Thomas Schiex

202

Documents

Publications

	Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium Helit Cohen , Claire Hoede , Felix Scharte , Charles Coluzzi , Emiliano Cohen PLoS Pathogens, 2022, 18 (4), 35 p. ⟨10.1371/journal.ppat.1010425⟩ Journal articles hal-03690615v1
	Iterated local search with partition crossover for computational protein design François Beuvin , Simon De Givry , Thomas Schiex , Sébastien Verel , David Simoncini Proteins - Structure, Function and Bioinformatics, 2021, 89 (11), pp.1522-1529. ⟨10.1002/prot.26174⟩ Journal articles hal-03298736v1
	A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases Jelena Vucinic , Gleb Novikov , Cédric Montanier , Claire Dumon , Thomas Schiex International Journal of Molecular Sciences, 2021, 22 (11), ⟨10.3390/ijms22115961⟩ Journal articles hal-03244138v1
	Protein Design with Deep Learning Marianne Defresne , Sophie Barbe , Thomas Schiex International Journal of Molecular Sciences, 2021, 22 (21), ⟨10.3390/ijms222111741⟩ Journal articles hal-03602603v1
	Guaranteed Diversity and Optimality in Cost Function Network Based Computational Protein Design Methods Manon Ruffini , Jelena Vucinic , Simon De Givry , George Katsirelos , Sophie Barbe Algorithms, 2021, 14 (6), pp.168. ⟨10.3390/a14060168⟩ Journal articles hal-03244149v1
	Molecular flexibility in computational protein design: an algorithmic perspective Younes Bouchiba , Juan Cortés , Thomas Schiex , Sophie Barbe Protein Engineering, Design and Selection, 2021, 34, pp.gzab011. ⟨10.1093/protein/gzab011⟩ Journal articles hal-03221838v1
	Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase Sota Yagi , Aditya K Padhi , Jelena Vucinic , Sophie Barbe , Thomas Schiex Journal of the American Chemical Society, inPress, 143 (39), pp.15998-16006. ⟨10.1021/jacs.1c05367⟩ Journal articles hal-03360584v1
	Positive multistate protein design Jelena Vucinic , David Simoncini , Manon Ruffini , Sophie Barbe , Thomas Schiex Bioinformatics, 2020, ⟨10.1093/bioinformatics/btz497⟩ Journal articles hal-02625007v1
	Aide à la conception Juan Cortés , Thomas Schiex Le petit illustré, regards croisés de chercheur.es, 2020 Journal articles hal-03436420v1
	Graphical Models: Queries, Complexity, Algorithms Martin Cooper , Simon de Givry , Thomas Schiex Leibniz International Proceedings in Informatics , 2020, 154, pp.4:1--4:22. ⟨10.4230/LIPIcs.STACS.2020.4⟩ Journal articles hal-02547692v1
	A structural homology approach for computational protein design with flexible backbone David Simoncini , Kam y J Zhang , Thomas Schiex , Sophie Barbe Bioinformatics, 2019, 35 (14), ⟨10.1093/bioinformatics/bty975⟩ Journal articles hal-02114756v1
	Computational design of symmetrical eight-bladed β-propeller proteins Hiroki Noguchi , Christine Addy , David Simoncini , Staf Wouters , Bram Mylemans International Union of Crystallography journal, 2019, 6 (1), pp.46-55. ⟨10.1107/S205225251801480X⟩ Journal articles hal-02154353v1
	Exact or approximate inference in graphical models: why the choice is dictated by the treewidth, and how variable elimination can be exploited Nathalie Dubois Peyrard Peyrard , Marie-Josée Cros , Simon de Givry , Alain Franc , Stephane S. Robin Australian and New Zealand Journal of Statistics, 2019, 61 (2), pp.89-133. ⟨10.1111/anzs.12257⟩ Journal articles hal-02433018v1
	Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems Antoine Charpentier , David Mignon , Sophie Barbe , Juan Cortés , Thomas Schiex Journal of Chemical Information and Modeling, 2019, 59 (1), pp.127-136. ⟨10.1021/acs.jcim.8b00510⟩ Journal articles hal-01943616v1
	Cost function network-based design of protein–protein interactions: predicting changes in binding affinity Clément Viricel , Simon de Givry , Thomas Schiex , Sophie Barbe Bioinformatics, 2018, 34 (15), pp.2581-2589. ⟨10.1093/bioinformatics/bty092⟩ Journal articles hal-02154341v1
	Contraintes, incertitudes et modèles graphiques Thomas Schiex Bulletin de l'Association Française pour l'Intelligence Artificielle, 2018, 100, pp.40-42 Journal articles hal-02617623v1
	Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes Romain Blanc-Mathieu , Laetitia Zurletto , Jean-Marc Aury , Martine da Rocha , Jerome Gouzy PLoS Genetics, 2017, 13 (6), pp.e1006777. ⟨10.1371/journal.pgen.1006777⟩ Journal articles hal-01602779v1
	Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction David Simoncini , Thomas Schiex , Kam Y.J. Zhang Proteins, 2017, 85 (5), pp.852-858. ⟨10.1002/prot.25244⟩ Journal articles hal-01607119v1
	The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution Hélène Badouin , Jerome Gouzy , Christopher Grassa , Florent Murat , S Evan Staton Nature, 2017, 546 (7656), pp.148-152. ⟨10.1038/nature22380⟩ Journal articles hal-01603287v1
	Triangle-based consistencies for cost function networks  Christian Bessiere , Simon de Givry , Thomas Schiex , Thi Hông Hiêp Nguyên Constraints, 2017, 22 (2), pp.230-264. ⟨10.1007/s10601-016-9250-1⟩ Journal articles lirmm-01374514v1
	Multi-language evaluation of exact solvers in graphical model discrete optimization Barry Hurley , Barry O'Sullivan , David Allouche , George Katsirelos , Thomas Schiex Constraints, 2016, 21 (3), pp.413-434. ⟨10.1007/s10601-016-9245-y⟩ Journal articles hal-02633083v1
	Fast search algorithms for computational protein design Seydou Traore , Kyle E. Roberts , David Allouche , Bruce R. Donald , Isabelle André Journal of Computational Chemistry, 2016, 37 (12), pp.1048 - 1058. ⟨10.1002/jcc.24290⟩ Journal articles hal-01886385v1
	Tractability-preserving Transformations of Global Cost Functions David Allouche , Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Gutierrez Artificial Intelligence, 2016, 238, pp.166-189. ⟨10.1016/j.artint.2016.06.005⟩ Journal articles lirmm-01374533v1
	Guaranteed Discrete Energy Optimization on Large Protein Design Problems David Simoncini , David Allouche , Simon de Givry , Céline Delmas , Sophie Barbe Journal of Chemical Theory and Computation, 2015, 11 (12), pp.5980 - 5989. ⟨10.1021/acs.jctc.5b00594⟩ Journal articles hal-02637306v1
	Computational protein design as an optimization problem David Allouche , Isabelle André , Sophie Barbe , Jessica Davies , Simon de Givry Artificial Intelligence, 2014, 212, pp.59-79. ⟨10.1016/j.artint.2014.03.005⟩ Journal articles hal-01268554v1
	EuGene-PP: a next generation automated annotation pipeline for prokaryotic genomes. Erika Sallet , Jerome Gouzy , Thomas Schiex Bioinformatics, 2014, 30 (18), pp.2659-2661. ⟨10.1093/bioinformatics/btu366⟩ Journal articles hal-02632297v1
	Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011 Erika Sallet , Brice Roux , Laurent Sauviac , M.-F. Jardinaud , S. Carrere DNA Research, 2013, 20 (4), pp.339-353. ⟨10.1093/dnares/dst014⟩ Journal articles hal-03082947v1
	A new framework for computational protein design through cost function network optimization Seydou Traore , David Allouche , Isabelle André , Simon de Givry , George Katsirelos Bioinformatics, 2013, 29 (17), pp.2129-2136. ⟨10.1093/bioinformatics/btt374⟩ Journal articles hal-01268153v1
	Detecting long tandem duplications in genomic sequences Eric Audemard , Thomas Schiex , Thomas Faraut BMC Bioinformatics, 2012, 13, online (may), Non paginé. ⟨10.1186/1471-2105-13-83⟩ Journal articles hal-02650334v1
	The tomato genome sequence provides insights into fleshy fruit evolution Shusei Sato , Satoshi Tabata , Hideki Hirakawa , Erika Asamizu , Kenta Shirasawa Nature, 2012, 485 (7400), pp.635-641. ⟨10.1038/nature11119⟩ Journal articles hal-02651748v1
	The tomato genome sequence provides insights into fleshy fruit evolution Shusei Sato , Satoshi Tabata , Hideki Hirakawa , Erika Asamizu , Kenta Shirasawa Nature, 2012, 485 (7400), pp.635-641. ⟨10.1038/nature11119⟩ Journal articles hal-04198562v1
	Le séquençage du génome humain Thomas Schiex Tangente (Paris), 2012, pp.104-109 Journal articles hal-02641811v1
	Gene regulatory network reconstruction using Bayesian networks, the Dantzig selector, the Lasso and their meta-analysis Matthieu Vignes , Jimmy Vandel , David Allouche , Nidal Ramadan-Alban , Christine Cierco-Ayrolles PLoS ONE, 2011, 6 (12), pp.1-15. ⟨10.1371/journal.pone.0029165⟩ Journal articles hal-02649016v1
	The genome of Theobroma cacao. Xavier Argout , Jerome Salse , Jean-Marc Aury , Mark J Guiltinan , Gaetan Droc Nature Genetics, 2011, 43 (2), pp.101-8. ⟨10.1038/ng.736⟩ Journal articles hal-00855922v1
	The Medicago genome provides insight into the evolution of rhizobial symbioses Nevin D. Young , Frederic Debellé , Giles E. D. Oldroyd , Rene Geurts , Steven Cannon Nature, 2011, 480 (7378), pp.520-524. ⟨10.1038/nature10625⟩ Journal articles hal-02652790v1
	Le cadre PFU, un modèle et des algorithmes génériques pour la décision séquentielle incluant incertitudes, faisabilités et utilités Cédric Pralet , Gérard Verfaillie , Thomas Schiex Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, 2010, 29 (1), pp.85-114. ⟨10.3166/tsi.29.85-114⟩ Journal articles hal-02661485v1
	Soft arc consistency revisited Martin Cooper , Simon de Givry , Marti Sanchez , Thomas Schiex , Matthias Zytnicki Artificial Intelligence, 2010, 174, pp.449-478. ⟨10.1016/j.artint.2010.02.001⟩ Journal articles hal-02662237v1
	Introduction to the special issue on constraint-based approaches to preference modelling and reasoning Pedro Meseguer , Francesca Rossi , Thomas Schiex Constraints, 2010, 15 (4), pp.453-455. ⟨10.1007/s10601-010-9096-x⟩ Journal articles hal-02657736v1
	FrameDP: sensitive peptide detection on noisy matured sequences Jerome Gouzy , Sebastien Carrere , Thomas Schiex Bioinformatics, 2009, 25 (5), pp.670-671. ⟨10.1093/bioinformatics/btp024⟩ Journal articles hal-02665259v1
	Bounds arc consistency for weighted CSPs Matthias Zytnicki , Christine Gaspin , Simon de Givry , Thomas Schiex Journal of Artificial Intelligence Research, 2009, 35, pp.593-621. ⟨10.1613/jair.2797⟩ Journal articles hal-02668467v1
	Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals. Thomas Faraut , Simon de Givry , Christophe Hitte , Yvette Lahbib Mansais , Mireille Morisson Cytogenetic and Genome Research, 2009, 126 (1-2), pp.21-33. ⟨10.1159/000245904⟩ Journal articles inserm-00442389v1
	LeARN : a platform for detecting, clustering and annotating non-coding RNAs Céline Noirot , Christine Gaspin , Thomas Schiex , Jerome Gouzy BMC Bioinformatics, 2008, 9 (21), pp.1-11. ⟨10.1186/1471-2105-9-21⟩ Journal articles hal-02661357v1
	Genome annotation in plants and fungi: EuGène as a model platform Sylvain Foissac , Jerome Gouzy , Stephane Rombauts , Catherine Mathé , Joelle J. Amselem Current Bioinformatics, 2008, 3 (2), pp.87-97. ⟨10.2174/157489308784340702⟩ Journal articles hal-02658120v1
	2006 and 2007 Max-SAT evaluations: contributed instances Federico Heras , Javier Larrosa , Simon de Givry , Thomas Schiex Journal on Satisfiability, Boolean Modeling and Computation, 2008, 4, pp.239-250 Journal articles hal-02656247v1
	Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita Pierre Abad , Jerome Gouzy , Jean-Marc Aury , Philippe Castagnone-Sereno , Etienne Danchin Nature Biotechnology, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩ Journal articles hal-01189285v1
	A comparative genome approach to marker ordering Thomas Faraut , Simon de Givry , Patrick P. Chabrier , Thomas Derrien , Francis Galibert Bioinformatics, 2007, 23 (2), pp.E50-E56. ⟨10.1093/bioinformatics/btl321⟩ Journal articles hal-02667668v1
	Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome Sebastien S. Aubourg , Marie-Laure Martin-Magniette , Veronique V. Brunaud , Ludivine Taconnat , Frederique Bitton BMC Genomics, 2007, 8 (401), pp.1-9. ⟨10.1186/1471-2164-8-401⟩ Journal articles hal-02668276v1
	Searching RNA motifs and their intermolecular contacts with constraint networks P. Thébault , S. de Givry , Thomas Schiex , C. Gaspin Bioinformatics, 2006, 22, pp.2074-2080 Journal articles hal-00428036v1
	Searching RNA motifs and their intermolecular contacts with constraint networks. Patricia Thebault , Simon de Givry , Thomas Schiex , Christine Gaspin Bioinformatics, 2006, 22 (17), pp.2074-80. ⟨10.1093/bioinformatics/btl354⟩ Journal articles hal-00355512v1
	CAR(H)(T)AGene: multipopulation integrated genetic and radiation hybrid mapping Simon de Givry , Martin Bouchez , Patrick P. Chabrier , Denis Milan , Thomas Schiex Bioinformatics, 2005, 21 (5), pp.1703-1704. ⟨10.1093/bioinformatics/bti222⟩ Journal articles hal-02682633v1
	Integrating alternative splicing detection into gene prediction Sylvain Foissac , Thomas Schiex BMC Bioinformatics, 2005, 6, Non paginé. ⟨10.1186/1471-2105-6-25⟩ Journal articles hal-01417735v1
	Rearranged gene order between pig and human in a QTL region on SSC 7 Olivier O. Demeure , Christine Renard , Martine M. Yerle , Thomas Faraut , Juliette Riquet Mammalian Genome, 2003, 14, pp.71-80. ⟨10.1007/s00335-002-3034-1⟩ Journal articles hal-02679052v1
	EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences Sylvain Foissac , Philippe Bardou , Annick Moisan , Marie-Josée Cros , Thomas Schiex Nucleic Acids Research, 2003, 31 (13), pp.3742-3745. ⟨10.1093/nar/gkg586⟩ Journal articles hal-02675508v1
	Current methods of gene prediction their strengths and weaknesses C. Mathé , M.-F. Sagot , Thomas Schiex , P. Rouzé Nucleic Acids Research, 2002, 30, pp.4103-4117 Journal articles hal-00427288v1
	Gene finding in eukaryotes C. Mathé , Thomas Schiex , P. Rouzé , P. Blayo , M.-F. Sagot incollection, 2002, --, pp.27-43 Journal articles hal-00427230v1
	Genome sequence of the plant pathogen Ralstonia solanacearum. Marcel Salanoubat , S. Genin , François Artiguenave , J. Gouzy , S. Mangenot Nature, 2002, 415 (6871), pp.497-502. ⟨10.1038/415497a⟩ Journal articles hal-00427300v2
	Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis Etienne-Pascal Journet , Diederik van Tuinen , Jerome Gouzy , Hervé Crespeau , V. Carreau Nucleic Acids Research, 2002, 30 (24), pp.5579-5592. ⟨10.1093/nar/gkf685⟩ Journal articles hal-02678310v1
	Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis E.P. Journet , D. van Tuinen , J. Gouzy , H. Crespeau , V. Carreau Nucleic Acids Research, 2002, 30, pp.5579-5592 Journal articles hal-00427223v1
	Maintaining reversible DAC for Max-CSP J. Larrosa , P. Meseguer , Thomas Schiex Artificial Intelligence, 1999, 107, pp.149-163 Journal articles hal-02690806v1
	Radio link frequency assignment Bertrand Cabon , Simon de Givry , Lionel Lobjois , Thomas Schiex , Joost P. Warners Constraints, 1999, 4 (1), pp.79-89. ⟨10.1023/A:1009812409930⟩ Journal articles hal-02695373v1
	A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers V. Laurent , Eric Wajnberg , Brigitte B. Mangin , Thomas Schiex , Christine Gaspin Genetics, 1998, 150, pp.275-282 Journal articles hal-02687913v1
	Nonmonotonic Reasoning: from Complexity to Algorithms Claudette Cayrol , Marie-Christine Lagasquie-Schiex , Thomas Schiex Annals of Mathematics and Artificial Intelligence, 1998, 22 (3-4), pp.207-236. ⟨10.1023/A:1018939502485⟩ Journal articles hal-02908181v1
	Problèmes de satisfaction de contraintes valués Thomas Schiex , Hélène Fargier , Gérard Verfaillie Revue des Sciences et Technologies de l'Information - Série RIA : Revue d'Intelligence Artificielle, 1997, 11 (2), pp.339-373 Journal articles hal-02689261v1
	Traitement de problèmes de décision sous incertitude par des problèmes de satisfaction de contraintes Hélène Fargier , Jérôme Lang , Roger Martin Clouaire , Thomas Schiex Revue des Sciences et Technologies de l'Information - Série RIA : Revue d'Intelligence Artificielle, 1997, 11 (2), pp.375-398 Journal articles hal-02688777v1
	Maintien de solution dans les problèmes dynamiques de satisfaction de contraintes : bilan de quelques approches G. Verfaillie , Thomas Schiex Revue des Sciences et Technologies de l'Information - Série RIA : Revue d'Intelligence Artificielle, 1995, 9 (3), pp.269-309 Journal articles hal-02703826v1
	Nogood recording for static and dynamic constraint satisfaction problems Thomas Schiex , G. Verfaillie International Journal on Artificial Intelligence Tools, 1994, 3 (2), pp.187-207 Journal articles hal-02709865v1
	A fixed point semantics for the ATMS M. Cayrol , O. Palmade , Thomas Schiex Journal of Logic and Computation, 1993, 3 (2), pp.115-130 Journal articles hal-02700521v1

	Scalable Coupling of Deep Learning with Logical Reasoning Marianne Defresne , Sophie Barbe , Thomas Schiex First International Workshop on Discrete Optimization with Soft Constraint., Sep 2024, Girona, Spain Conference papers hal-04787313v1
	AI-powered de novo design of miniprotein binders Younes Bouchiba , Juan Cortés , Thomas Schiex , Sophie Barbe Biosynsys, Jun 2024, Montpellier, France Conference papers hal-04787310v1
	Design of symmetrical multi-component proteins using a hybrid generative AI approach. Delphine Dessaux , Samuel Buchet , Marianne Defresne , Lucie Barthe , Gianluca Cioci AI Methods and Models for (Bio)Catalysis and Synthetic Biology Workshop, Jun 2024, Montpellier, France Conference papers hal-04787319v1
	Bi-Objective Discrete Graphical Model Optimization Samuel Buchet , David Allouche , Simon de Givry , Thomas Schiex The 21st International Conference on the Integration of Constraint Programming, Artificial Intelligence, and Operations Research, May 2024, Uppsala (Suède), Sweden Conference papers hal-04556832v1
	Learning how to design biomolecules using a neuro-symbolic architecture Marianne Defresne , Sophie Barbe , Thomas Schiex AISSAI - Heterogeneous Data and Large Representation Models in Science, Sep 2024, Toulouse, France Conference papers hal-04787315v1
	Design of symmetrical multi-component proteins using a hybrid generative AI approach Delphine Dessaux , Samuel Buchet , Marianne Defresne , Lucie Barthe , Gianluca Cioci Biosynsys, Jun 2024, Montpellier, France Conference papers hal-04787317v1
	Learning to Reason: Predict-then-Optimize vs Predict-and-Optimize Marianne Defresne , Thomas Schiex , Sophie Barbe AAAI 2023 Bridge on Constraint Programming and Machine Learning, Feb 2023, Washington DC, United States Conference papers hal-04222883v1
	Coupling CP with Deep Learning for Molecular Design and SARS-CoV2 Variants Exploration Thomas Schiex International Conference on Principles and Practice of Constraint Programming (CP), Aug 2023, Toronto ( CA ), Canada. ⟨10.4230/LIPIcs.CP.2023.4⟩ Conference papers hal-04556854v1
	Scalable Coupling of Deep Learning with Logical Reasoning Marianne Defresne , Thomas Schiex , Sophie Barbe PFIA'23, Jul 2023, Strasbourg, France Conference papers hal-04223509v1
	Scalable Coupling of Deep Learning with Logical Reasoning * Marianne Defresne , Sophie Barbe , Thomas Schiex Thirty-Second International Joint Conference on Artificial Intelligence (IJCAI-23), Edith Elkind, University of Oxford, UK, Aug 2023, Macao, China. ⟨10.24963/ijcai.2023/402⟩ Conference papers hal-04222857v1
	Computational Protein Design with Artificial Intelligence Marianne Defresne , Thomas Schiex , Sophie Barbe GGMM 2023, May 2023, Toulouse, France Conference papers hal-04223563v1
	Computational Design of miniprotein binders Younes Bouchiba , Juan Cortés , Thomas Schiex , Sophie Barbe Journées Scientifiques du GDR ChemBio, Jun 2022, Toulouse, France Conference papers hal-04223586v1
	Neural Learning of Graphical Models for Protein Design Marianne Defresne , Thomas Schiex , Sophie Barbe ANITI workshop on Automated Reasoning & Decision Making (ARDM), Jun 2022, Toulouse, France Conference papers hal-04787578v1
	Protein Design with Automated Reasoning and Deep Learning Marianne Defresne , Delphine Dessaux , Thomas Schiex , Sophie Barbe Symposium on Systems and Synthetic Biology (BioSynSys2022), Sep 2022, Paris, France Conference papers hal-04223575v1
	Computational Protein Design with Automated Reasoning and Deep Learning Marianne Defresne , Thomas Schiex , Sophie Barbe Journées thématiques “machine learning/Deep learning in structural bioinformatics) du GDR BIM/ GT MASIM, Paris, 5-6 December 2022, Dec 2022, Paris, France Conference papers hal-04787572v1
	Constraint and Cost Function Networks: feasibility, optimization and learning. Thomas Schiex Journées francophones de programmation par contraintes (JFPC), Association Française pour la Programmation par Contraintes (AFPC), Jun 2021, Nice, France Conference papers hal-03737195v1
	Computer-aided Protein Design (by combining automated reasoning and learning) Thomas Schiex Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2021, Jul 2021, Paris (Colloque virtuel), France Conference papers hal-03737198v1
	Computational Design of miniprotein binders Younes Bouchiba , Manon Ruffini , Juan Cortés , Thomas Schiex , Sophie Barbe GGMM 2021, Sep 2021, Villeneuve d’Ascq, France Conference papers hal-04223596v1
	Pushing Data into CP Models Using Graphical Model Learning and Solving Celine Brouard , Simon de Givry , Thomas Schiex International Conference on Principles and Practice of Constraint Programming, Sep 2020, Louvain La Neuve, Belgium Conference papers hal-02942378v1
	Guaranteed Diversity & Quality for the Weighted CSP Manon Ruffini , Jelena Vucinic , Simon de Givry , George Katsirelos , Sophie Barbe 2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), Nov 2019, Portland, United States. pp.18-25, ⟨10.1109/ICTAI.2019.00012⟩ Conference papers hal-03181764v1
	Intelligence Artificielle: entre logique et intuition Thomas Schiex Journée Science pour tous, Mar 2019, Castanet-Tolosan, France Conference papers hal-02788712v1
	Pushing the computational frontiers of multistate protein design Jelena Vucinic , Manon Ruffini , David Simoncini , Thomas Schiex , Sophie Barbe GGMM 2019, Apr 2019, Nice, France Conference papers hal-04223606v1
	Designing molecules with cost function networks - Bridging symbolic and numerical AI. Thomas Schiex Journées plénières du GDR IA du CNRS, Oct 2018, Paris, France Conference papers hal-02785414v1
	Constraint Programming and Graphical models - Pushing data into your models, The protein design case. Thomas Schiex , Sophie Barbe , David Simoncini , Jelena Vucinic , Manon Ruffini 23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France Conference papers hal-02154354v1
	Fitness Landscape Analysis around the Optimum in Computational Protein Design David Simoncini , Sophie Barbe , Thomas Schiex , Sébastien Verel Genetic and Evolutionary Computation Conference (GECCO) 2018, Jul 2018, Kyoto, Japan. pp.355-362 Conference papers hal-01823638v1
	Recent algorithmic advances for combinatorial optimization in graphical models David Allouche , Simon de Givry , Georgios Katsirelos , Thomas Schiex , Matthias Zytnicki 23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France. 80 p Conference papers hal-02785380v1
	How Computers Break (Serious) Puzzles with logic and (a different breed of) learning Thomas Schiex French Académie des sciences Symposium on « Machine Learning for Artificial Intelligence », Feb 2018, Paris, France Conference papers hal-02786911v1
	Exact and approximate inference in graphical models Régis Sabbadin , Nathalie Peyrard , Marie-Josée Cros , Simon de Givry , Alain Franc 10th International Conference on Scalable Uncertainty Management (SUM), Oct 2017, Granada, Spain Conference papers hal-02116334v1
	Removing Ded Ends in (re)search - Emeritate of Marc de Maeyer Thomas Schiex Eméritat de Marc de Maeyer, Sep 2016, Leuven, Belgium Conference papers hal-01603888v1
	Optimization in Graphical Models - NP-complete optimization and its applications Thomas Schiex Assemblée générale de l'Association Française d'Intelligence Artificielle, Oct 2016, Paris, France Conference papers hal-02794159v1
	Guaranteed Weighted Counting for Affinity Computation: Beyond Determinism and Structure Clement Viricel , David Simoncini , Sophie Barbe , Thomas Schiex CP16 - 22nd International Conference on the Principles and Practice of Constraint Programming, Sep 2016, Toulouse, France. pp.18, ⟨10.1007/978-3-319-44953-1_46⟩ Conference papers hal-01828389v1
	Guaranteed Optimization on Large Protein Design Problems Thomas Schiex Séminaire au Baker Lab (Institute for Protein Design), Jul 2016, Seattle, United States Conference papers hal-01603273v1
	Guaranteed energetic optimization, exploration and counting of sequence-conformation in Computational Protein Design Thomas Schiex 4th Prague Protein Spring Meeting 2016, May 2016, Prague, Czech Republic Conference papers hal-01603552v1
	Optimization in Graphical Models - Connecting NP-complete frameworks Thomas Schiex Séminaire Université Catholique de Louvain, Sep 2016, Louvain, Belgium Conference papers hal-01603551v1
	Optimization in Graphical Models Thomas Schiex 34e Journée Francilienne de Recherche Opérationnelle (JFRO), Sep 2015, Paris, France Conference papers hal-01602147v1
	Computational protein design as an optimization problem Thomas Schiex BAI 2015 : Advance in Bioinformatics and Artificial Intelligence, Jul 2015, Buenos Aires, Argentina Conference papers hal-01603297v1
	Anytime hybrid best-first search with tree decomposition for weighted CSP David Allouche , Simon de Givry , George Katsirelos , Thomas Schiex , Matthias Zytnicki CP 2015 - 21st International Conference on Principles and Practice of Constraint Programming, Aug 2015, Cork, Ireland. 17 p., ⟨10.1007/978-3-319-23219-5_2⟩ Conference papers hal-01198361v1
	Computational Design as an Optimization Problem Thomas Schiex Séminaire INRIA-IRISA, May 2015, Rennes, France Conference papers hal-01602148v1
	Optimization in Graphical Models Thomas Schiex 27th IEEE International Conference on Tools with Artificial Intelligence, Nov 2015, Vietri sul Mare, Italy Conference papers hal-01602150v1
	Computational Enzyme Design through deterministic optimization and counting Thomas Schiex , Seydou Traoré , David Simoncini , Sophie Barbe , Simon de Givry 3DSig Structural Bioinformatics and Computational Biophysics 2015, Jul 2015, Dublin, Ireland Conference papers hal-01605405v1
	Approximate counting with deterministic guarantees for affinity computation Clément Viricel , David Simoncini , David Allouche , Simon de Givry , Sophie Barbe 3. International Conference on Modelling, Computation and Optimization in Information Systems and Management Sciences - MCO 2015, Université de Lorraine (UL). FRA., May 2015, Metz, France. 500 p., ⟨10.1007/978-3-319-18167-7_15⟩ Conference papers hal-01269259v1
	An integer linear programming approach for genome scaffolding Nicolas Briot , Annie Chateau , Remi Coletta , Simon de Givry , Philippe Leleux WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2014, Lyon, France. 16 p Conference papers hal-01198359v1
	Une comparaison de logiciels d'optimisation sur une large collection de modèles graphiques David Allouche , Simon de Givry , Barry Hurley , George Katsirelos , Barry O'Sullivan JFPC 2014 - Dixièmes Journées Francophones de Programmation par Contraintes, Jun 2014, Angers, France. 10 p Conference papers hal-01198360v1
	Maintaining Virtual Arc Consistency Dynamically During Search Thi Hông Hiêp Nguyên , Simon de Givry , Thomas Schiex , Christian Bessiere ICTAI 2014 - 26th IEEE International Conference on Tools with Artificial Intelligence, Nov 2014, Limassol, Cyprus Conference papers hal-02743901v1
	Maintaining Virtual Arc Consistency Dynamically during Search Simon de Givry , Thomas Schiex , Christian Bessiere , Thi Hông Hiêp Nguyên ICTAI: International Conference on Tools with Artificial Intelligence, Nov 2014, Limassol, Cyprus. pp.8-15, ⟨10.1109/ICTAI.2014.13⟩ Conference papers lirmm-01228369v1
	An Experimental Evaluation of CP/AI/OR Solvers for Optimization in Graphical Models Simon de Givry , Barry Hurley , David Allouche , George Katsirelos , Thomas Schiex ROADEF - 15ème congrès annuel de la Société française de recherche opérationnelle et d'aide à la décision, Société française de recherche opérationnelle et d'aide à la décision, Feb 2014, Bordeaux, France Conference papers hal-00946323v1
	An experimental evaluation of CP/AI/OR solvers for optimization in graphical models Simon de Givry , Barry Hurley , David Allouche , Georgios Katsirelos , Barry O'Sullivan Congrès ROADEF'2014, Feb 2014, Bordeaux, France. 1 p Conference papers hal-02742905v1
	Dynamic virtual arc consistency Thi Hông Hiêp Nguyên , Thomas Schiex , Christian Bessiere 28th Annual ACM Symposium on Applied Computing, Mar 2013, Coimbra, Portugal. pp.6, ⟨10.1145/2480362.2480384⟩ Conference papers hal-02745649v1
	Computational protein design as a cost function network optimization problem Thomas Schiex , David Allouche , Simon de Givry , George Katsirelos , Sophie Barbe Séminaire MOGISA du LAAS/CNRS, Centre National de la Recherche Scientifique (CNRS). FRA., Jun 2013, Toulouse, France Conference papers hal-01268632v1
	Dynamic Virtual Arc Consistency Christian Bessiere , Thomas Schiex , Thi Hông Hiêp Nguyên SAC: Symposium on Applied Computing, Mar 2013, Coimbra, Portugal. pp.098-103 Conference papers lirmm-00830307v1
	Cohérence d'arc virtuelle dynamique Thomas Schiex , Christian Bessiere , Thi Hông Hiêp Nguyên JFPC 2013 - 9es Journées Francophones de Programmation par Contraintes, Jun 2013, Aix-en-Provence, France. pp.249-258 Conference papers lirmm-00830411v1
	Cohérence d'arc virtuelle dynamique Thi Hông Hiêp Nguyên , Christian Bessiere , Thomas Schiex JFPC 2013 - Neuvièmes Journées Francophones de Programmation par Contraintes, Association Française pour la Programmation par Contraintes (AFPC). FRA., Jun 2013, Aix-en -Provence, France Conference papers hal-02749182v1
	A new framework for computational protein design through cost function network optimization Seydou Traore , David Allouche , Isabelle André , Simon de Givry , George Katsirelos JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Société Française de Bio-Informatique (SFBI). FRA., Jul 2013, Toulouse, France. 2 p Conference papers hal-01268555v1
	From hosts to symbionts: integrated gene prediction for prokaryotic genomes using EuGene Erika Sallet , Jerome Gouzy , Brice Roux , Delphine Capela , Laurent Sauviac XX. PAG Plant & Animal Genome, Jan 2012, San-Diego, United States Conference papers hal-02807348v1
	Filtrage de fonctions de coût globales décomposables David Allouche , Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Gutierrez JFPC 2012 - 8es Journées Francophones de Programmation par Contraintes, May 2012, Toulouse, France Conference papers hal-00809789v1
	Filtering decomposable global cost functions David Allouche , Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Gutierrez Twenty-Sixth Conference on Artificial Intelligence, Jul 2012, Toronto, Canada. pp.7 Conference papers hal-02747813v1
	Filtering Decomposable Global Cost Functions David Allouche , Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Gutierrez AAAI Conference on Artificial Intelligence, Jul 2012, Toronto, ON, Canada Conference papers lirmm-00748187v1
	Computational protein design as a cost function network optimization problem David Allouche , Seydou Traore , Isabelle André , Simon de Givry , George Katsirelos CP 2012 - 18th International Conference on Principles and Practice of Constraint Programming, Oct 2012, Québec, Canada. pp.10, ⟨10.1007/978-3-642-33558-7_60⟩ Conference papers hal-01191320v1
	Combining exact WCSP techniques and VNS search for solving MPE David Allouche , Aurélie Favier , Mathieu Fontaine , Simon de Givry , Jean-Philippe Metivier Conference on Uncertainty in Artificial Intelligence (UAI'12), Aug 2012, Catalina Island, United States Conference papers hal-01022649v1
	Genomic resources for functional analysis in Medicago truncatula and related crop species Frederic Debellé , C. Belser , J.M. Aury , K. Labadie , Brice Roux 6. International Conference on Legume Genetics and Genomics, International Crops Research Institute for the Semi-Arid Tropics, CGIAR (ICRISAT). Patancheru, IND., Oct 2012, Hyderabad, India Conference papers hal-02747944v1
	Filtrage de fonctions de coût globales décomposables David Allouche , Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Gutierrez Huitièmes Journées Francophones de Programmation par Contraintes (JFPC), Association Française de Programmation par Contraintes (AFPC). FRA., May 2012, Toulouse, France. pp.358 Conference papers hal-02747133v1
	Pairwise decomposition for combinatorial optimization in graphical models Aurélie Favier , Simon de Givry , Andres Legarra , Thomas Schiex IJCAI 2011 - Twenty-second International Joint Conference on Artificial Intelligence, Labo/service de l'auteur, Ville service, Pays service., 2011, Barcelona, Spain Conference papers hal-02744861v1
	Decomposing Global Cost Functions Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Guttiriez , Samir Loudni 11th Workshop on Preferences and Soft Constraints (Soft'11) in 17th Int. Conf. on Principles and Practice of Constraint Programming, Sep 2011, Perugia, Italy. pp.16-30 Conference papers hal-01017977v1
	Decomposing global cost functions Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Gutierrez , Samir Loudini 11th Workshop on Preferences and Soft Contraints (Soft), Labo/service de l'auteur, Ville service, Pays service., Sep 2011, Perugia, Italy Conference papers hal-02747863v1
	Integrated gene prediction for prokaryotic genomes using EuGene Erika Sallet , Jerome Gouzy , Brice Roux , Delphine Capela , Laurent Sauviac JOBIM 2011 - 12e édition du Colloque - Journées Ouvertes en Biologie, Informatique et Mathématiques, Labo/service de l'auteur, Ville service, Pays service., Jun 2011, Paris, France Conference papers hal-02748784v1
	Décomposition par paire pour l'optimisation combinatoire dans les modèles graphiques Aurélie Favier , Simon de Givry , Andres Legarra , Thomas Schiex JFPC 2011 - Septièmes Journées Francophones de Programmation par Contraintes, Labo/service de l'auteur, Ville service, Pays service., 2011, Lyon, France Conference papers hal-02744726v1
	Development of genomic resources for Medicago truncatula and related legume crops Frederic Debellé , Marion Verdenaud , Anne-Marie Dudez , Nicolas Samson , Olivier Saurat Model Legume Congress 2011, Institut National Polytechnique (Toulouse) (Toulouse INP). Castanet Tolosan, FRA., May 2011, Sainte Maxime, France Conference papers hal-02746654v1
	Sélection de tagSNP: une approche PLNE David Allouche , Simon de Givry , Thomas Schiex Congrès ROADEF'2010, Feb 2010, Toulouse, France. pp.2 Conference papers hal-02812620v1
	An introduction to valued constraint satisfaction Thomas Schiex Workshop on Optimization in Markov Random Fields, Sep 2010, Koncha-Zaspa, Ukraine. 78 p Conference papers hal-02812930v1
	Towards parallel non serial dynamic programming for solving hard weighted CSP David Allouche , Simon de Givry , Thomas Schiex 16th Annual International Conference on the Principles and Practice of Constraint Programming, Sep 2010, St. Andrews, Scotland, United Kingdom. pp.8, ⟨10.1007/978-3-642-15396-9_7⟩ Conference papers hal-02753702v1
	Détection de régions génomiques homologues par un algorithme de flots avec coûts Eric Audemard , Thomas Faraut , Thomas Schiex Congrès ROADEF'2010, Société Française de Recherche Opérationnelle et d'Aide à la Décision (SFROAD). FRA., Feb 2010, Toulouse, France. 2 p Conference papers hal-02752130v1
	Algorithme des Poupées Russes exploitant une décomposition arborescente M. Sanchez , David Allouche , Simon de Givry , Thomas Schiex Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans, juin 2009, Jun 2009, France. pp.15-25 Conference papers hal-00387845v1
	Russian doll search with tree decomposition Marti Sanchez , David Allouche , Simon de Givry , Thomas Schiex 21st International Joint Conference on Artificial Intelligence, Jul 2009, Pasadena, United States. pp.6 Conference papers hal-02755904v1
	Combinatorial optimization for graphical models Rina Dechter , Radu Marinescu , Thomas Schiex , Simon de Givry IJCAI 2009 - International Joint Conference on Artificial Intelligence, Jul 2009, Pasadena, United States. 196 p Conference papers hal-02820716v1
	TagSNP selection using weighted CSP and russian doll search with tree decomposition David Allouche , Thomas Schiex , Simon de Givry , Martin Sanchez CP-09 workshop on Constraint Based Methods for Bioinformatics, Sep 2009, Lisbonne, Portugal. pp.9 Conference papers hal-02813239v1
	Virtual arc consistency for weighted CSP Martin Cooper , Simon de Givry , Marti Sanchez , Thomas Schiex , Matthias Zytnicki Twenty-third AAAI Conference on Artificial Intelligence, Jul 2008, Chicago, United States. pp.6 Conference papers hal-02752851v1
	Cohérence d'arc virtuelle pour les CSP pondérés Martin Cooper , Simon de Givry , Marti Sanchez , Thomas Schiex , Matthias Zytnicki JFPC 2008- Quatrièmes Journées Francophones de Programmation par Contraintes, LINA - Université de Nantes - Ecole des Mines de Nantes, Jun 2008, Nantes, France. pp.237-246 Conference papers inria-00292640v1
	Optimal soft arc consistency Martin Cooper , Simon de Givry , Thomas Schiex 20th International Joint Conference on Artificial Intelligence - IJCAI 2007, Jan 2007, Hyderabad, India. pp.6 Conference papers hal-02754114v1
	Décomposition arborescente et cohérence locale souple dans les CSP pondérés Simon de Givry , Thomas Schiex , Gérard Verfaillie Deuxièmes Journées Francophones de Programmation par Contraintes (JFPC06), 2006, Nîmes - Ecole des Mines d'Alès / France, France Conference papers inria-00085804v1
	Mendelsoft: Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques. Simon de Givry , Zulma Vitezica , Isabelle Palhiere Palhière , Thomas Schiex 8. World Congress on Genetics Applied to Livestock Production, 2006, Belo Horizonte, Brazil Conference papers hal-02813118v1
	Exploiting tree decomposition and soft local consistency in weighted CSP Simon de Givry , Thomas Schiex , Gerard Verfaillie Twenty-first National Conference on Artificial Intelligence - AAAI 2006, Jul 2006, Boston, United States. 1115 p Conference papers hal-02755023v1
	A new local consistency for weighted CSP applied to ncRNA detection. Christine Gaspin , Simon de Givry , Thomas Schiex , Patricia Thebault , Matthias Zytnicki Workshop on Constraint Based Methods for Bioinformatics October 5, 2005, Sitges (Spain), May 2005, Sitges, Spain Conference papers hal-00362190v1
	Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques Simon de Givry , Isabelle Palhiere , Z. Vitezica , Thomas Schiex Workshop on constraint based methods for bioinformatics, Oct 2005, Sitges, Spain Conference papers hal-02760634v1
	Combining constraint processing and pattern matching to describe and locate structured motifs in genomic sequences. Patricia Thebault , Simon de Givry , Thomas Schiex , Christine Gaspin Fifth IJCAI-05 Workshop on Modelling and Solving Problems with Constraints, Edindurgh, Scotland, 2005., 2005, Edimbourg, United Kingdom. 8p Conference papers hal-00362194v1
	Requêtes complexes sur des réseaux de Croyance-Faisabilité-Désir Cédric Pralet , Gerard Verfaillie , Thomas Schiex Premières Journées Francophones de Programmation par Contraintes, CRIL - CNRS FRE 2499, Jun 2005, Lens, France. pp.129-138 Conference papers inria-00000053v1
	Integration of genetic and radiation hybrid maps of the pig: The second generation IMpRH maps Denis Milan , Thomas Schiex , Martine M. Yerle , A. Rink , C. Beattie Plant and Animal Genome Conference XII, 2004 Conference papers hal-02829410v1
	Solving Max-SAT as weighted CSP Simon de Givry , Javier Larrosa , Pedro Meseguer , Thomas Schiex 9th International Conference on Principles and Practice of Constraint Programming - CP2003, Sep 2003, Kinsale, Ireland. pp.14, ⟨10.1007/978-3-540-45193-8_25⟩ Conference papers hal-02763945v1
	Cohérence d'arc pour contraintes molles Thomas Schiex Journées Nationales pour la Résolution Pratique des Problèmes, 2000, Marseille, France Conference papers hal-02765509v1
	EuGene an eurocaryotic gene finder that combines several sources of evidence Thomas Schiex , A. Moisan , L. Duret , Pierre Rouzé Journées ouvertes biologie informatique mathématiques, May 2000, Montpellier, France Conference papers hal-02770502v1
	CARTHAGENE : Constructing and joining maximum likelihood genetic maps Thomas Schiex , Christine Gaspin Intelligent Systems in Molecular Biology, Jun 1997, Halkidiki, Greece Conference papers hal-02765754v1
	Bounding the optimum of constraint optimization problems Simon de Givry , G. Verfaillie , Thomas Schiex International Conference on Principles and Practice of Constraint Programming, 1997, Schloss Hagenberg, Austria Conference papers hal-02768589v1
	Genetic algorithms for genetic mapping Christine Gaspin , Thomas Schiex 3. Conference on Evolutionary Algorithms, 1997, Nîmes, France Conference papers hal-02765613v1
	Décision et représentation des connaissances C. da Costa Pereira , F. Garcia , Roger Martin Clouaire , Sidy Ndiaye , Thomas Schiex 6. Journées Nationales du PRC-GDR Intelligence Artificielle Pôle de Recherches Coordonnées-Groupe de Recherche Intelligence Artificielle, Mar 1997, Grenoble, France Conference papers hal-02769900v1
	Russian doll search for solving constraint optimization problems G. Verfaillie , M. Lemaitre , Thomas Schiex National American Conference on Artificial Intelligence, 1996, Portland, United States Conference papers hal-02766400v1
	Lazy arc consistency Thomas Schiex , J.C. Régin , Christine Gaspin , G. Verfaillie National American Conference on Artificial Intelligent, 1996, Portland, United States Conference papers hal-02771457v1
	Mixed constraint satisfaction : a framework for decision problems under incomplete knowledge Hélène Fargier , Jérôme Lang , Thomas Schiex National American Conference on Artificial Intelligence (AAAI 1996), Association for the Advancement of Artificial Intelligence, Aug 1996, Portland, United States. pp.175-180 Conference papers hal-02770543v1
	Valued constraint satisfaction problems : hard and easy problems Thomas Schiex , Hélène Fargier , Gérard Verfaillie 14th International joint conference on artificial intelligence (IJCAI 1995), International Joint Conferences on Artificial Intelligence Organization, Aug 1995, Montreal, Canada. pp.631-637 Conference papers hal-02778456v1
	Semiring-based CSPs and valued CSPs: basic properties and comparison Stefano Bistarelli , Hélène Fargier , Ugo Montanari , Francesca Rossi , Thomas Schiex International Workshop on Over-Constrained Systems (OCS 1995), Sep 1995, Cassis, France. pp.111-150, ⟨10.1007/3-540-61479-6_19⟩ Conference papers hal-02838379v1
	A constraint satisfaction framework for decision under uncertainty Hélène Fargier , Jérôme Lang , Roger Martin Clouaire , Thomas Schiex 11th Annual Conference on Uncertainty in Artificial Intelligence (UAI 1995), Aug 1995, Montreal, Canada. pp.167-174 Conference papers hal-02774878v1
	Solution reuse in dynamic constraint satisfaction problems G. Verfaillie , Thomas Schiex American Association for Artificial Intelligence (AAAI), 1994, Seattle, United States Conference papers hal-02775349v1
	Autour du problème de satisfaction de contraintes Christine Gaspin , Jean-Pierre Rellier , Roger Martin Clouaire , Thomas Schiex 5e Journées nationales du PRC GDR intelligence artificielle, Nov 1994, Paris, France Conference papers hal-02774000v1
	Stubbornness : a possible enhancement for backjumping and nogood recording Thomas Schiex , G. Verfaillie 11. European Conference on Artificial Intelligence, 1994, Toulouse, France Conference papers hal-02774709v1
	Gestion de l'inconsistance dans les bases de connaissances : une approche syntaxique basée sur la logique des pénalités Florence Dupin de Saint-Cyr , Jérôme Lang , Thomas Schiex 9ème Congrès "Reconnaissance des Formes et Intelligence Artificielle" (RFIA 1994), Association française pour la cybernétique économique et technique; Association française pour l'intelligence artificielle, 1994, Toulouse, France. pp.507-518 Conference papers hal-02778823v1
	Nogood recording for static and dynamic constraint satisfaction problems Thomas Schiex , G. Verfaillie 5. International Conference on Tools with Artificial Intelligence, 1993, Boston, United States Conference papers hal-02847674v1
	Possibilistic constraint satisfaction problems or "How to handle soft constraints ?" Thomas Schiex 8. Conference of Uncertainty in Artificial Intelligence, Jul 1992, Stanford, United States Conference papers hal-02773457v1
	Représentation et traitement pratique de la flexibilité dans les problèmes sous contraintes Gérard Bel , Eric Bensana , Khaled Ghédira , David Lesaint , Thomas Schiex 4èmes Journées du PRC-Intelligence Artificielle 1992, PRC-IA : Pôle de Recherches Coordonnées - Intelligence Artificielle, Oct 1992, Marseille, France Conference papers hal-02778063v1
	Satisfaction de contraintes souples Hélène Fargier , Roger Martin Clouaire , Thomas Schiex Journées nationales sur les Applications des Ensembles Flous (AEF 1992), Nov 1992, Nimes, France Conference papers hal-02774966v1

	AI-powered de novo design of miniprotein binders Younes Bouchiba , Juan Cortés , Thomas Schiex , Sophie Barbe Biosynsys, Jun 2024, Montpellier, France Conference poster hal-04787355v1
	Scalable Coupling of Deep Learning with Logical Reasoning Marianne Defresne , Sophie Barbe , Thomas Schiex Thirty-Second International Joint Conference on Artificial Intelligence (IJCAI-23), Aug 2023, Macao, China. 2023 Conference poster hal-04223508v1
	Computational strategy for protein design based on structure-dynamics-activity relationship insights: GH11Xylanases as a casestudy Gleb Novikov , Jelena Vucinic , Cedric Montanier , Thomas Schiex , Claire Dumon 13. Carbohydrate Bioengineering Meeting, May 2019, Toulouse, France Conference poster hal-02928929v1
	New computational methods and tools for structure-based protein design Clement Viricel , David Simoncini , Simon De Givry , Thomas Schiex , Sophie Barbe GGMM 2019, Apr 2019, Nice, France Conference poster hal-04225657v1
	Fitness landscape analysis to improve computational protein design David Simoncini , Thomas Schiex , Sophie Barbe , Sébastien Verel GGMM 2019, Apr 2019, Nice, France Conference poster hal-04225651v1
	Variable Neighborhood Search with Cost Function Networks to Solve Large Computational Protein Design Problems David Allouche , Antoine Charpentier , Thomas Schiex , Thomas Simonson Rencontre des Chimistes Théoriciens Francophones, Oct 2018, Toulouse, France. 2018 Conference poster hal-02733727v1
	Host tropism and host-pathogen interplay of typhoidal Salmonella enterica Ludovic Mallet , Claire Hoede , Franck Cerruti , Annick Moisan , Christine Gaspin JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. , 2017, Journées Ouvertes en Biologie, Informatique et Mathématiques. JOBIM 2017 Conference poster hal-01603254v1
	EU COST Action TD0801: statistical challenges on the 1000 euro genome sequences in plants Marco Bink , Thomas Schiex SeqAhead Scientific Meeting (COST Action BM1006), Nov 2011, Bruxelles, Belgium. EMBnet journal, 17 (Suppl. B), 2012, Proceedings SeqAhead Scientific Meeting (COST Action BM1006). ⟨10.14806/ej.17.B.280⟩ Conference poster hal-02747129v1
	MENDELSOFT : Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques. Simon de Givry , M. Sanchez , Zulma Vitezica , Isabelle Palhiere Palhière , Thomas Schiex GénoToul 2006, Nov 2006, Toulouse, France. 2006, GénoToul 2006, Bioinformatique, Recueil des Posters Conference poster hal-02750733v1

	Sequential decision-making problems : representation and solution Cédric Pralet , Thomas Schiex , Gérard Verfaillie ISTE Ltd, 384 p., 2010, 978-1-84821-174-2 Books hal-02818397v1
	Quelques expérimentations sur des problèmes de satisfaction de contraintes académiques et réels Thomas Schiex , G. Verfaillie 9 p., 1997 Books hal-02837978v1

	Cost Function Networks to Solve Large Computational Protein Design Problems David Allouche , Sophie Barbe , Simon de Givry , George Katsirelos , Yahia Lebbah Malek Masmoudi, Bassem Jarboui, Patrick Siarry. Operations Research and Simulation in healthcare, Springer, pp.81-102, 2021, 978-3-030-45223-0. ⟨10.1007/978-3-030-45223-0_4⟩ Book sections hal-02177634v1
	Valued Constraint Satisfaction Problems Martin Cooper , Simon de Givry , Thomas Schiex A Guided Tour of Artificial Intelligence Research, 2, Springer International Publishing, pp.185-207, 2020, AI Algorithms, 978-3-030-06167-8. ⟨10.1007/978-3-030-06167-8_7⟩ Book sections hal-02942366v1
	EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes Erika Sallet , Thomas Schiex , Jerome Gouzy Gene Prediction : Methods and Protocols, Humana Press INC., Springer Science, 2019, Methods in Molecular Biology, 978-1-4939-9173-0. ⟨10.1007/978-1-4939-9173-0_6⟩ Book sections hal-02790731v1
	Deterministic search methods for computational protein design Seydou Traore , David Allouche , Isabelle André , Thomas Schiex , Sophie Barbe Computational Protein Design, Chapter 4, Editions Springer, 2017, Methods in Molecular Biology, 978-1-4939-6635-6. ⟨10.1007/978-1-4939-6637-0_4⟩ Book sections hal-01605191v1
	Bioinformatique François Coste , Claire Nédellec , Thomas Schiex , Jean-Philippe Vert Pierre Marquis and Odile Papini and Henri Prade. Panorama de l'intelligence artificielle Ses bases méthodologiques, ses développements, 3, Cépaduès, 374 p., 2014, 9782364930438 Book sections hal-00857379v1
	Réseaux de contraintes valués Thomas Schiex , Simon de Givry , Martin Cooper Panorama de l'intelligence artificielle : Vol 2 : Algorithmes pour l'intelligence artificielle, Cepaduès Editions, 364 p., 2014, 9782364930421 Book sections hal-02795963v1
	A panel of learning methods for the reconstruction of gene regulatory networks in a systems genetics David Allouche , Christine Cierco-Ayrolles , Simon de Givry , Gérald Guillermin , Brigitte B. Mangin Gene network inference, verification of methods for systems genetics data, Editions Springer, 130 p., 2013, 978-3-642-45161-4. ⟨10.1007/978-3-642-45161-4⟩ Book sections hal-02808635v1
	Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques Marti Sanchez , Simon de Givry , Thomas Schiex Artificial Intelligence Research and Development, 163, IOS Press, pp.22, 2007, Frontiers in Artificial Intelligence and Applications, 978-1-60750-285-2 978-1-58603-798-7 Book sections hal-02814634v1
	Gene finding in eukaryotes C. Mathé , Thomas Schiex , Pierre Rouzé , Philippe Blayo , Marie-France Sagot Lu Q., Weiner M. Cloning and expression technologies, Eaton Publishing, pp.27-43, 2002 Book sections hal-00620804v1

	Qualité et diversité garanties dans les réseaux de fonctions de coût Manon Ruffini , Jelena Vucinic , Simon De Givry , George Katsirelos , Sophie Barbe 2019 Other publications hal-02963117v1
	Conclusion complétes des groupes de travail France IA - République Française , Thomas Schiex 2017, 350 p Other publications hal-02785477v1
	Rapport de synthèse France IA . République Française , Thomas Schiex 2017, 350 p Other publications hal-02785723v1
	Constraint programming Patrick Esquirol , Pierre Lopez , Hélène Fargier , Thomas Schiex 1995 Other publications hal-02850710v1

	Designing symmetrical multi-component proteins using a hybrid generative AI approach Delphine Dessaux , Samuel Buchet , Lucie Barthe , Marianne Defresne , Gianluca Cioci 2024 Preprints, Working Papers, ... hal-04646620v1
	Exact and approximate inference in graphical models: variable elimination and beyond Nathalie Dubois Peyrard , Simon de Givry , Alain Franc , Stephane Robin , Régis Sabbadin 2015 Preprints, Working Papers, ... hal-01197655v1

	Non-monotonic reasoning: from complexity to algorithms Claudette Cayrol , Marie-Christine Lagasquie-Schiex , Thomas Schiex [Research Report] Rapport IRIT--96.07R, IRIT : Institut de recherche en informatique de Toulouse; Toulouse 3 Paul Sabatier. 1996 Reports hal-02842327v1

	Algorithms for Computational Protein Design Thomas Schiex 3rd cycle. International Winter School on “Algorithms in Structural Bioinformatics – Computational Protein Design" (Algorithms for Computational Protein Design), 2017 Lectures hal-02786907v1

Thomas Schiex

Publications

Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium

Iterated local search with partition crossover for computational protein design

A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases

Protein Design with Deep Learning

Guaranteed Diversity and Optimality in Cost Function Network Based Computational Protein Design Methods

Molecular flexibility in computational protein design: an algorithmic perspective

Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

Positive multistate protein design

Aide à la conception

Graphical Models: Queries, Complexity, Algorithms

A structural homology approach for computational protein design with flexible backbone

Computational design of symmetrical eight-bladed β-propeller proteins

Exact or approximate inference in graphical models: why the choice is dictated by the treewidth, and how variable elimination can be exploited

Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems

Cost function network-based design of protein–protein interactions: predicting changes in binding affinity

Contraintes, incertitudes et modèles graphiques

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Triangle-based consistencies for cost function networks

Multi-language evaluation of exact solvers in graphical model discrete optimization

Fast search algorithms for computational protein design

Tractability-preserving Transformations of Global Cost Functions

Guaranteed Discrete Energy Optimization on Large Protein Design Problems

Computational protein design as an optimization problem

EuGene-PP: a next generation automated annotation pipeline for prokaryotic genomes.

Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

A new framework for computational protein design through cost function network optimization

Detecting long tandem duplications in genomic sequences

The tomato genome sequence provides insights into fleshy fruit evolution

The tomato genome sequence provides insights into fleshy fruit evolution

Le séquençage du génome humain

Gene regulatory network reconstruction using Bayesian networks, the Dantzig selector, the Lasso and their meta-analysis

The genome of Theobroma cacao.

The Medicago genome provides insight into the evolution of rhizobial symbioses

Le cadre PFU, un modèle et des algorithmes génériques pour la décision séquentielle incluant incertitudes, faisabilités et utilités

Soft arc consistency revisited

Introduction to the special issue on constraint-based approaches to preference modelling and reasoning

FrameDP: sensitive peptide detection on noisy matured sequences

Bounds arc consistency for weighted CSPs

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals.

LeARN : a platform for detecting, clustering and annotating non-coding RNAs

Genome annotation in plants and fungi: EuGène as a model platform

2006 and 2007 Max-SAT evaluations: contributed instances

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

A comparative genome approach to marker ordering

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome

Searching RNA motifs and their intermolecular contacts with constraint networks

Searching RNA motifs and their intermolecular contacts with constraint networks.

CAR(H)(T)AGene: multipopulation integrated genetic and radiation hybrid mapping

Integrating alternative splicing detection into gene prediction

Rearranged gene order between pig and human in a QTL region on SSC 7

EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences

Current methods of gene prediction their strengths and weaknesses

Gene finding in eukaryotes

Genome sequence of the plant pathogen Ralstonia solanacearum.

Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis

Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis

Maintaining reversible DAC for Max-CSP

Radio link frequency assignment

A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers

Nonmonotonic Reasoning: from Complexity to Algorithms

Problèmes de satisfaction de contraintes valués

Traitement de problèmes de décision sous incertitude par des problèmes de satisfaction de contraintes

Maintien de solution dans les problèmes dynamiques de satisfaction de contraintes : bilan de quelques approches

Nogood recording for static and dynamic constraint satisfaction problems

A fixed point semantics for the ATMS

Scalable Coupling of Deep Learning with Logical Reasoning

AI-powered de novo design of miniprotein binders

Design of symmetrical multi-component proteins using a hybrid generative AI approach.

Bi-Objective Discrete Graphical Model Optimization

Learning how to design biomolecules using a neuro-symbolic architecture

Design of symmetrical multi-component proteins using a hybrid generative AI approach

Learning to Reason: Predict-then-Optimize vs Predict-and-Optimize

Coupling CP with Deep Learning for Molecular Design and SARS-CoV2 Variants Exploration

Scalable Coupling of Deep Learning with Logical Reasoning

Scalable Coupling of Deep Learning with Logical Reasoning *

Computational Protein Design with Artificial Intelligence

Triangle-based consistencies for cost function networks 