20 research outputs found

    LIPIcs, Volume 261, ICALP 2023, Complete Volume

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    LIPIcs, Volume 261, ICALP 2023, Complete Volum

    Advances in Condition Monitoring, Optimization and Control for Complex Industrial Processes

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    The book documents 25 papers collected from the Special Issue “Advances in Condition Monitoring, Optimization and Control for Complex Industrial Processes”, highlighting recent research trends in complex industrial processes. The book aims to stimulate the research field and be of benefit to readers from both academic institutes and industrial sectors

    Scaling the development of large ontologies : identitas and hypernormalization

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    PhD ThesisDuring the last decade ontologies have become a fundamental part of the life sciences to build organised computational knowledge. Currently, there are more than 800 biomedical ontologies hosted by the NCBO BioPortal repository. However, the proliferation of ontologies in the biomedical and biological domains has highlighted a number of problems. As ontologies become large, their development and maintenance becomes more challenging and time-consuming. Therefore, the scalability of ontology development has become problematic. In this thesis, we examine two new approaches that can help address this challenge. First, we consider a new approach to identi ers that could signi cantly facilitate the scalability of ontologies and overcome some related issues with monotonic, numeric identi ers while remaining semantics-free. Our solutions are described, along with the Identitas library, which allows concurrent development, pronounceability and error checking. The library integrated into two ontology development environments, Prot eg e and Tawny-OWL. This thesis also discusses the ways in which current ontological practices could be migrated towards the use of this scheme. Second, we investigate the usage of the hypernormalisation, patternisation and programatic approaches by asking how we could use this approach to rebuild the Gene Ontology (GO). The aim of the hypernormalisation and patternisation techniques is to allow the ontology developer to manage its maintainability and evolution. To apply this approach we had to analyse the ontology structure, starting with the Molecular Function Ontology (MFO). The MFO is formed from several large and tangled hierarchies of classes, each of which describe a broad molecular activity. The exploitation of the hypernormalisation approach resulted in the creation of a hypernormalised form of the Transporter Activity (TA) and Catalytic Activity (CA) hierarchies, together they constitute 78% of all classes in MFO. The hypernormalised structure of the TA and CA are generated based on developed higher-level patterns and novel content-speci c patterns, and exploit ontology logical reasoners. The gen- erated ontologies are robust, easy to maintain and can be developed and extended freely. Although, there are a variety of ontologies development tools, Tawny-OWL is a programmatic interactive tool for ontology creation and management and provides a set of patterns that explicitly support the creation of a hypernormalised ontology. Finally, the investigation of the hypernormalisation highlighted inconsistent classi- cations and identi cation of signi cant semantic mismatch between GO and the Chemical Entities of Biological Interest (ChEBI). Although both ontologies describe the same real entities, GO often refers to the form most common in biology, while ChEBI is more speci c and precise. The use of hypernormalisation forces us to deal with this mismatch, we used the equivalence axioms created by the GO-Plus ontology. To sum up, to address the scalability and ease development of ontologies we propose a new identi er scheme and investigate the use of the hypernormalisation methodology. Together, the Identitas and the hypernormalisation technique should enable the construction of large-scale ontologies in the future.Northern Borders University, Saudi Arabia

    Calibración de un algoritmo de detección de anomalías marítimas basado en la fusión de datos satelitales

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    La fusión de diferentes fuentes de datos aporta una ayuda significativa en el proceso de toma de decisiones. El presente artículo describe el desarrollo de una plataforma que permite detectar anomalías marítimas por medio de la fusión de datos del Sistema de Información Automática (AIS) para seguimiento de buques y de imágenes satelitales de Radares de Apertura Sintética (SAR). Estas anomalías son presentadas al operador como un conjunto de detecciones que requieren ser monitoreadas para descubrir su naturaleza. El proceso de detección se lleva adelante primero identificando objetos dentro de las imágenes SAR a través de la aplicación de algoritmos CFAR, y luego correlacionando los objetos detectados con los datos reportados mediante el sistema AIS. En este trabajo reportamos las pruebas realizadas con diferentes configuraciones de los parámetros para los algoritmos de detección y asociación, analizamos la respuesta de la plataforma y reportamos la combinación de parámetros que reporta mejores resultados para las imágenes utilizadas. Este es un primer paso en nuestro objetivo futuro de desarrollar un sistema que ajuste los parámetros en forma dinámica dependiendo de las imágenes disponibles.XVI Workshop Computación Gráfica, Imágenes y Visualización (WCGIV)Red de Universidades con Carreras en Informática (RedUNCI

    AUTOMATED ANALYSIS OF NATURAL-LANGUAGE REQUIREMENTS USING NATURAL LANGUAGE PROCESSING

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    Natural Language (NL) is arguably the most common vehicle for specifying requirements. This dissertation devises automated assistance for some important tasks that requirements engineers need to perform in order to structure, manage, and elaborate NL requirements in a sound and effective manner. The key enabling technology underlying the work in this dissertation is Natural Language Processing (NLP). All the solutions presented herein have been developed and empirically evaluated in close collaboration with industrial partners. The dissertation addresses four different facets of requirements analysis: • Checking conformance to templates. Requirements templates are an effective tool for improving the structure and quality of NL requirements statements. When templates are used for specifying the requirements, an important quality assurance task is to ensure that the requirements conform to the intended templates. We develop an automated solution for checking the conformance of requirements to templates. • Extraction of glossary terms. Requirements glossaries (dictionaries) improve the understandability of requirements, and mitigate vagueness and ambiguity. We develop an auto- mated solution for supporting requirements analysts in the selection of glossary terms and their related terms. • Extraction of domain models. By providing a precise representation of the main concepts in a software project and the relationships between these concepts, a domain model serves as an important artifact for systematic requirements elaboration. We propose an automated approach for domain model extraction from requirements. The extraction rules in our approach encompass both the rules already described in the literature as well as a number of important extensions developed in this dissertation. • Identifying the impact of requirements changes. Uncontrolled change in requirements presents a major risk to the success of software projects. We address two different dimen- sions of requirements change analysis in this dissertation: First, we develop an automated approach for predicting how a change to one requirement impacts other requirements. Next, we consider the propagation of change from requirements to design. To this end, we develop an automated approach for predicting how the design of a system is impacted by changes made to the requirements

    Logics and Models for Stochastic Analysis Beyond Markov Chains

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    Application of information extraction techniques to pharmacological domain : extracting drug-drug interactions

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    Una interacción farmacológica ocurre cuando los efectos de un fármaco se modifican por la presencia de otro. Las consecuencias pueden ser perjudiciales si la interacción causa un aumento de la toxicidad del fármaco o la disminución de su efecto, pudiendo provocar incluso la muerte del paciente en los peores casos. Las interacciones farmacológicas no sólo suponen un grave problema para la seguridad del paciente, sino que además también conllevan un importante incremento en el gasto médico. En la actualidad, el personal sanitario tiene a su disposición diversas bases de datos sobre interacciones que permiten evitar posibles interacciones a la hora de prescribir un determinado tratamiento, sin embargo, estas bases de datos no están completas. Por este motivo, médicos y farmacéuticos se ven obligados a revisar una gran cantidad de artículos científicos e informes sobre seguridad de medicamentos para estar al día de todo lo publicado en relación al tema. Desgraciadamente, el gran volumen de información al respecto hace que estos profesionales estén desbordados ante tal avalancha. El desarrollo de métodos automáticos que permitan recopilar, mantener e interpretar toda esta información es crucial a la hora de conseguir una mejora real en la detección temprana de las interacciones entre fármacos. Por tanto, la extracción de información podría reducir el tiempo empleado por el personal médico en la revisión de la literatura médica. Sin embargo, la extracción de interacciones farmacológicas a partir textos biomédicos no ha sido dirigida hasta el momento. Motivados por estos aspectos, en esta tesis hemos realizado un estudio detallado sobre diversas técnicas de extracción de información aplicadas al dominio farmacológico. Basándonos en este estudio, hemos propuesto dos aproximaciones distintas para la extracción de interacciones farmacológicas de los textos. Nuestra primera aproximación propone un enfoque híbrido, que combina análisis sintáctico superficial y la aplicación de patrones léxicos definidos por un farmacéutico. La segunda aproximación se aborda mediante aprendizaje supervisado, concretamente, el uso de métodos kernels. Además, se han desarrollado las siguientes tareas auxiliares: (1) el análisis de los textos utilizando la herramienta UMLS MetaMap Transfer (MMTx), que proporciona información sintáctica y semántica, (2) un proceso para identificar y clasificar los nombres de fármacos que ocurren en los textos, y (3) un proceso para reconoger las expresiones anafóricas que se refieren a fármacos. Un prototipo ha sido desarrollado para integrar y combinar las distintas técnicas propuestas en esta tesis. Para la evaluación de las dos propuestas, con la ayuda de un farmacéutico desarrollamos y anotamos un corpus con interacciones farmacológicas. El corpus DrugDDI es una de las principales aportaciones de la tesis, ya que es el primer corpus en el dominio biomédico anotado con este tipo de información y porque creemos que puede alentar la investigación sobre extracción de información en el dominio farmacológico. Los experimentos realizados demuestran que el enfoque basado en kernels consigue mejores resultados que los reportados por el enfoque que utiliza información sintáctica y patrones léxicos. Además, los kernels consiguen resultados comparables a los obtenidos en dominios similares como son las interacciones entre proteínas. Esta tesis se ha llevado a cabo en el marco del consorcio de investigación MAVIRCM (Mejorando el acceso y visibilidad de la información multilingüe en red para la Comunidad de Madrid, www.mavir.net) dentro del Programa de Actividades de I+D en Tecnologías 2005-2008 de la Comunidad de Madrid (S-0505/TIC-0267) así como en el proyecto de investigación BRAVO: ”Búsqueda de Respuestas Avanzada Multimodal y Multilingüe” (TIN2007-67407-C03-01).----------------------------------------------------------------------------------------A drug-drug interaction occurs when one drug influences the level or activity of another drug. The detection of drug interactions is an important research area in patient safety since these interactions can become very dangerous and increase health care costs. Although there are different databases supporting health care professionals in the detection of drug interactions, this kind of resource is rarely complete. Drug interactions are frequently reported in journals of clinical pharmacology, making medical literature the most effective source for the detection of drug interactions. However, the increasing volume of the literature overwhelms health care professionals trying to keep an up-to-date collection of all reported drug-drug interactions. The development of automatic methods for collecting, maintaining and interpreting this information is crucial for achieving a real improvement in their early detection. Information Extraction (IE) techniques can provide an interesting way of reducing the time spent by health care professionals on reviewing the literature. Nevertheless, no approach has been carried out to extract drug-drug interactions from biomedical texts. In this thesis, we have conducted a detailed study on various IE techniques applied to biomedical domain. Based on this study, we have proposed two different approximations for the extraction of drug-drug interactions from texts. The first approximation proposes a hybrid approach, which combines shallow parsing and pattern matching to extract relations between drugs from biomedical texts. The second approximation is based on a supervised machine learning approach, in particular, kernel methods. In addition, we have created and annotated the first corpus, DrugDDI, annotated with drug-drug interactions, which allow us to evaluate and compare both approximations. To the best of our knowledge, the DrugDDI corpus is the only available corpus annotated for drug-drug interactions and this thesis is the first work which addresses the problem of extracting drug-drug interactions from biomedical texts. We believe the DrugDDI corpus is an important contribution because it could encourage other research groups to research into this problem. We have also defined three auxiliary processes to provide crucial information, which will be used by the aforementioned approximations. These auxiliary tasks are as follows: (1) a process for text analysis based on the UMLS MetaMap Transfer tool (MMTx) to provide shallow syntactic and semantic information from texts, (2) a process for drug name recognition and classification, and (3) a process for drug anaphora resolution. Finally, we have developed a pipeline prototype which integrates the different auxiliary processes. The pipeline architecture allows us to easily integrate these modules with each of the approaches proposed in this thesis: pattern-matching or kernels. Several experiments were performed on the DrugDDI corpus. They show that while the first approximation based on pattern matching achieves low performance, the approach based on kernel-methods achieves a performance comparable to those obtained by approaches which carry out a similar task such as the extraction of protein-protein interactions. This work has been partially supported by the Spanish research projects: MAVIR consortium (S-0505/TIC-0267, www.mavir.net), a network of excellence funded by the Madrid Regional Government and TIN2007-67407-C03-01 (BRAVO: Advanced Multimodal and Multilingual Question Answering)

    GSI Scientific Report 2009 [GSI Report 2010-1]

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    GSI Scientific Report 2009 [GSI Report 2010-1]

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    Displacement design response spectrum is an essential component for the currently-developing displacement-based seismic design and assessment procedures. This paper proposes a new and simple method for constructing displacement design response spectra on soft soil sites. The method takes into account modifications of the seismic waves by the soil layers, giving due considerations to factors such as the level of bedrock shaking, material non-linearity, seismic impedance contrast at the interface between soil and bedrock, and plasticity of the soil layers. The model is particularly suited to applications in regions with a paucity of recorded strong ground motion data, from which empirical models cannot be reliably developed
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