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Number of documents

46

David Allouche


Journal articles14 documents

  • Abdelkader Ouali, David Allouche, Simon de Givry, Samir Loudni, Yahia Lebbah, et al.. Variable neighborhood search for graphical model energy minimization. Artificial Intelligence, Elsevier, 2020, 278, pp.103194. ⟨10.1016/j.artint.2019.103194⟩. ⟨hal-02463467⟩
  • Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortés, Thomas Schiex, et al.. Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. Journal of Chemical Information and Modeling, American Chemical Society, 2019, 59 (1), pp.127-136. ⟨10.1021/acs.jcim.8b00510⟩. ⟨hal-01943616⟩
  • Seydou Traore, Kyle E. Roberts, David Allouche, Bruce R. Donald, Isabelle André, et al.. Fast search algorithms for computational protein design. Journal of Computational Chemistry, Wiley, 2016, 37 (12), pp.1048 - 1058. ⟨10.1002/jcc.24290⟩. ⟨hal-01886385⟩
  • Barry Hurley, Barry O'Sullivan, David Allouche, George Katsirelos, Thomas Schiex, et al.. Multi-language evaluation of exact solvers in graphical model discrete optimization. Constraints, Springer Verlag, 2016, 21 (3), pp.413-434. ⟨10.1007/s10601-016-9245-y⟩. ⟨hal-02633083⟩
  • David Allouche, Christian Bessière, Patrice Boizumault, Simon de Givry, Patricia Gutierrez, et al.. Tractability-preserving Transformations of Global Cost Functions. Artificial Intelligence, Elsevier, 2016, 238, pp.166-189. ⟨10.1016/j.artint.2016.06.005⟩. ⟨lirmm-01374533⟩
  • David Simoncini, David Allouche, Simon de Givry, Céline Delmas, Sophie Barbe, et al.. Guaranteed Discrete Energy Optimization on Large Protein Design Problems. Journal of Chemical Theory and Computation, American Chemical Society, 2015, 11 (12), pp.5980 - 5989. ⟨10.1021/acs.jctc.5b00594⟩. ⟨hal-02637306⟩
  • David Allouche, Isabelle André, Sophie Barbe, Jessica Davies, Simon de Givry, et al.. Computational protein design as an optimization problem. Artificial Intelligence, Elsevier, 2014, 212, pp.59-79. ⟨10.1016/j.artint.2014.03.005⟩. ⟨hal-01268554⟩
  • Seydou Traore, David Allouche, Isabelle André, Simon de Givry, George Katsirelos, et al.. A new framework for computational protein design through cost function network optimization. Bioinformatics, Oxford University Press (OUP), 2013, 29 (17), pp.2129-2136. ⟨10.1093/bioinformatics/btt374⟩. ⟨hal-01268153⟩
  • Matthieu Vignes, Jimmy Vandel, David Allouche, Nidal Ramadan-Alban, Christine Cierco-Ayrolles, et al.. Gene regulatory network reconstruction using Bayesian networks, the Dantzig selector, the Lasso and their meta-analysis. PLoS ONE, Public Library of Science, 2011, 6 (12), pp.1-15. ⟨10.1371/journal.pone.0029165⟩. ⟨hal-02649016⟩
  • Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, et al.. BioMAJ: a flexible framework for databanks synchronization and processing. Bioinformatics, Oxford University Press (OUP), 2008, 24 (16), pp.1823-1825. ⟨10.1093/bioinformatics/btn325⟩. ⟨inria-00327502⟩
  • David Allouche, Joseph Parello, Yves-Henri Sanejouand. Ca 2+ /Mg 2+ exchange in parvalbumin and other EF-hand proteins. A theoretical study. Journal of Molecular Biology, Elsevier, 1999, 285 (2), pp.857-873. ⟨10.1006/jmbi.1998.2329⟩. ⟨hal-02116336⟩
  • Xavier Periole, David Allouche, A. Ramírez-Solís, I. Ortega-Blake, J. P. Daudey, et al.. New Effective Potentials Extraction Method for the Interaction between Cations and Water. Journal of Physical Chemistry B, American Chemical Society, 1998, 102 (43), pp.8579-8587. ⟨10.1021/jp981688t⟩. ⟨hal-02694207⟩
  • X. Periole, David Allouche, J.-P. Daudey, Y.-H. Sanejouand. Simple Two-Body Cation−Water Interaction Potentials Derived from ab Initio Calculations. Comparison to Results Obtained with an Empirical Approach. Journal of Physical Chemistry B, American Chemical Society, 1997, 101 (25), pp.5018-5025. ⟨10.1021/jp9701855⟩. ⟨hal-02694213⟩
  • Anne-Sylvie Fabiano, David Allouche, Yves-Henri Sanejouand, Nicole Paillous. Synthesis of a New Cationic Pyropheophorbide Derivative and Studies of its Aggregation Process in Aqueous Solution. Photochemistry and Photobiology, Wiley, 1997, 66 (3), pp.336-345. ⟨10.1111/j.1751-1097.1997.tb03156.x⟩. ⟨hal-02694209⟩

Conference papers27 documents

  • David Allouche. Cost function network for molecular design an IA method for discret search space exploration. Symposium on Molecular Design and Bioinformatics 2019 (SEADIM), Jun 2019, Santa María Key, Cuba. ⟨hal-02734749⟩
  • Thomas Schiex, Sophie Barbe, David Simoncini, Jelena Vucinic, Manon Ruffini, et al.. Constraint Programming and Graphical models - Pushing data into your models, The protein design case.. 23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France. ⟨hal-02154354⟩
  • Abdelkader Ouali, David Allouche, Simon de Givry, Samir Loudni, Yahia Lebbah, et al.. Recherche complète à voisinages variables guidée par la décomposition arborescente pour la minimisation d'énergie dans les modèles graphiques. 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⟩. ⟨hal-02733676⟩
  • David Allouche, Simon de Givry, Georgios Katsirelos, Thomas Schiex, Matthias Zytnicki, et al.. Recent algorithmic advances for combinatorial optimization in graphical models. 23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France. 80 p. ⟨hal-02785380⟩
  • David Allouche. Pourquoi les MATH et l’intelligence artificielle sont important pour comprend et améliorer le fonctionnement de protéine ?. Fête de la science, Oct 2018, Castanet-Tolosan, France. 18 p. ⟨hal-02733726⟩
  • David Allouche. Euclidean Variable Neighborhood Search: A method for large computation protein design. Deciphering complex energy landscape and kinetic network from single molecules to cells: a new challenge to make theories meet experiments, Sep 2017, Dijon, France. ⟨hal-02733686⟩
  • Abdelkader Ouali, David Allouche, Simon de Givry, Samir Loudni, Yahia Lebbah, et al.. Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization. Conference on Uncertainty in Artificial Intelligence, UAI 2017, Aug 2017, Sydney, Australia. ⟨hal-01628162⟩
  • Abdelkader Ouali, David Allouche, Simon de Givry, Samir Loudni, Yahia Lebbah, et al.. Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization. Conference on Uncertainty in Artificial Intelligence (UAI'17), Aug 2017, Sydney, Australia. 10 p. ⟨hal-02733961⟩
  • David Allouche, Simon de Givry, George Katsirelos, Thomas Schiex, Matthias Zytnicki. Anytime hybrid best-first search with tree decomposition for weighted CSP. 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⟩. ⟨hal-01198361⟩
  • Clément Viricel, David Simoncini, David Allouche, Simon de Givry, Sophie Barbe, et al.. Approximate counting with deterministic guarantees for affinity computation. 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⟩. ⟨hal-01269259⟩
  • Thomas Schiex, Seydou Traoré, David Simoncini, Sophie Barbe, Simon de Givry, et al.. Computational Enzyme Design through deterministic optimization and counting. 3DSig Structural Bioinformatics and Computational Biophysics 2015, Jul 2015, Dublin, Ireland. ⟨hal-01605405⟩
  • David Allouche, Simon de Givry, Barry Hurley, George Katsirelos, Barry O'Sullivan, et al.. Une comparaison de logiciels d'optimisation sur une large collection de modèles graphiques. JFPC 2014 - Dixièmes Journées Francophones de Programmation par Contraintes, Jun 2014, Angers, France. 10 p. ⟨hal-01198360⟩
  • Simon de Givry, Barry Hurley, David Allouche, Georgios Katsirelos, Barry O'Sullivan, et al.. An experimental evaluation of CP/AI/OR solvers for optimization in graphical models. Congrès ROADEF'2014, Feb 2014, Bordeaux, France. 1 p. ⟨hal-02742905⟩
  • Simon de Givry, Barry Hurley, David Allouche, George Katsirelos, Thomas Schiex, et al.. An Experimental Evaluation of CP/AI/OR Solvers for Optimization in Graphical Models. 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. ⟨hal-00946323⟩
  • Thomas Schiex, David Allouche, Simon de Givry, George Katsirelos, Sophie Barbe, et al.. Computational protein design as a cost function network optimization problem. Séminaire MOGISA du LAAS/CNRS, Centre National de la Recherche Scientifique (CNRS). FRA., Jun 2013, Toulouse, France. ⟨hal-01268632⟩
  • Seydou Traore, David Allouche, Isabelle André, Simon de Givry, George Katsirelos, et al.. A new framework for computational protein design through cost function network optimization. JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Société Française de Bio-Informatique (SFBI). FRA., Jul 2013, Toulouse, France. 2 p. ⟨hal-01268555⟩
  • David Allouche, Christian Bessière, Patrice Boizumault, Simon de Givry, Patricia Gutierrez, et al.. Filtering Decomposable Global Cost Functions. AAAI Conference on Artificial Intelligence, Jul 2012, Toronto, ON, Canada. ⟨lirmm-00748187⟩
  • David Allouche, Christian Bessière, Patrice Boizumault, Simon de Givry, Patricia Gutierrez, et al.. Filtrage de fonctions de coût globales décomposables. 8èmes Journées Francophones de Programmation par Contraintes (JFPC 2012), May 2012, Toulouse, France. ⟨hal-00809789⟩
  • David Allouche, Christian Bessière, Patrice Boizumault, Simon de Givry, Patricia Gutierrez, et al.. Filtering decomposable global cost functions. Twenty-Sixth Conference on Artificial Intelligence, Jul 2012, Toronto, Canada. pp.7. ⟨hal-02747813⟩
  • David Allouche, Christian Bessière, Patrice Boizumault, Simon de Givry, Patricia Gutierrez, et al.. Filtrage de fonctions de coût globales décomposables. Huitièmes Journées Francophones de Programmation par Contraintes (JFPC), Association Française de Programmation par Contraintes (AFPC). FRA., May 2012, Toulouse, France. pp.358. ⟨hal-02747133⟩
  • David Allouche, Aurélie Favier, Mathieu Fontaine, Simon de Givry, Jean-Philippe Metivier, et al.. Combining exact WCSP techniques and VNS search for solving MPE. Conference on Uncertainty in Artificial Intelligence (UAI'12), Aug 2012, Catalina Island, United States. ⟨hal-01022649⟩
  • David Allouche, Seydou Traore, Isabelle André, Simon de Givry, George Katsirelos, et al.. Computational protein design as a cost function network optimization problem. 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⟩. ⟨hal-01191320⟩
  • David Allouche, Simon de Givry, Thomas Schiex. Towards parallel non serial dynamic programming for solving hard weighted CSP. 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⟩. ⟨hal-02753702⟩
  • David Allouche, Simon de Givry, Thomas Schiex. Sélection de tagSNP: une approche PLNE. Congrès ROADEF'2010, Feb 2010, Toulouse, France. pp.2. ⟨hal-02812620⟩
  • M. Sanchez, David Allouche, Simon de Givry, Thomas Schiex. Algorithme des Poupées Russes exploitant une décomposition arborescente. Cinquièmes Journées Francophones de Programmation par Contraintes, Orléans, juin 2009, Jun 2009, France. pp.15-25. ⟨hal-00387845⟩
  • David Allouche, Thomas Schiex, Simon de Givry, Martin Sanchez. TagSNP selection using weighted CSP and russian doll search with tree decomposition. CP-09 workshop on Constraint Based Methods for Bioinformatics, Sep 2009, Lisbonne, Portugal. pp.9. ⟨hal-02813239⟩
  • Marti Sanchez, David Allouche, Simon de Givry, Thomas Schiex. Russian doll search with tree decomposition. 21st International Joint Conference on Artificial Intelligence, Jul 2009, Pasadena, United States. pp.6. ⟨hal-02755904⟩

Poster communications1 document

  • David Allouche, Antoine Charpentier, Thomas Schiex, Thomas Simonson. Variable Neighborhood Search with Cost Function Networks to Solve Large Computational Protein Design Problems: we explored various mutator for improving VNS robustness for the protein design . But the method is generic and can be used very likely in various context of molecular modelling if energy table can be precomputed. Rencontre des Chimistes Théoriciens Francophones, Oct 2018, Toulouse, France. 2018. ⟨hal-02733727⟩

Book sections3 documents

  • David Allouche, Sophie Barbe, Simon de Givry, George Katsirelos, Yahia Lebbah, et al.. Cost Function Networks to Solve Large Computational Protein Design Problems. Malek Masmoudi, Bassem Jarboui, Patrick Siarry. Operations Research and Simulation in healthcare, Springer, In press. ⟨hal-02177634⟩
  • Seydou Traore, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe. Deterministic search methods for computational protein design. Computational Protein Design, Editions Springer, 2017, Methods in Molecular Biology, 978-1-4939-6635-6. ⟨10.1007/978-1-4939-6637-0_4⟩. ⟨hal-01605191⟩
  • David Allouche, Christine Cierco-Ayrolles, Simon de Givry, Gérald Guillermin, Brigitte Mangin, et al.. A panel of learning methods for the reconstruction of gene regulatory networks in a systems genetics. 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⟩. ⟨hal-02808635⟩

Other publications1 document

  • David Allouche, Anthony Assi, Yoann Beausse, Christophe Caron, Olivier Filangi, et al.. BioMAJ : A workflow engine dedicated to biological bank management. 2007. ⟨inria-00176506⟩