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Thomas Schiex

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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

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
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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

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

Manon Ruffini , Jelena Vucinic , Simon De de Givry , George Katsirelos , Sophie Barbe
Algorithms, 2021, 14 (6), pp.168. ⟨10.3390/a14060168⟩
Journal articles hal-03244149v1
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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
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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
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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
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Positive multistate protein design

Jelena Vucinic , David Simoncini , Manon Ruffini , Sophie Barbe , Thomas Schiex
Journal articles hal-02625007v1
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Aide à la conception

Juan Cortés , Thomas Schiex
Le petit illustré, regards croisés de chercheur.es, 2020
Journal articles hal-03436420v1
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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
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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
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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
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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
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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

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
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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
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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

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
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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
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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

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

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
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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
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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
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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-04198562v1
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Le séquençage du génome humain

Thomas Schiex
Tangente (Paris), 2012, pp.104-109
Journal articles hal-02641811v1

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
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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 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

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

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

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

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
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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
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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

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
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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
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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
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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
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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
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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
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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

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

Gene finding in eukaryotes

C. Mathé , Thomas Schiex , P. Rouzé , P. Blayo , M.-F. Sagot
incollection, 2002, --, pp.27-43
Journal articles hal-00427230v1

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

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
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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
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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
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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, United States
Conference papers hal-04222883v1

Scalable Coupling of Deep Learning with Logical Reasoning

Marianne Defresne , Thomas Schiex , Sophie Barbe
PFIA'23, Jul 2023, Strasbourg, France
Conference papers hal-04223509v1
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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-04223570v1
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Computational Protein Design with Artificial Intelligence

Marianne Defresne , Thomas Schiex , Sophie Barbe
GGMM 2023, May 2023, Toulouse, France
Conference papers hal-04223563v1
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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 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

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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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

Optimization in Graphical Models - Connecting NP-complete frameworks

Thomas Schiex
Séminaire Université Catholique de Louvain, Sep 2016, Louvain, Belgium
Conference papers hal-01603551v1

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

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

Computational Design as an Optimization Problem

Thomas Schiex
Séminaire INRIA-IRISA, May 2015, Rennes, France
Conference papers hal-01602148v1
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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

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
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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
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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
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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
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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

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

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
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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
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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
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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
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Cohérence d'arc virtuelle dynamique

Thomas Schiex , Christian Bessiere , Thi Hông Hiêp Nguyên
9èmes Journées Francophones de Programmation par Contraintes (JFPC 2013), Jun 2013, Aix-en-Provence, France. pp.249-258
Conference papers lirmm-00830411v1
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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

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

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
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Filtrage de fonctions de coût globales décomposables

David Allouche , Christian Bessiere , Patrice Boizumault , Simon de Givry , Patricia Gutierrez
8èmes Journées Francophones de Programmation par Contraintes (JFPC 2012), May 2012, Toulouse, France
Conference papers hal-00809789v1
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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
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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
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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

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
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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
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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
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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
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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
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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
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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
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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
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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
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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

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
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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
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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
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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
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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
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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

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
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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
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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

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

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
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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
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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

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
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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

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

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
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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
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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

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

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

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

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
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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
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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
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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
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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
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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
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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
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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