Bibliography

Structure Learning and Gene Regulatory Networks

2
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

3
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

4
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

6
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

7
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

Bioinformatics

9
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

10
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

11
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
http://bioinformatics.oxfordjournals.org/content/29/17/2129.abstract?keytype=ref&ijkey=6s5WwvLNn88x2ZB

12
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

13
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 http://www.springerlink.com

14
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

15
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

16
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

18
S de Givry and G Katsirelos
Clique Cuts in Weighted Constraint Satisfaction
In Proc. of CP-17, pages 97-113, Melbourne, Australia, 2017

19
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

20
Hiep Nguyen, Christian Bessiere, Simon de Givry, and Thomas Schiex
Triangle-based Consistencies for Cost Function Networks
Constraints, 22(2):230-264, 2017

21
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

22
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, http://www.inra.fr/mia/T/degivry/cpaior16sdg.pdf

23
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

24
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

25
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

26
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

27
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
http://www.inra.fr/mia/T/degivry/Ficolofo2012poster.pdf (poster)

28
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 http://www.inra.fr/mia/T/degivry/Favier11.mov

29
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

30
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

31
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

32
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

33
R. Marinescu, R. Dechter, S. de Givry, and T. Schiex
Combinatorial optimization for graphical models
IJCAI-09 tutorial, July 2009
http://www.inra.fr/mia/T/degivry/tutorial_optimization_ijcai09.ppt

34
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
http://www.inra.fr/mia/T/degivry/rdsbtd_ijcai09_sdg.ppt

35
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

36
J. Larrosa, F. Heras, and S. de Givry
A logical approach to efficient max-sat solving
Artificial Intelligence, 172(2-3):204-233, 2008

37
M. Cooper, S. de Givry, and T. Schiex
Optimal soft arc consistency
In Proc. of IJCAI-07, pages 68-73, Hyderabad, India, 2007

38
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
http://www.inra.fr/mia/T/degivry/VerfaillieAAAI06pres.pdf (slides)

39
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

40
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

41
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

42
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

44
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

45
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
http://planet.dfki.de/service/Resources/Rome/degivry.pdf (slides)

46
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

47
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