RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case

International audienceThe rapid expansion of biomedical literature has provoked an increased development of advanced text mining tools to rapidly extract relevant events from the continuously increasing amount of knowledge published periodically in PubMed. However, bioinvestigators are still reluctant to use these tools for two reasons: i) a large volume of events is often extracted upon a query, and this volume is hard to manage, and ii) background events dominate search results and overshadow more pertinent published information, especially for domain experts. In this paper, we propose an approach that incorporates the temporal dimension of published events to the process of information extraction to improve data selection and prioritize more pertinent periodically published knowledge for scientists. Indeed, instead of providing the total knowledge associated with a PubMed query, which is usually a mix of trivial background information and non-background information, we propose a method that incorporates time and selects non background and highly relevant biological entities and events published over time for bioinvestigators. Before excluding background events from the total knowledge extracted, a quantification of their amount is also provided. This work is illustrated by a case study regarding Hepcidin gene publications over a decade, a duration that is sufficiently long enough to generate alternative views on the overall data extracted

Multi-level and multi-objective design optimization tools for handling complex systems

La conception d'un système électrique est une tâche très complexe qui relève d’expertises dans différents domaines de compétence. Dans un contexte compétitif où l’avance technologique est un facteur déterminant, l’industrie cherche à réduire les temps d'étude et à fiabiliser les solutions trouvées par une approche méthodologique rigoureuse fournissant une solution optimale systémique.Il est alors nécessaire de construire des modèles et de mettre au point des méthodes d'optimisation compatibles avec ces préoccupations. En effet, l’optimisation unitaire de sous-systèmes sans prendre en compte les interactions ne permet pas d'obtenir un système optimal. Plus le système est complexe plus le travail est difficile et le temps de développement est important car il est difficile pour le concepteur d'appréhender le système dans toute sa globalité. Il est donc nécessaire d'intégrer la conception des composants dans une démarche systémique et globale qui prenne en compte à la fois les spécificités d’un composant et ses relations avec le système qui l’emploie.Analytical Target Cascading est une méthode d'optimisation multi niveaux de systèmes complexes. Cette approche hiérarchique consiste à décomposer un système complexe en sous-systèmes, jusqu’au niveau composant dont la conception relève d’algorithmes d'optimisation classiques. La solution optimale est alors trouvée par une technique de coordination qui assure la cohérence de tous les sous-systèmes. Une première partie est consacrée à l'optimisation de composants électriques. L'optimisation multi niveaux de systèmes complexes est étudiée dans la deuxième partie où une chaîne de traction électrique est choisie comme exempleThe design of an electrical system is a very complex task which needs experts from various fields of competence. In a competitive environment, where technological advance is a key factor, industry seeks to reduce study time and to make solutions reliable by way of a rigorous methodology providing a systemic solution.Then, it is necessary to build models and to develop optimization methods which are suitable with these concerns. Indeed, the optimization of sub-systems without taking into account the interaction does not allow to achieve an optimal system. More complex the system is more the work is difficult and the development time is important because it is difficult for the designer to understand and deal with the system in its complexity. Therefore, it is necessary to integrate the design components in a systemic and holistic approach to take into account, in the same time, the characteristics of a component and its relationship with the system it belongs to.Analytical Target Cascading is a multi-level optimization method for handling complex systems. This hierarchical approach consists on the breaking-down of a complex system into sub-systems, and component where their optimal design is ensured by way of classical optimization algorithms. The optimal solution of the system must be composed of the component's solutions. Then a coordination strategy is needed to ensure consistency of all sub-systems. First, the studied and proposed optimization algorithms are tested and compared on the optimization of electrical components. The second part focuses on the multi-level optimization of complex systems. The optimization of railway traction system is taken as a test cas

Méthodologie et algorithmes adaptés à l’optimisation multi-niveaux et multi-objectif de systèmes complexes

The design of an electrical system is a very complex task which needs experts from various fields of competence. In a competitive environment, where technological advance is a key factor, industry seeks to reduce study time and to make solutions reliable by way of a rigorous methodology providing a systemic solution.Then, it is necessary to build models and to develop optimization methods which are suitable with these concerns. Indeed, the optimization of sub-systems without taking into account the interaction does not allow to achieve an optimal system. More complex the system is more the work is difficult and the development time is important because it is difficult for the designer to understand and deal with the system in its complexity. Therefore, it is necessary to integrate the design components in a systemic and holistic approach to take into account, in the same time, the characteristics of a component and its relationship with the system it belongs to.Analytical Target Cascading is a multi-level optimization method for handling complex systems. This hierarchical approach consists on the breaking-down of a complex system into sub-systems, and component where their optimal design is ensured by way of classical optimization algorithms. The optimal solution of the system must be composed of the component's solutions. Then a coordination strategy is needed to ensure consistency of all sub-systems. First, the studied and proposed optimization algorithms are tested and compared on the optimization of electrical components. The second part focuses on the multi-level optimization of complex systems. The optimization of railway traction system is taken as a test caseLa conception d'un système électrique est une tâche très complexe qui relève d’expertises dans différents domaines de compétence. Dans un contexte compétitif où l’avance technologique est un facteur déterminant, l’industrie cherche à réduire les temps d'étude et à fiabiliser les solutions trouvées par une approche méthodologique rigoureuse fournissant une solution optimale systémique.Il est alors nécessaire de construire des modèles et de mettre au point des méthodes d'optimisation compatibles avec ces préoccupations. En effet, l’optimisation unitaire de sous-systèmes sans prendre en compte les interactions ne permet pas d'obtenir un système optimal. Plus le système est complexe plus le travail est difficile et le temps de développement est important car il est difficile pour le concepteur d'appréhender le système dans toute sa globalité. Il est donc nécessaire d'intégrer la conception des composants dans une démarche systémique et globale qui prenne en compte à la fois les spécificités d’un composant et ses relations avec le système qui l’emploie.Analytical Target Cascading est une méthode d'optimisation multi niveaux de systèmes complexes. Cette approche hiérarchique consiste à décomposer un système complexe en sous-systèmes, jusqu’au niveau composant dont la conception relève d’algorithmes d'optimisation classiques. La solution optimale est alors trouvée par une technique de coordination qui assure la cohérence de tous les sous-systèmes. Une première partie est consacrée à l'optimisation de composants électriques. L'optimisation multi niveaux de systèmes complexes est étudiée dans la deuxième partie où une chaîne de traction électrique est choisie comme exempl

Quality-Aware Integration and Warehousing of Genomic Data

International audienceIn human health and life sciences, researchers extensively collaborate with each other, sharing biomedical and genomic data and their experimental results. This necessitates dynamically integrating different databases or warehousing them into a single repository. Based on our past experience of building a data warehouse called GEDAW (Gene Expression Data Warehouse) that stores data on genes expressed in the liver during iron overload and liver pathologies, and also relevant information from public databanks (mostly in XML format), DNA chips home experiments and medical records, we present the lessons learned, the data quality issues in this context and the current solutions we propose for integrating and warehousing biomedical data. This paper provides a functional and modular architecture for data quality enhancement and awareness in the complex processes of integration and warehousing of biomedical data

Multi-level and multi-objective design optimization tools for handling complex systems

La conception d'un système électrique est une tâche très complexe qui relève d expertises dans différents domaines de compétence. Dans un contexte compétitif où l avance technologique est un facteur déterminant, l industrie cherche à réduire les temps d'étude et à fiabiliser les solutions trouvées par une approche méthodologique rigoureuse fournissant une solution optimale systémique.Il est alors nécessaire de construire des modèles et de mettre au point des méthodes d'optimisation compatibles avec ces préoccupations. En effet, l optimisation unitaire de sous-systèmes sans prendre en compte les interactions ne permet pas d'obtenir un système optimal. Plus le système est complexe plus le travail est difficile et le temps de développement est important car il est difficile pour le concepteur d'appréhender le système dans toute sa globalité. Il est donc nécessaire d'intégrer la conception des composants dans une démarche systémique et globale qui prenne en compte à la fois les spécificités d un composant et ses relations avec le système qui l emploie.Analytical Target Cascading est une méthode d'optimisation multi niveaux de systèmes complexes. Cette approche hiérarchique consiste à décomposer un système complexe en sous-systèmes, jusqu au niveau composant dont la conception relève d algorithmes d'optimisation classiques. La solution optimale est alors trouvée par une technique de coordination qui assure la cohérence de tous les sous-systèmes. Une première partie est consacrée à l'optimisation de composants électriques. L'optimisation multi niveaux de systèmes complexes est étudiée dans la deuxième partie où une chaîne de traction électrique est choisie comme exempleThe design of an electrical system is a very complex task which needs experts from various fields of competence. In a competitive environment, where technological advance is a key factor, industry seeks to reduce study time and to make solutions reliable by way of a rigorous methodology providing a systemic solution.Then, it is necessary to build models and to develop optimization methods which are suitable with these concerns. Indeed, the optimization of sub-systems without taking into account the interaction does not allow to achieve an optimal system. More complex the system is more the work is difficult and the development time is important because it is difficult for the designer to understand and deal with the system in its complexity. Therefore, it is necessary to integrate the design components in a systemic and holistic approach to take into account, in the same time, the characteristics of a component and its relationship with the system it belongs to.Analytical Target Cascading is a multi-level optimization method for handling complex systems. This hierarchical approach consists on the breaking-down of a complex system into sub-systems, and component where their optimal design is ensured by way of classical optimization algorithms. The optimal solution of the system must be composed of the component's solutions. Then a coordination strategy is needed to ensure consistency of all sub-systems. First, the studied and proposed optimization algorithms are tested and compared on the optimization of electrical components. The second part focuses on the multi-level optimization of complex systems. The optimization of railway traction system is taken as a test caseVILLENEUVE D'ASCQ-ECLI (590092307) / SudocSudocFranceF

Integration of Biological Data on Transcriptome

International audienc

RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case

The rapid expansion of biomedical literature has provoked an increased development of advanced text mining tools to rapidly extract relevant events from the continuously increasing amount of knowledge published periodically in PubMed. However, bioinvestigators are still reluctant to use these tools for two reasons: i) a large volume of events is often extracted upon a query, and this volume is hard to manage, and ii) background events dominate search results and overshadow more pertinent published information, especially for domain experts. In this paper, we propose an approach that incorporates the temporal dimension of published events to the process of information extraction to improve data selection and prioritize more pertinent periodically published knowledge for scientists. Indeed, instead of providing the total knowledge associated with a PubMed query, which is usually a mix of trivial background information and nonbackground information, we propose a method that incorporates time and selects non background and highly relevant biological entities and events published over time for bioinvestigators. Before excluding background events from the total knowledge extracted, a quantification of their amount is also provided. This work is illustrated by a case study regarding Hepcidin gene publications over a decade, a duration that is sufficiently long enough to generate alternative views on the overall data extracted

QDex: A Database Profiler for Generic Bio-data Exploration and Quality Aware Integration

International audienc