Linked Data). El uso de las descripciones semánticas y las aproximaciones basadas en el contenido publicado por la comunidad geoespacial pueden ayudar en la búsqueda de información sobre los fenómenos geográficos, y en la búsqueda de recursos geoespaciales en general. El trabajo comienza con un análisis de una aproximación para mejorar la búsqueda de las entidades geoespaciales desde la perspectiva de geocodificación tradicional. La arquitectura de geocodificación compuesta propuesta en este trabajo asegura una mejora de los resultados de geocodificación gracias a la utilización de diferentes proveedores de información geográfica. En este enfoque, el uso de patrones estructurales de diseño y ontologías en esta aproximación permite una arquitectura avanzada en términos de extensibilidad, flexibilidad y adaptabilidad. Además, una arquitectura basada en la selección de servicio de geocodificación permite el desarrollo de una metodología de la georreferenciación de diversos tipos de información geográfica (por ejemplo, direcciones o puntos de interés). A continuación, se presentan dos aplicaciones representativas que requieren una caracterización semántica adicional de los recursos geoespaciales. El enfoque propuesto en este trabajo utiliza contenidos basados en heurísticas para el muestreo de un conjunto de recursos geopesaciales. La primera parte se dedica a la idea de la abstracción de un fenómeno geográfico de su definición espacial. La investigación muestra que las buenas prácticas de la Web Semántica se puede reutilizar en el ámbito de una Infraestructura de Datos Espaciales para describir los servicios geoespaciales estandarizados por Open Geospatial Consortium por medio de geoidentificadores (es decir, por medio de las entidades de una ontología geográfica). La segunda parte de este capítulo desglosa la aquitectura y componentes de un servicio de geoprocesamiento para la identificación automática de ortoimágenes ofrecidas a través de un servicio estándar de publicación de mapas (es decir, los servicios que siguen la especificación OGC Web Map Service). Como resultado de este trabajo se ha propuesto un método para la identificación de los mapas ofrecidos por un Web Map Service que son ortoimágenes. A continuación, el trabajo se dedica al análisis de cuestiones relacionadas con la creación de los metadatos de recursos de la Web en el contexto del dominio geográfico. Este trabajo propone una arquitectura para la generación automática de conocimiento geográfico de los recursos Web. Ha sido necesario desarrollar un método para la estimación de la cobertura geográfica de las páginas Web. Las heurísticas propuestas están basadas en el contenido publicado por os proveedores de información geográfica. El prototipo desarrollado es capaz de generar metadatos. El modelo generado contiene el conjunto mínimo recomendado de elementos requeridos por un catálogo que sigue especificación OGC Catalogue Service for the Web, el estandar recomendado por deiferentes Infraestructuras de Datos Espaciales (por ejemplo, the Infrastructure for Spatial Information in the European Community (INSPIRE)). Además, este estudio determina algunas características de la Web Geoespacial actual. En primer lugar, ofrece algunas características del mercado de los proveedores de los recursos Web de la información geográfica. Este estudio revela algunas prácticas de la comunidad geoespacial en la producción de metadatos de las páginas Web, en particular, la falta de metadatos geográficos. Todo lo anterior es la base del estudio de la cuestión del apoyo a los usuarios no expertos en la búsqueda de recursos de la Web Geoespacial. El motor de búsqueda dedicado a la Web Geoespacial propuesto en este trabajo es capaz de usar como base un motor de búsqueda existente. Por otro lado, da soporte a la búsqueda exploratoria de los recursos geoespaciales descubiertos en la Web. El experimento sobre la precisión y la recuperación ha demostrado que el prototipo desarrollado en este trabajo es al menos tan bueno como el motor de búsqueda remoto. Un estudio dedicado a la utilidad del sistema indica que incluso los no expertos pueden realizar una tarea de búsqueda con resultados satisfactorios