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david allouche

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Variable neighborhood search for graphical model energy minimization

Abdelkader Ouali , David Allouche , Simon de Givry , Samir Loudni , Yahia Lebbah et al.
Artificial Intelligence, 2020, 278, pp.103194. ⟨10.1016/j.artint.2019.103194⟩
Journal articles hal-02463467v1
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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 et al.
Journal of Chemical Information and Modeling, 2019, 59 (1), pp.127-136. ⟨10.1021/acs.jcim.8b00510⟩
Journal articles hal-01943616v1

Fast search algorithms for computational protein design

Seydou Traore , Kyle E. Roberts , David Allouche , Bruce R. Donald , Isabelle André et al.
Journal of Computational Chemistry, 2016, 37 (12), pp.1048 - 1058. ⟨10.1002/jcc.24290⟩
Journal articles hal-01886385v1
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Tractability-preserving Transformations of Global Cost Functions

David Allouche , Christian Bessière , Patrice Boizumault , Simon de Givry , Patricia Gutierrez et al.
Artificial Intelligence, 2016, 238, pp.166-189. ⟨10.1016/j.artint.2016.06.005⟩
Journal articles lirmm-01374533v1

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

Barry Hurley , Barry O'Sullivan , David Allouche , George Katsirelos , Thomas Schiex et al.
Constraints, 2016, 21 (3), pp.413-434. ⟨10.1007/s10601-016-9245-y⟩
Journal articles hal-02633083v1

Guaranteed Discrete Energy Optimization on Large Protein Design Problems

David Simoncini , David Allouche , Simon de Givry , Céline Delmas , Sophie Barbe et al.
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 et al.
Artificial Intelligence, 2014, 212, pp.59-79. ⟨10.1016/j.artint.2014.03.005⟩
Journal articles hal-01268554v1
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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 et al.
Bioinformatics, 2013, 29 (17), pp.2129-2136. ⟨10.1093/bioinformatics/btt374⟩
Journal articles hal-01268153v1
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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 et al.
PLoS ONE, 2011, 6 (12), pp.1-15. ⟨10.1371/journal.pone.0029165⟩
Journal articles hal-02649016v1
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BioMAJ: a flexible framework for databanks synchronization and processing

Olivier Filangi , Yoann Beausse , Anthony Assi , Ludovic Legrand , Jean-Marc Larré et al.
Bioinformatics, 2008, 24 (16), pp.1823-1825. ⟨10.1093/bioinformatics/btn325⟩
Journal articles inria-00327502v1
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Ca 2+ /Mg 2+ exchange in parvalbumin and other EF-hand proteins. A theoretical study

David Allouche , Joseph Parello , Yves-Henri Sanejouand
Journal of Molecular Biology, 1999, 285 (2), pp.857-873. ⟨10.1006/jmbi.1998.2329⟩
Journal articles hal-02116336v1
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New Effective Potentials Extraction Method for the Interaction between Cations and Water

Xavier Periole , David Allouche , A. Ramírez-Solís , I. Ortega-Blake , J. P. Daudey et al.
Journal of Physical Chemistry B, 1998, 102 (43), pp.8579-8587. ⟨10.1021/jp981688t⟩
Journal articles hal-02694207v1
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Simple Two-Body Cation−Water Interaction Potentials Derived from ab Initio Calculations. Comparison to Results Obtained with an Empirical Approach

X. Periole , David Allouche , J.-P. Daudey , Y.-H. Sanejouand
Journal of Physical Chemistry B, 1997, 101 (25), pp.5018-5025. ⟨10.1021/jp9701855⟩
Journal articles hal-02694213v1

Synthesis of a New Cationic Pyropheophorbide Derivative and Studies of its Aggregation Process in Aqueous Solution

Anne-Sylvie Fabiano , David Allouche , Yves-Henri Sanejouand , Nicole Paillous
Photochemistry and Photobiology, 1997, 66 (3), pp.336-345. ⟨10.1111/j.1751-1097.1997.tb03156.x⟩
Journal articles hal-02694209v1

Cost function network for molecular design an IA method for discret search space exploration

David Allouche
Symposium on Molecular Design and Bioinformatics 2019 (SEADIM), Jun 2019, Santa María Key, Cuba
Conference papers hal-02734749v1
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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 et al.
23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France
Conference papers hal-02154354v1
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Recherche complète à voisinages variables guidée par la décomposition arborescente pour la minimisation d'énergie dans les modèles graphiques

Abdelkader Ouali , David Allouche , Simon de Givry , Samir Loudni , Yahia Lebbah et al.
9e Journées Francophones sur les Réseaux Bayésiens et les Modèles Graphiques Probabilistes 2018 (JFRB 2018), May 2018, Toulouse, France. 114 p., ⟨10.3166/RIA.-.1-7⟩
Conference papers hal-02733676v1
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Pourquoi les MATH et l’intelligence artificielle sont important pour comprend et améliorer le fonctionnement de protéine ?

David Allouche
Fête de la science, Oct 2018, Castanet-Tolosan, France. 18 p
Conference papers hal-02733726v1
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Recent algorithmic advances for combinatorial optimization in graphical models

David Allouche , Simon de Givry , Georgios Katsirelos , Thomas Schiex , Matthias Zytnicki et al.
23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France. 80 p
Conference papers hal-02785380v1
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Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization

Abdelkader Ouali , David Allouche , Simon de Givry , Samir Loudni , Yahia Lebbah et al.
Conference on Uncertainty in Artificial Intelligence, UAI 2017, Aug 2017, Sydney, Australia
Conference papers hal-01628162v1
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Euclidean Variable Neighborhood Search: A method for large computation protein design

David Allouche
Deciphering complex energy landscape and kinetic network from single molecules to cells: a new challenge to make theories meet experiments, Sep 2017, Dijon, France
Conference papers hal-02733686v1
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Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization

Abdelkader Ouali , David Allouche , Simon de Givry , Samir Loudni , Yahia Lebbah et al.
Conference on Uncertainty in Artificial Intelligence (UAI'17), Aug 2017, Sydney, Australia. 10 p
Conference papers hal-02733961v1

Anytime hybrid best-first search with tree decomposition for weighted CSP

David Allouche , Simon de Givry , George Katsirelos , Thomas Schiex , Matthias Zytnicki et al.
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 Enzyme Design through deterministic optimization and counting

Thomas Schiex , Seydou Traoré , David Simoncini , Sophie Barbe , Simon de Givry et al.
3DSig Structural Bioinformatics and Computational Biophysics 2015, Jul 2015, Dublin, Ireland
Conference papers hal-01605405v1
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Approximate counting with deterministic guarantees for affinity computation

Clément Viricel , David Simoncini , David Allouche , Simon de Givry , Sophie Barbe et al.
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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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 et al.
JFPC 2014 - Dixièmes Journées Francophones de Programmation par Contraintes, Jun 2014, Angers, France. 10 p
Conference papers hal-01198360v1

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 et al.
Congrès ROADEF'2014, Feb 2014, Bordeaux, France. 1 p
Conference papers hal-02742905v1

An Experimental Evaluation of CP/AI/OR Solvers for Optimization in Graphical Models

Simon de Givry , Barry Hurley , David Allouche , George Katsirelos , Thomas Schiex et al.
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

Computational protein design as a cost function network optimization problem

Thomas Schiex , David Allouche , Simon de Givry , George Katsirelos , Sophie Barbe et al.
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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A new framework for computational protein design through cost function network optimization

Seydou Traore , David Allouche , Isabelle André , Simon de Givry , George Katsirelos et al.
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 Bessière , Patrice Boizumault , Simon de Givry , Patricia Gutierrez et al.
Twenty-Sixth Conference on Artificial Intelligence, Jul 2012, Toronto, Canada. pp.7
Conference papers hal-02747813v1
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Filtrage de fonctions de coût globales décomposables

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

Combining exact WCSP techniques and VNS search for solving MPE

David Allouche , Aurélie Favier , Mathieu Fontaine , Simon de Givry , Jean-Philippe Metivier et al.
Conference on Uncertainty in Artificial Intelligence (UAI'12), Aug 2012, Catalina Island, United States
Conference papers hal-01022649v1
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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 et al.
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
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Filtering Decomposable Global Cost Functions

David Allouche , Christian Bessière , Patrice Boizumault , Simon de Givry , Patricia Gutierrez et al.
AAAI Conference on Artificial Intelligence, Jul 2012, Toronto, ON, Canada
Conference papers lirmm-00748187v1
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Filtrage de fonctions de coût globales décomposables

David Allouche , Christian Bessière , Patrice Boizumault , Simon de Givry , Patricia Gutierrez et al.
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
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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

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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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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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
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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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Cost Function Networks to Solve Large Computational Protein Design Problems

David Allouche , Sophie Barbe , Simon de Givry , George Katsirelos , Yahia Lebbah et al.
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

Deterministic search methods for computational protein design

Seydou Traore , David Allouche , Isabelle André , Thomas Schiex , Sophie Barbe et al.
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

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 et al.
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