Skip to Main content Skip to Navigation
Theses

Étude de la dynamique des réseaux biologiques : apprentissage des modèles, intégration des données temporelles et analyse formelle des propriétés dynamiques

Abstract : Over the last few decades, the emergence of a wide range of new technologies has produced a massive amount of biological data (genomics, proteomics...). Thus, a very large amount of time series data is now produced every day. The newly produced data can give us new ideas about the behavior of biological systems. This leads to considerable developments in the field of bioinformatics that could benefit from these enormous data. This justifies the motivation to develop efficient methods for learning Biological Regulatory Networks (BRN) modeling a biological system from its time series data. Then, in order to understand the nature of system functions, we study, in this thesis, the dynamics of their BRN models. Indeed, we focus on developing original and scalable logical methods (implemented in Answer Set Programming) to deciphering the emerging complexity of dynamics of biological systems. The main contributions of this thesis are enumerated in the following. (i) Refining the dynamics of the BRN, modeling with the automata Network (AN) formalism, by integrating a temporal parameter (delay) in the local transitions of the automata. We call the extended formalism a Timed Automata Network (T-AN). This integration allows the parametrization of the transitions between each automata local states as well as between the network global states. (ii) Learning BRNs modeling biological systems from their time series data. (iii) Model checking of discrete dynamical properties of BRN (modeling with AN and T-AN) by dynamical formal analysis : attractors identification (minimal trap domains from which the network cannot escape) and reachability verification of an objective from a network global initial state.
Document type :
Theses
Complete list of metadatas

Cited literature [314 references]  Display  Hide  Download

https://tel.archives-ouvertes.fr/tel-02506943
Contributor : Abes Star :  Contact
Submitted on : Thursday, March 12, 2020 - 4:16:08 PM
Last modification on : Wednesday, June 24, 2020 - 4:19:35 PM
Long-term archiving on: : Saturday, June 13, 2020 - 5:25:28 PM

File

E_BENABDALLAH.pdf
Version validated by the jury (STAR)

Identifiers

  • HAL Id : tel-02506943, version 1

Citation

Emna Ben Abdallah. Étude de la dynamique des réseaux biologiques : apprentissage des modèles, intégration des données temporelles et analyse formelle des propriétés dynamiques. Bio-Informatique, Biologie Systémique [q-bio.QM]. École centrale de Nantes, 2017. Français. ⟨NNT : 2017ECDN0041⟩. ⟨tel-02506943⟩

Share

Metrics

Record views

124

Files downloads

87