Structure Learning and Gene Regulatory Networks

David Allouche, Christine Cierco-Ayrolles, Simon de Givry, G Guillermin, Brigitte Mangin, Thomas Schiex, Jimmy Vandel, and Matthieu Vignes
Gene Network Inference, chapter A Panel of Learning Methods for the Reconstruction of Gene Regulatory Networks in a Systems Genetics Contex
Springer, 2014

J Vandel, B Mangin, and S de Givry
New Local Move Operators for Bayesian Network Structure Learning
In Proc. of PGM-12, Granada, Spain, 2012

Matthieu Vignes, Jimmy Vandel, David Allouche, Nidal Ramadan-Alban, Christine Cierco-Ayrolles, Thomas Schiex, Brigitte Mangin, and Simon de Givry
Gene regulatory network reconstruction using bayesian networks, the dantzig selector, the lasso and their meta-analysis
PLoS ONE, 6(12), 2011

Agronomy and Operations Research

Sara Maqrot, Simon de Givry, Gauthier Quesnel, and Marc Tchamitchian
A Mixed Integer Programming Reformulation of the Mixed Fruit-Vegetable Crop Allocation Problem
In 30th International Conference on Industrial, Engineering, and Other Applications of Applied Intelligent Systems (IEA/AIE), page 12 pages, Arras, France, June 2017

Mahuna Akplogan, Simon de Givry, Jean-Philippe Métivier, Gauthier Quesnel, Alexandre Joannon, and Frédérick Garcia
Solving the crop allocation problem using hard and soft constraints
RAIRO - Operations Research, 47:151-172, 2013


Clément Viricel, Simon de Givry, Thomas Schiex, and Sophie Barbe
Cost function network-based design of protein-protein interactions: predicting changes in binding affinity
Bioinformatics, 34(15):2581-2589, 2018

D. Simoncini, D. Allouche, S. de Givry, C. Delmas, S. Barbe, and T. Schiex
Guaranteed discrete energy optimization on large protein design problems
Journal of Chemical Theory and Computation, 11(12):5980-5989, 2015

Seydou Traoré, David Allouche, Isabelle André, Simon de Givry, George Katsirelos, Thomas Schiex, and Sophie Barbe
A new framework for computational protein design through cost function network optimization
Bioinformatics, 29(17):2129-2136, 2013

B. Servin, S. de Givry, and T. Faraut
Statistical confidence measures for genome maps: application to the validation of genome assemblies
Bioinformatics, 26(24):3035-3042, 2010

M. Sanchez, S. de Givry, and T. Schiex
Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques
Constraints, 13(1):130-154, 2008
Special issue on Bioinformatics and Constraints. The original publication is available at

Patricia Thébault, Simon de Givry, Thomas Schiex, and Christine Gaspin
Searching RNA motifs and their intermolecular contacts with constraint networks
Bioinformatics, 22(17):2074-2080, 2006

T. Faraut, S. de Givry, P. Chabrier, T. Derrien, F. Galibert, C. Hitte, and T. Schiex
A comparative genome approach to marker ordering
Bioinformatics, 23(2):50-56, 2007

Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, and Thomas Schiex
CARTHAGENE: multipopulation integrated genetic and radiated hybrid mapping
Bioinformatics, 21(8):1703-1704, 2005

Valued Constraint Satisfaction Problems

S de Givry and G Katsirelos
Clique Cuts in Weighted Constraint Satisfaction
In Proc. of CP-17, pages 97-113, Melbourne, Australia, 2017

Abdelkader Ouali, David Allouche, Simon de Givry, Samir Loudni, Yahia Lebbah, Francisco Eckhardt, and Lakhdar Loukil
Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization
In Proc. of UAI-17, pages 550-559, Sydney, Australia, 2017

Hiep Nguyen, Christian Bessiere, Simon de Givry, and Thomas Schiex
Triangle-based Consistencies for Cost Function Networks
Constraints, 22(2):230-264, 2017

David Allouche, Christian Bessière, Patrice Boizumault, Simon de Givry, Patricia Gutierrez, Jimmy H.M. Lee, Ka Lun Leung, Samir Loudni, Jean-Philippe Métivier, Thomas Schiex, and Yi Wu
Tractability-preserving transformations of global cost functions
Artificial Intelligence, 238:166-189, 2016

B Hurley, B O'Sullivan, D Allouche, G Katsirelos, T Schiex, M Zytnicki, and S de Givry
Multi-Language Evaluation of Exact Solvers in Graphical Model Discrete Optimization
Constraints, 21(3):413-434, 2016
Presentation at CPAIOR'16, Banff, Canada,

D Allouche, S de Givry, G Katsirelos, T Schiex, and M Zytnicki
Anytime Hybrid Best-First Search with Tree Decomposition for Weighted CSP
In Proc. of CP-15, pages 12-28, Cork, Ireland, 2015

David Allouche, Jessica Davies, Simon de Givry, George Katsirelos, Thomas Schiex, Seydou Traoré, Isabelle André, Sophie Barbe, Steve Prestwich, and Barry O'Sullivan
Computational protein design as an optimization problem
Artificial Intelligence, 212:59-79, 2014

S de Givry, S Prestwich, and B O'Sullivan
Dead-End Elimination for Weighted CSP
In Proc. of CP-13, pages 263-272, Uppsala, Sweden, 2013

D Allouche, S Traoré, I André, S de Givry, G Katsirelos, S Barbe, and T Schiex
Computational protein design as a cost function network optimization problem
In Proc. of CP-12, Quebec City, Canada, 2012

D Allouche, C Bessiere, P Boizumault, S de Givry, P Gutierrez, S Loudni, JP Métivier, and T Schiex
Decomposing global cost functions
In Proc. of AAAI-12, Toronto, Canada, 2012 (poster)

A Favier, S de Givry, A Legarra, and T Schiex
Pairwise decomposition for combinatorial optimization in graphical models
In Proc. of IJCAI-11, Barcelona, Spain, 2011
Video demonstration at

A. Favier, S. de Givry, and P. Jégou
Solution counting for CSP and SAT with large tree-width
Control Systems and Computers, (2):4-13, 2011

D. Allouche, S. de Givry, and T. Schiex
Towards parallel non serial dynamic programming for solving hard weighted csp
In Proc. of CP-10, St Andrews, Scotland, 2010

M. Cooper, S. de Givry, M. Sanchez, T. Schiex, M. Zytnicki, and T. Werner
Soft arc consistency revisited
Artificial Intelligence, (7-8):449-478, 2010

M. Zytnicki, C. Gaspin, S. de Givry, and T. Schiex
Bounds Arc Consistency for Weighted CSPs
Journal of Artificial Intelligence Research, 35:593-621, 2009

R. Marinescu, R. Dechter, S. de Givry, and T. Schiex
Combinatorial optimization for graphical models
IJCAI-09 tutorial, July 2009

M Sanchez, D Allouche, S de Givry, and T Schiex
Russian doll search with tree decomposition
In Proc. of IJCAI'09, Pasadena (CA), USA, 2009

M. Cooper, S. de Givry, M. Sanchez, T. Schiex, and M. Zytnicki
Virtual arc consistency for weighted csp
In Proc. of AAAI-08, Chicago, IL, 2008

J. Larrosa, F. Heras, and S. de Givry
A logical approach to efficient max-sat solving
Artificial Intelligence, 172(2-3):204-233, 2008

M. Cooper, S. de Givry, and T. Schiex
Optimal soft arc consistency
In Proc. of IJCAI-07, pages 68-73, Hyderabad, India, 2007

Simon de Givry, Thomas Schiex, and Gérard Verfaillie
Exploiting tree decomposition and soft local consistency in weighted csp
In Proc. of AAAI-06, Boston, MA, 2006 (slides)

S. de Givry, M. Zytnicki, F. Heras, and J. Larrosa
Existential arc consistency: Getting closer to full arc consistency in weighted csps
In Proc. of IJCAI-05, pages 84-89, Edinburgh, Scotland, 2005

S. de Givry, J. Larrosa, P. Meseguer, and T. Schiex
Solving max-sat as weighted csp
In Proc. of CP-03, pages 363-376, Kinsale, County Cork, Ireland, 2003

Bertrand Cabon, Simon de Givry, and Gérard Verfaillie
Anytime Lower Bounds for Constraint Optimization Problems
In Proc. of CP-98, pages 117-131, Pisa, Italy, October 26-30 1998

Simon de Givry, Gérard Verfaillie, and Thomas Schiex
Bounding the Optimum of Constraint Optimization Problems
In Proc. of CP-97, pages 405-419, Schloss Hagenberg, Austria, October 29 - November 1 1997

Constraint Programming

S. de Givry and L. Jeannin
A unified framework for partial and hybrid search methods in constraint programming
Computer & Operations Research, 33(10):2805-2833, 2006

S. de Givry, L. Jeannin, F. Josset, J. Mattioli, N. Museux, and P. Savéant
The thales constraint programming framework for hard and soft real-time applications
The PLANET Newsletter, Issue 5 ISSN 1610-0212, pages 5-7, December 2002 (slides)

S. de Givry, Y. Hamadi, J. Mattioli, P. Gérard, M. Lemaître, G. Verfaillie, A. Aggoun, I. Gouachi, T. Benoist, E. Bourreau, F. Laburthe, P. David, S. Loudni, and S. Bourgault
Towards an on-line optimisation framework
In CP-2001 Workshop on On-Line combinatorial problem solving and ConstraintProgramming (OLCP'01), pages 45-61, Paphos, Cyprus, December 1 2001

Jean Jourdan, Simon de Givry, and Pierre Savéant
Designing limited search algorithms for time constrained combinatorial optimization problems
Technical report, Thales Research & Development, 1999

Simon Degivry 2019-04-12