Permanent researcher (CRHC, HdR) at INRAE MIAT
Head of Statistics and Algorithms for Biology (SaAB) team
Co-chair with T. Schiex in Artificial and Natural Intelligence Toulouse Institute (ANITI)

INRAE
Centre de recherches de Toulouse
Unité de Mathématiques et Informatique Appliquées de Toulouse
24, chemin de borde rouge
B.P. 52627 - 31326 CASTANET-TOLOSAN CEDEX FRANCE
Phone: (+33) (0)5 61 28 50 74
Secr.: (+33) (0)5 61 28 52 75
Email: simon.de-givry_AT_inrae.fr
Access from Toulouse: metro line B (Ramonville exit) then bus Linéo 6 (INRAE exit in Castanet-Tolosan, then follow this)

Events

Soft 2024, First Workshop on Discrete Optimization with Soft Constraints, Girona, Spain, September 2nd, 2024.

Past Events

CPDP2022, invited presentation on Interdisciplinary Research: Cost Function Networks for Life Sciences, CP'2022 Doctoral Program, Haïfa, Israël, August 1st, 2022.
ANITI2021, presentation on cost function network solver toulbar2, ANITI seminar for industrials, November 19th, 2021 (slides in English and talk in French).
MIAT2021, présentation sur la résolution d'un problème d'optimisation exprimé par un réseau de fonctions de coûts avec toulbar2 et les services Web, séminaire INRAE -MIAT, 15 octobre, 2021.
JFRB2021, présentation sur l'apprentissage du réseau de gènes du tournesol aux 10èmes Journées Francophones sur les Réseaux Bayésiens et les Modèles Graphiques Probabilistes, île de Porquerolles, 11 octobre, 2021.
CP 2019, 25th International Conference on Principles and Practice of Constraint Programming, Stamford (CT), USA, September 30-October 4th, 2019.
PFIA 2019, tutorial on Cost Function Networks (part1, part2, demo), Plate-Forme Intelligence Artificielle, Toulouse, July 4th, 2019.
JFPC 2019, 15èmes Journées Francophones de Programmation par Contraintes, IMT Mines Albi, 12-14 juin, 2019.
ISMP18, presentation on recent algorithmic advances for combinatorial optimization in graphical models, 23rd International Symposium opn Mathematical Programming, Bordeaux, France, July 6th, 2018.
ROSa17, invited presentation on Combinatorial Optimization for Life Sciences, ROSa (Operations Research for Health Care), LAAS, Toulouse, November 7th, 2017.
CARTABLE16, invited presentation on Exact Structure Learning of Bayesian Networks, INRA Toulouse, October 13th 2016.
Heidelberg14, invited presentation on Multi-Paradigm Evaluation of Solvers in Graphical Model Discrete Optimization, workshop on Discrete Graphical Models, Heidelberg, Germany, November 14th, 2014.
CUHK13, invited presentation on Combinatorial Optimization for Life Sciences, Chinese University of Hong-Kong, China, November 1st, 2013.
JFPC'12, program chair of the French conference on Constraint Programming, Toulouse, May 22-24th, 2012.
HDR(slides), Habilitation à dirigé des recherches (in French), UPS, Toulouse, March 29th, 2011.
KIEV10, tutorial on Search Methods Exploiting the Problem Structure at Theoretical and Applied Problems of Structural Pattern Recognition Workshop, Kiev, Ukraine, September 26th, 2010.
CP10VCSP, tutorial on Valued Constraint Satisfaction Problems by Martin Cooper & Peter Jeavons & Simon de Givry at CP'10, St Andrews, Scotland, September 7th, 2010.
IJCAI09OPTIM, tutorial on Combinatorial Optimization for Graphical Models by Rina Dechter & Radu Marinescu & Simon de Givry & Thomas Schiex at IJCAI'09, Pasadena, USA, July 12th, 2009.

WCB'16, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CP 2016, Toulouse, France, September 5th, 2016.
WCB15, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CP 2015, Cork, Ireland, August 31st, 2015.
WCB14, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CP 2014, Lyon, France, September 8th, 2014.
WCB13, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CP 2013, Uppsala, Sweden, September 16th, 2013.
WCB11, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CP 2011, Perugia, Italy, September 12th, 2011.
WCB10, workshop on Constraint Based Methods for Bioinformatics held in conjunction with ICLP 2010, Edinburgh, Scotland, July 21th, 2010.
WCB09, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CP 2009, Lisbon, Portugal, September 20th, 2009.
WCB08, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CPAIOR 2008, Paris, France, May 22th, 2008.
WCB07, workshop on Constraint Based Methods for Bioinformatics held in conjunction with ICLP 2007, Porto, Portugal, September 13, 2007.
WCB06, workshop on Constraint Based Methods for Bioinformatics held in conjunction with CP 2006, Nantes, France, September 25th, 2006.

JFRB 2018, 9èmes Journées Francophones sur les Réseaux Bayésiens et les Modèles Graphiques Probabilistes, INRA Castanet-Tolosan, May 31st-June 1st, 2018.
AIGM15, workshop on Algorithmic issues for Inference in Graphical Models, Paris, France, September 28th, 2015.
AIGM14, workshop on Algorithmic issues for Inference in Graphical Models, Paris, France, September 22th, 2014.
AIGM13, workshop on Algorithmic issues for Inference in Graphical Models, Paris, France, September 13th, 2013.
AIGM12, workshop on Algorithmic issues for Inference in Graphical Models held in conjunction with ECAI 2012, Montpellier, France, August 28th, 2012.
AIGM10, workshop on Graphical models for reasoning on biological systems: computational challenges, held in conjunction with ECCS 2012, Lisbon, Portugal, September 16th, 2010.

BAI 2017, workshop on Advances in Bioinformatics and Artificial Intelligence: Bridging the Gap, held in conjunction with IJCAI-17, Melbourne, Australia, August 21, 2017.
BAI 2016, workshop on Advances in Bioinformatics and Artificial Intelligence: Bridging the Gap, held in conjunction with IJCAI-16, New York City, USA, July 11th, 2016.
BAI 2015, workshop on Advances in Bioinformatics and Artificial Intelligence: Bridging the Gap, held in conjunction with IJCAI-15, Buenos Aires, Argentina, July 27th, 2015.

Soft 2011, CP-2011 workshop on Preferences and Soft Constraints, Perugia, Italy, September 12th, 2011.
Soft 2010, CP-2010 workshop on Preferences and Soft Constraints, St Andrews, Scotland, September 6th, 2010.
Soft 2008, CP-2008 workshop on Preferences and Soft Constraints, Sydney, Australia, September 15th, 2008. Special year on Cost Function Processing.
Alenya 2008, The Unique Informal Workshop on Cost Function processing, Alenya, France, February 14-15th, 2008.
Soft 2006, CP-2006 workshop on Preferences and Soft Constraints, Nantes, France, September 25th, 2006. Special year on Structural decomposition and Tractability.
Soft 2005, CP-2005 workshop on Preferences and Soft Constraints, Sitges, Spain, October 1st, 2005.

CARTABLE, colloque sur Apprentissage de Réseaux : de la Théorie aux Applications en Biologie et Ecologie, INRA Toulouse, October 12-14th 2016.
NETBIO, atelier du réseau méthodologique MIA sur Inférence de réseaux biologiques.

Publications

Teaching

Past courses

Graphes et réseaux (in French), mineur OPTA, ENAC, Toulouse.
Théorie des graphes (in French), module Systèmes informatique et décision, ENSAE, Toulouse.
Méthodes de preuves, Optimisation et Satisfaction de contraintes (in French), M2R IA, Université Paul Sabatier, Toulouse. Also includes several tutorials from the constraint programming community.
Algorithmes et Modèles probabilistes pour la Biologie (in French), M2R IA, Université Paul Sabatier, Toulouse.
Cartographie génétique (in French), M1 Bioinformatique et biologie des Systèmes, module Génomique et génétique statistique, Université Paul Sabatier, Toulouse.

Softwares

Softwares in which I have been involved.

baryonyx: an approximate open-source C++ solver written by Gauthier Quesnel (INRAE MIA Toulouse, France) for binary and integer linear programming based on the Dag Wedelin heuristic (Ann. Oper. Res., 1995) and revisited in (Bastert et al, INFORMS J. on Computing, 2010). It reads cplex lp format.
toulbar2: an exact open-source C++ solver for cost function networks. It solves various combinatorial optimization problems such as Weighted CSP, Weighted Partial Max-Sat, Bayesian Networks (MPE task), Markov Random Fields (MPA task), and Quadratic Pseudo-Boolean Optimization. This is a collaborative work open to additional developpers (see the toulbar2 github source forge).
numberjack/Toulbar2: A python-based combinatorial optimisation platform. It is designed to support a number of underlying C/C++ solvers including MIP solvers (SCIP,CPLEX,Gurobi), two SAT solvers (MiniSat) and (Walksat), a CP solver (Mistral, versions 1 and 2), and a WCSP solver (Toulbar2). It includes a simple portfolio approach reading flatzinc format.
GeneBayesNet: demonstrates the reconstruction of gene regulatory networks from genetical genomics data using Bayesian network structure learning techniques. It aims at recovering the underlying gene regulation network given measures of expression data and SNP occurrences for a set of related individuals.
CARThAGENE: solves marker ordering problems and can also join maps (genetic or radiated hybrid) on simple pedigrees: backcross, RI (ri self, ri sib), F2 intercross, phase known outbreds and radiated hybrids.
MendelSoft: detects Mendelian errors in complex pedigree using weighted constraint satisfaction techniques.

Darn!: from Matthias Zytnicki, searches RNA motifs and their intermolecular contacts, dealing with preferences for sorting RNA motif solutions in the weighted CSP framework.
ToolBar: is an exact open-source C solver for cost function networks. It is no more developed.
Eclair©/ToOLS©: solves combinatorial optimization problems in a constraint programming framework. Eclair is a finite domain constraint solver with real-time features and is written in the Claire programming language. ToOLS is part of Eclair and is dedicated to the design of partial and hybrid search algorithms. Eclair and ToOLS are copyright THALES Research & Technology.

Benchmarks

EvalGM: 3026 discrete optimization benchmarks available in various formats (wcsp, wcnf, uai, lp, mzn).
Cost Function Library: an on-going collection of benchmarks from various domains of Artificial Intelligence, Constraint Programming, and Operations Research (formats in wcsp, wcnf, lp, qpbo, uai).

CostFunction: a collection of benchmarks from various domains: WCSP, Bayesian Networks, Markov Random Fields, Max-SAT,...
WCSP: a collection of benchmarks, problem generators and input langages/translators for ToolBar and other soft constraint solvers (lvcsp, vcsp, and incop).

Projects, Collaborations and Students

CostFunction, a constraint programming extension to combinatorial optimization.
SoftCSP, a (wiki) collaborative web site dedicated to Soft Constraint Satisfaction Problems.

French ANR project ANDES (february 2023-february 2026) on Artificial-Intelligence-based Methods for Nanobody Design.
French ANR project SpaceHex (february 2020-february 2024) on spatial control of hexameric proteins.
French PIA3 project ANITI (2019-2023) on Design using intuition and logic.
French ANR project DEMOGRAPH (april 2017-april 2021) on decomposition of graphical models.
4C visitor (2013), a 6-month research experience in the 4C lab to combine WCSP and CP approaches, Cork, Ireland.
French-Hong-Kong Procore project (2012-2014) towards a practical library of global cost functions.
French ANR project SUNRISE (2012-2020) on genetic and molecular discovery (WP6) to develop the economic competitiveness of the sunflower crop.
French ANR project (janv 2011-juillet 2014) on introducing stronger local consistency filtering algorithms for solving constraint optimization problems with global cost functions and for bounding the normalization constant in probabilistic graphical models.
Structure learning of gene networks (in French, 2009-), a research working group supported by INRA MIA.
French ANR project (dec 2005-dec 2008) on strategies and algorithms for decomposing and solving constraint optimization problems.
French ARC project (2005-2007) on integrated biological networks.
French-Ireland Ulysse project (2006, 2008) on conditional preferences and soft constraints. Also explore new valuation structures.

Martin Cooper, IRIT, Toulouse, France. Weighted CSP.
Thomas Faraut, INRA LGC, Toulouse, France. Comparative RH mapping.
Hélène Fargier, IRIT, Toulouse, France. Valued CSP and compilation.
Christine Gaspin, INRA MIA, Toulouse, France. RNA Structured Motifs Search.
Christophe Hitte, CNRS / UMR 6061, Rennes, France. Comparative RH mapping applied to the Dog genome.
Laurent Jeannin, THALES Research & Technology FRANCE, Orsay. Partial and hybrid search algorithms in constraint programming.
Philippe Jégou, LSIS - Université Paul Cézanne, Marseille, France. Tree decomposition and counting.
Javier Larrosa, UPC, Barcelona, Spain. Weighted CSP.
Jimmy Lee, The Chinese University of Hong-Kong, China. Weighted CSP.
Brigitte Mangin, INRA MIA, Toulouse, France. Genetics.
Pedro Meseguer, IIIA-CSIC, Bellaterra, Spain. Weighted CSP.
Barry O'Sullivan, UCC, head of the 4C team at Cork, Ireland.
Steve Prestwich, UCC, Cork, Ireland.
Thomas Schiex, INRA MIA, former head of the bioinformatics team at Toulouse, France.
Gérard Verfaillie, ONERA CERT, Toulouse, France. Weighted CSP.

Post Doctoral Students

Vincent Rocher, Gene Regulatory Network Inference Methods in Bacillus Subtilis, August 2023-December 2024.
Samuel Buchet, Multi-objective Weighted CSP and Protein Design, October 2022-October 2024.
Lise Pomiès, Gene regulatory network inference applied to sunflower, October 2017-March 2020.
Clément Carré, Gene regulatory network inference applied to sunflower, May-July 2017.
Marti Sanchez, Weighted CSP processing, July 2006-May 2008.

Ph.D. Students

Pierre Montalbano, école doctorale MITT, ANITI, Université de Toulouse, Pseudo-Boolean Learning from Conflicts in Cost Function Networks (original version in English, extended summary in French), October 2020 - December 15th 2023 (co-supervised with George Katsirelos, INRA MIA). See toulbar2.
Fulya Ural, école doctorale MITT, Université Paul Sabatier, Toulouse, Exact Methods for Bayesian Network Structure Learning (original version in English, also translated in French), September 2018 - March 31st 2022 (co-supervised with George Katsirelos, INRA MIA). See toulbar2.
Sara Maqrot, école doctorale MITT, Université Paul Sabatier, Toulouse, Approximation methods in combinatorial mathematical programming. Application to mixed fruit-vegetable cropping system design (in French), October 2015 - September 23rd 2019 (co-supervised with Gauthier Quesnel, INRA MIA). See baryonyx and crop models and results from IEA-AIE 2017 paper.
Jimmy Vandel, école doctorale MITT, Université Paul Sabatier, Toulouse, Learning gene regulatory networks in genetical genomics experiments (in French), October 2009 - December 7th 2012 (co-supervised with Brigitte Mangin, INRA MIA). See GeneBayesNet.
Aurélie Favier, école doctorale MITT, Université Paul Sabatier, Toulouse, Bayesian Network processing, applications in genetics (haplotype inference) (in French), October 2008 - December 12th 2011 (co-supervised with Andres Legarra, INRA SAGA). See toulbar2 and Haplotype inference in half-sib families.

Licence/Master Students

Julien Guidihounme, ENAC/M2R RO UPS, Parcours de graphe de pangénome et score d'affinité d'hybrides, Mars-Aout 2024.
Tuan-Ahn Vu, ENAC/M2R RO UPS, Exploitation d'une décomposition dynamique dans une recherche arborescente, April-September 2021.
Pierre Montalbano, Polytech Clermont-Ferrand, ANITI, Linear Constraints in Weighted Constraint Satisfaction, March-September 2020.
Auxane Calmont, IUT d'Aurillac, Validation du réseau de régulation de gènes du tournesol, April-June 2019.
Abdelkader Beldjilali, ENAC/M2R RO UPS, Parallélisation d'une recherche arborescente hybride et partielle, March-September 2019.
Fulya Ural, M2R ORCO INP - ENSIMAG Grenoble, Contrainte pondérée d'acyclicité pour l'apprentissage de réseaux bayésiens, February-July 2018.
Miezan Thomas Miezan, M2R RO Université Paul Sabatier, Adaptation en ligne des paramètres du solveur toulbar2 en optimisation discrète, April-September 2016.
Sara Maqrot, M2R RO Université Paul Sabatier, Méthode approchéee en programmation mathématique. Application à la conception de vergers maraîchers, March-August 2015.
Abdallah Mechati, M2R IAICI Université Paul Sabatier, Reconstruction exacte de réseaux bayésiens à partir d'observations complètes, February-August 2015.
Philippe Leleux, M2R IAICI Université Paul Sabatier, Assemblage de génome à l'aide des réseaux de fonctions de coûts (in French), March 2014-September 25th 2014.
Mickaël Gomes, L3 IUT de Toulouse, Intégration du solver ToulBar2 dans NumberJack, March 2012-August 2012.
Jimmy Vandel, Université Paul Sabatier, Toulouse, Reconstruction de réseau de régulation de gènes à l'aide de données génomiques, February 2009-June 2009.
Rony Rozas, Université Paul Sabatier, Toulouse, Algorithmes pour la satisfaction de contraintes flexibles ; Optimisation de préférences multi-critères, February 2009-June 2009.
Joëlson Randriamparany, Université de Fianarantsoa, Madagascar, Etude de la classe des problèmes sous-modulaires pour la résolution des CSP pondérés binaires, September 2006-November 2006.
Laetitia Albenque, ENSEEIHT, Toulouse, Problème du voyageur de commerce multi-objectifs avec données manquantes, application en bio-informatique à la cartographie comparée, June 2006-August 2006.

Personal links

GomaEsperance

http://www.gomaesperance.org -- Help us with a school in Africa (Goma, RDC) (in French)

Hans Universalis

http://www.hansuniversalis.org -- Read Robinson des glaces (in French)

Lyon Urban Kayak

http://www.lyonurbankayak.com -- See expeditions in Stockholm Archipelago (in French)

Contact: Simon de Givry
Last Update: June 2024