- E-mail: loic.pauleve lri.fr – PGP key: E7E7D63A – ORCID:0000-0002-7219-2027.
- LRI, Bât 650 Ada Lovelace, Université Paris-Sud, 91405 Orsay Cedex, France.
- Office: 140.
- Formal analysis of dynamics of large-scale biological networks.
- Abstract interpretation of traces in concurrent systems.
- Stochastic simulation and parameters estimation.
My main research focuses on the abstract interpretation of traces in automata networks. I introduced the Local Causality Graphs (Graphes de Causalité Locale) which represent necessary and/or sufficient intermediary steps for changing a local state of a given automaton. Local Causality Graphs bring a very compact representation of all the possible traces of an Automata Network. They have been applied for deriving highly scalable necessary or sufficient conditions for reachability properties in Automata Networks. Local Causality Graphs have also been applied for deducing correct cut sets for transient reachability, i.e. sets of mutations that make impossible the concerned reachability to occur; and for goal-oriented model reduction preserving minimal traces for reachability. Such analysis have been applied to networks ranging from 100 to 10,000 nodes, which was unprecedented.
During my PhD studies, I introduced the Process Hitting (Frappes de Processus) framework for modeling the qualitative dynamics of Biological Regulatory Networks (Boolean and multi-valued networks) possibly without a complete knowledge of the interactions. The Process Hitting is a particular class of Asynchronous Automata Networks or Petri nets where transitions modify the state of only one automaton at a time and are triggered by at most one other automaton of the network. Several extensions (priorities, stochastic) are investigated. See also my PhD thesis, and [PCFMR14-chapterLMBS].
I created and maintain the software Pint which provides a language for specifying Automata Networks and Process Hitting models, and several static analysis tools (reachability, fixed point, stochastic simulation). Recently, I supervised the development of the software CausaLex for visualizing and scripting Local Causality Graphs that can be generated using Pint.
I am coordinator of the project AlgoReCell (ANR-FNR, 2017-2020). I am involved in the projects HyClock (ANR, 2015-2017); RNALands (ANR-FWF, 2015-2017). Previously, I was involved in the projects BioTempo (ANR Blanc, 2011-2014); CirClock (PEPII CNRS, 2011-2012).
I am co-supervising the PhD studies of Juraj Kolčák (2017-2020; funded by ANR-FNR AlgoReCell project) on parametric regulatory networks and Hugues Mandon (2016-2019; funded by Digicosme Labex) on Boolean network reprogramming.
I am PC member of CMSB'17; SASB'17; JOBIM'17. I was PC co-chair of SASB'15; SASB'14; PC member of SASB'16; CMSB'15; MEMICS'15; SASB'13; SASB'12; and organizing committee member of SeqBio 2015. I was member of the PhD commitee of Adrien Rougny (Univ. Paris-Saclay, 2016); Séverine Affeldt (Institut Curie, 2015).
I got my M.Sc. in computer science from École Normale Supérieure de Cachan, Brittany extension, France, in 2008 and my Ph.D. from École Centrale de Nantes, France, in 2011, supervised by Olivier Roux and Morgan Magnin. Between 2011 and 2012, I have been a postdoc at Laboratoire d'Informatique de l'École Polytechnique (LIX), France, in the AMIB group. Between 2012 and 2013, I have been a postdoc at ETH Zürich, Switzerland, in the BISON group of Heinz Koeppl. Since 2013, I am a researcher at CNRS in LRI laboratory in the Bioinfo group.