Welcome to my website !

I'm a PhD Student at IFP Énergies nouvelles (IFPEN) in the Control, Signal and System Department and Univerité Paris-Est in the Laboratoire d'Informatique Gaspard Monge (LIGM).

My PhD advisors are Jean-Christophe Pesquet (LIGM), Laurent Duval (IFPEN - Math.), Camille Couprie (Facebook, AI Research) and Frédérique Bidard-Michelot (IFPEN - Bio).

PhD Work

Reconstruction and Clustering with Graph optimization and Priors on Gene networks and Images

We propose to address network inference problems with recently developed techniques pertaining to graph (nodes and edges) optimization with biological and structural priors, leading to a vari- ational analysis. Those choices are driven by an apparent simplicity of certain basic biological mechanisms in cells, and the ability to operate with conditions allowing variations in the studied enzyme production mechanisms. Given all the pairwise gene regulation information available, we propose to determine the presence of edges in the final GRN by adopting an energy optimization formulation. To refine inference results by restricting the space of possible solutions, additional constraints are incor- porated into our models. Some constraints, reflecting either biological (information about gene interactions) or structural (information about node connectivity) a priori, have been considered. Different priors lead to different mathematical properties of the global cost function, for which various optimization strategies can be applied. Optimization strategies are inspired by recent graph optimization works in image processing and computer vision, where pixels and their con- nectivity are used to interpret images at a higher level. We devote them the dedicated ?? for a more self-contained reading. The post-processing network refinements we proposed led to a software suite named BRANE *** for "Biologically-Related A priori for Network Enhancement".

My thesis in 3 minutes

3 minutes thesis

Useful Links

LIGM : Laboratoire d'Informatique Gaspard Monge

IFPEN : IFP Énergies nouvelles

Linked in: see my profil

BRANE Page: all you need to know about the suite of BRANE software

Contact

IFP Énergie nouvelles
Dir. Mécatronique et Numérique
1 & 4 avenue de Bois-Préau
92852 Rueil-Malmaison cedex - France
aurelie{dot}pirayre{at}ifpen{dot}fr
01 47 52 61 27

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