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Méthodes numériques et formelles pour l'ingénierie des réseaux biologiques : traitement de l'information par des populations d'oscillateurs. Approches par contraintes et Taxonomie des réseaux biologiques

Abstract : This thesis is concerned by the engineering of complex systems from a desired dynamics. Particularly, we are interested by populations of oscillators and genetical regulatory networks. In a first part, we start from a hypothesis introduced in neuroscience, which highlight the role of neural synchronization in the cognitive processing. We propose to use this hypothesis in a more general panorama to investigate the computing with populations of oscillators. We discuss about the isochrons of few oscillators selected according to their symmetry in the state space. Therefore, we define procedures for making footprints, for reading and for reorganizing information by a population of oscillators. As a perspective, we propose a system of lattices of Wilson-Cowan oscillators organized in several interconnected layers. This system properly mixes synchronization and desynchronization by using two types of coupling : pulsed and continuous coupling. At the end of this part, we propose to use this system in order to detect the edges of an image. In the second part, we propose a constraint-based approach to determine the structure of genetic regulatory networks starting from incomplete knowledge on their structure and their dynamics. The formalism we use is widely called thresholded Boolean automata networks or Hopfield-like networks. As an proof of concept, we apply this method to determine the regulatory network of Arabidopsis thaliana flower morphogenesis. We obtain 532 valid models instead of one unique solution and then classify them by using structural robustness criteria. By this way, we showed the potential of this approach in determining and classifying thresholded Boolean automata networks like genetic regulatory networks or neural networks. This works leads to many applications, in particular the developpement and the design of new methods for processing information and the design of systems of unconventional computing.
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Mohamed Hedi Ben Amor. Méthodes numériques et formelles pour l'ingénierie des réseaux biologiques : traitement de l'information par des populations d'oscillateurs. Approches par contraintes et Taxonomie des réseaux biologiques. Médecine humaine et pathologie. Université de Grenoble, 2012. Français. ⟨NNT : 2012GRENS020⟩. ⟨tel-00778673v2⟩

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