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ORCIDFrançois Fages
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- affiliation: INRIA, France
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2020 – today
- 2023
[i16]Marine Collery, Philippe Bonnard, François Fages, Remy Kusters:
Neural-based classification rule learning for sequential data. CoRR abs/2302.11286 (2023)- 2022
- [j41]Jeremy Grignard
, Véronique Lamamy, Eva Vermersch, Philippe Delagrange, Jean-Philippe Stephan, Thierry Dorval, François Fages:
Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design. PLoS Comput. Biol. 18(6) (2022) - [c77]Mathieu Hemery, François Fages:
Algebraic Biochemistry: A Framework for Analog Online Computation in Cells. CMSB 2022: 3-20 - [c76]Eléa Thibault Greugny, Georgios N. Stamatas, François Fages:
Stability Versus Meta-stability in a Skin Microbiome Model. CMSB 2022: 179-197 - 2021
- [j40]Julien Martinelli, Sandrine Dulong, Xiao-Mei Li, Michèle Teboul, Sylvain Soliman, Francis Lévi, François Fages, Annabelle Ballesta:
Model learning to identify systemic regulators of the peripheral circadian clock. Bioinform. 37(Supplement): 401-409 (2021) - [c75]Mathieu Hemery, François Fages, Sylvain Soliman:
Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs. CMSB 2021: 74-90 - 2020
- [c74]Elisabeth Degrand, François Fages, Sylvain Soliman:
Graphical Conditions for Rate Independence in Chemical Reaction Networks. CMSB 2020: 61-78 - [c73]Mathieu Hemery, François Fages, Sylvain Soliman:
On the Complexity of Quadratization for Polynomial Differential Equations. CMSB 2020: 120-140 - [i15]Mathieu Hemery, François Fages, Sylvain Soliman:
On the Complexity of Quadratization for Polynomial Differential Equations. CoRR abs/2007.08910 (2020) - [i14]Elisabeth Degrand, François Fages, Sylvain Soliman:
Graphical Conditions for Rate Independence in Chemical Reaction Networks. CoRR abs/2007.15642 (2020)
2010 – 2019
- 2019
- [c72]Wei-Chih Huang, Jie-Hong Roland Jiang, François Fages, Franck Molina:
Biochemical Threshold Function Implementation with Zero-Order Ultrasensitivity. BioCAS 2019: 1-4 - [c71]Elisabeth Degrand, Mathieu Hemery, François Fages:
On Chemical Reaction Network Design by a Nested Evolution Algorithm. CMSB 2019: 78-95 - [c70]Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages:
On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics. CMSB 2019: 352-355 - [i13]François Fages, Katsumi Inoue, Heinz Koeppl, Chris Myers, Yoshihiro Shimizu:
Formal methods for the synthesis of biomolecular circuits (NII Shonan Meeting 157). NII Shonan Meet. Rep. 2019 (2019) - 2018
- [j39]François Boulier, François Fages, Ovidiu Radulescu, Satya Swarup Samal, Andreas Schuppert, Werner M. Seiler, Thomas Sturm, Sebastian Walcher, Andreas Weber:
The SYMBIONT project: symbolic methods for biological networks. ACM Commun. Comput. Algebra 52(3): 67-70 (2018) - [j38]François Fages, Thierry Martinez, David A. Rosenblueth, Sylvain Soliman:
Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1138-1151 (2018) - [c69]François Fages, Sylvain Soliman:
On Robustness Computation and Optimization in BIOCHAM-4. CMSB 2018: 292-299 - [i12]Adrien Baudier, François Fages, Sylvain Soliman:
Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. CoRR abs/1809.08891 (2018) - 2017
- [c68]Chun-Ning Lai, Jie-Hong R. Jiang, François Fages:
Recombinase-based genetic circuit optimization. BioCAS 2017: 1-4 - [c67]Arthur Carcano, François Fages, Sylvain Soliman:
Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. CMSB 2017: 74-90 - [c66]François Fages, Guillaume Le Guludec, Olivier Bournez, Amaury Pouly:
Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs. CMSB 2017: 108-127 - 2016
- [j37]Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry:
Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. Bioinform. 32(17): 772-780 (2016) - [j36]Pauline Traynard, Céline Feillet, Sylvain Soliman, Franck Delaunay, François Fages:
Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis. Biosyst. 149: 59-69 (2016) - [j35]Faten Nabli, Thierry Martinez, François Fages, Sylvain Soliman:
On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity. Constraints An Int. J. 21(2): 251-276 (2016) - [c65]François Fages, Thierry Martinez, David A. Rosenblueth, Sylvain Soliman:
Influence Systems vs Reaction Systems. CMSB 2016: 98-115 - [c64]Thierry Martinez, François Fages, Abder Aggoun:
A Stochastic Continuous Optimization Backend for MiniZinc with Applications to Geometrical Placement Problems. CPAIOR 2016: 262-278 - [c63]Abderrahmane Aggoun, Ahmed Rhiat, François Fages:
Panorama of real-life applications in logistics embedding bin packing optimization algorithms, robotics and cloud computing technologies. GOL 2016: 1-4 - [i11]Abderrahmane Aggoun, Nicolas Beldiceanu, Gilles Chabert, François Fages:
Packing with Complex Shapes. ERCIM News 2016(105) (2016) - 2015
- [j34]François Fages, Steven Gay, Sylvain Soliman:
Inferring reaction systems from ordinary differential equations. Theor. Comput. Sci. 599: 64-78 (2015) - [j33]Hui-Ju Katherine Chiang, François Fages, Jie-Hong Roland Jiang, Sylvain Soliman:
Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Trans. Model. Comput. Simul. 25(2): 14:1-14:22 (2015) - [c62]Pauline Traynard, François Fages, Sylvain Soliman:
Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis. CMSB 2015: 208-221 - [c61]Hui-Ju Katherine Chiang, Jie-Hong R. Jiang, François Fages:
Reconfigurable neuromorphic computation in biochemical systems. EMBC 2015: 937-940 - [c60]Thierry Martinez, François Fages, Sylvain Soliman:
Search by constraint propagation. PPDP 2015: 173-183 - 2014
- [j32]Sylvain Soliman, François Fages, Ovidiu Radulescu:
A constraint solving approach to model reduction by tropical equilibration. Algorithms Mol. Biol. 9: 24 (2014) - [j31]Steven Gay, François Fages, Thierry Martinez, Sylvain Soliman, Christine Solnon:
On the subgraph epimorphism problem. Discret. Appl. Math. 162: 214-228 (2014) - [c59]Hui-Ju Katherine Chiang, Jie-Hong R. Jiang, François Fages:
Building reconfigurable circuitry in a biochemical world. BioCAS 2014: 560-563 - [c58]Pauline Traynard, François Fages, Sylvain Soliman:
Trace Simplifications Preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock. CMSB 2014: 114-128 - [c57]François Fages:
Cells as Machines: Towards Deciphering Biochemical Programs in the Cell. ICDCIT 2014: 50-67 - [e13]François Fages, Carla Piazza:
Formal Methods in Macro-Biology - First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Lecture Notes in Computer Science 8738, Springer 2014, ISBN 978-3-319-10397-6 [contents] - 2013
- [j30]François Fages, Simon de Givry, Christine Solnon:
Preface. RAIRO Oper. Res. 47(2): 89-90 (2013) - [j29]François Fages, Sylvain Soliman:
Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 10(2): 308-309 (2013) - [c56]Hui-Ju Katherine Chiang, François Fages, Jie-Hong R. Jiang, Sylvain Soliman:
On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models. CMSB 2013: 192-205 - [i10]Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman:
Un modèle booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri. CoRR abs/1304.2948 (2013) - 2012
- [j28]François Fages, Sylvain Soliman:
Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1314-1315 (2012) - [c55]François Fages, Steven Gay, Sylvain Soliman:
Inferring Reaction Models from ODEs. CMSB 2012: 370-373 - [c54]Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman:
A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets. CP 2012: 798-814 - [c53]Anthony José da Cunha Carneiro Lins, Fernando Buarque de Lima Neto, François Fages, Carmelo J. A. Bastos Filho:
A Comparative Analysis of FSS with CMA-ES and S-PSO in Ill-Conditioned Problems. IDEAL 2012: 416-422 - 2011
- [j27]Elisabetta De Maria, François Fages, Aurélien Rizk, Sylvain Soliman:
Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints. Theor. Comput. Sci. 412(21): 2108-2127 (2011) - [j26]Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures. Theor. Comput. Sci. 412(26): 2827-2839 (2011) - [c52]Jannis Uhlendorf, Samuele Bottani, François Fages, Pascal Hersen, Grégory Batt:
Towards Real-Time Control of Gene Expression: Controlling the Hog Signaling Cascade. Pacific Symposium on Biocomputing 2011: 338-349 - [e12]François Fages:
Computational Methods in Systems Biology, 9th International Conference, CMSB 2011, Paris, France, September 21-23, 2011. Proceedings. ACM 2011, ISBN 978-1-4503-0817-5 [contents] - 2010
- [j25]Steven Gay, Sylvain Soliman, François Fages:
A graphical method for reducing and relating models in systems biology. Bioinform. 26(18) (2010) - [c51]François Fages:
A Logical Paradigm for Systems Biology (Invited Talk). ICLP (Technical Communications) 2010: 2-3 - [i9]Abder Aggoun, Nicolas Beldiceanu, Mats Carlsson, François Fages:
Integrating Rule-Based Modelling and Constraint Programming for Solving Industrial Packing Problems. ERCIM News 2010(81) (2010) - [i8]François Fages, Grégory Batt, Elisabetta De Maria, Dragana Jovanovska, Aurélien Rizk, Sylvain Soliman:
Computational Systems Biology in BIOCHAM. ERCIM News 2010(82): 36 (2010)
2000 – 2009
- 2009
- [j24]Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
A general computational method for robustness analysis with applications to synthetic gene networks. Bioinform. 25(12) (2009) - [c50]Elisabetta De Maria, François Fages, Sylvain Soliman:
On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle. CMSB 2009: 142-157 - [c49]François Fages, Aurélien Rizk:
From Model-Checking to Temporal Logic Constraint Solving. CP 2009: 319-334 - [c48]François Fages, Julien Martin:
Modelling Search Strategies in Rules2CP. CPAIOR 2009: 321-322 - [c47]Julien Martin, Thierry Martinez, François Fages:
Procedural Code Generation vs Static Expansion in Modelling Languages for Constraint Programming. CSCLP 2009: 38-58 - [e11]Angelo Oddi, François Fages, Francesca Rossi:
Recent Advances in Constraints, 13th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2008, Rome, Italy, June 18-20, 2008, Revised Selected Papers. Lecture Notes in Computer Science 5655, Springer 2009, ISBN 978-3-642-03250-9 [contents] - 2008
- [j23]François Fages, Sylvain Soliman:
Abstract interpretation and types for systems biology. Theor. Comput. Sci. 403(1): 52-70 (2008) - [j22]François Fages, Aurélien Rizk:
On temporal logic constraint solving for analyzing numerical data time series. Theor. Comput. Sci. 408(1): 55-65 (2008) - [c46]Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman:
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology. CMSB 2008: 251-268 - [c45]François Fages, Julien Martin:
From Rules to Constraint Programs with the Rules2CP Modelling Language. CSCLP 2008: 66-83 - [c44]François Fages, Sylvain Soliman:
From Reaction Models to Influence Graphs and Back: A Theorem. FMSB 2008: 90-102 - [c43]François Fages, Sylvain Soliman:
Formal Cell Biology in Biocham. SFM 2008: 54-80 - [p1]François Fages, Sylvain Soliman:
Model Revision from Temporal Logic Properties in Computational Systems Biology. Probabilistic Inductive Logic Programming 2008: 287-304 - [e10]François Fages, Francesca Rossi, Sylvain Soliman:
Recent Advances in Constraints, 12th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2007, Rocquencourt, France, June 7-8, 2007, Revised Selected Papers. Lecture Notes in Computer Science 5129, Springer 2008, ISBN 978-3-540-89811-5 [contents] - 2007
- [j21]Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, L. Fosse, Sylvain Soliman:
Langages formels dans la machine abstraite biochimique BIOCHAM. Tech. Sci. Informatiques 26(1-2): 47-72 (2007) - [c42]François Fages, Aurélien Rizk:
On the Analysis of Numerical Data Time Series in Temporal Logic. CMSB 2007: 48-63 - [c41]Rémy Haemmerlé, François Fages, Sylvain Soliman:
Closures and Modules Within Linear Logic Concurrent Constraint Programming. FSTTCS 2007: 544-556 - [c40]Rémy Haemmerlé, François Fages:
Abstract Critical Pairs and Confluence of Arbitrary Binary Relations. RTA 2007: 214-228 - [e9]Francisco Azevedo, Pedro Barahona, François Fages, Francesca Rossi:
Recent Advances in Constraints, 11th Annual ERCIM International Workshop on Constraint Solving and Contraint Logic Programming, CSCLP 2006, Caparica, Portugal, June 26-28, 2006, Revised Selected and Invited Papers. Lecture Notes in Computer Science 4651, Springer 2007, ISBN 978-3-540-73816-9 [contents] - [e8]Stefano Spaccapietra, Paolo Atzeni, François Fages, Mohand-Said Hacid, Michael Kifer, John Mylopoulos, Barbara Pernici, Pavel Shvaiko, Juan Trujillo, Ilya Zaihrayeu:
Journal on Data Semantics VIII. Lecture Notes in Computer Science 4380, Springer 2007, ISBN 978-3-540-70663-2 [contents] - [e7]Stefano Spaccapietra, Paolo Atzeni, François Fages, Mohand-Said Hacid, Michael Kifer, John Mylopoulos, Barbara Pernici, Pavel Shvaiko, Juan Trujillo, Ilya Zaihrayeu:
Journal on Data Semantics IX. Lecture Notes in Computer Science 4601, Springer 2007, ISBN 978-3-540-74982-0 [contents] - [i7]François Fages, Abder Aggoun:
Net-WMS - A New Generation of Warehouse Management Systems Networked Services. ERCIM News 2007(68) (2007) - [i6]Jean Clairambault, François Fages, Sylvain Soliman:
Patient-Tailored Cancer Therapeutics - The Tempo Project. ERCIM News 2007(69) (2007) - 2006
- [j20]Laurence Calzone, François Fages, Sylvain Soliman:
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinform. 22(14): 1805-1807 (2006) - [j19]François Fages, Akash Lal:
A constraint programming approach to cutset problems. Comput. Oper. Res. 33(10): 2852-2865 (2006) - [j18]François Fages, Narendra Jussien, Christine Solnon:
Editorial. RAIRO Oper. Res. 40(4): 325-326 (2006) - [j17]François Fages:
From Syntax to Semantics in Systems Biology Towards Automated Reasoning Tools. Trans. Comp. Sys. Biology 4: 68-70 (2006) - [j16]Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman:
Machine Learning Biochemical Networks from Temporal Logic Properties. Trans. Comp. Sys. Biology 6: 68-94 (2006) - [c39]François Fages, Sylvain Soliman:
Type Inference in Systems Biology. CMSB 2006: 48-62 - [c38]Rémy Haemmerlé, François Fages:
Modules for Prolog Revisited. ICLP 2006: 41-55 - [e6]Brahim Hnich, Mats Carlsson, François Fages, Francesca Rossi:
Recent Advances in Constraints, Joint ERCIM/CoLogNET International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2005, Uppsala, Sweden, June 20-22, 2005, Revised Selected and Invited Papers. Lecture Notes in Computer Science 3978, Springer 2006, ISBN 3-540-34215-X [contents] - [e5]François Bry, François Fages, Massimo Marchiori, Hans Jürgen Ohlbach:
Principles and Practices of Semantic Web Reasoning, 11.-16. September 2005. Dagstuhl Seminar Proceedings 05371, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2006 [contents] - [i5]Grégory Batt, Jeremy T. Bradley, Roland Ewald, François Fages, Holger Hermanns, Jane Hillston, Peter Kemper, Alke Martens, Pieter J. Mosterman, Flemming Nielson, Oleg Sokolsky, Adelinde M. Uhrmacher:
06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification. Simulation and Verification of Dynamic Systems 2006 - 2005
- [c37]Emmanuel Coquery, François Fages:
A Type System for CHR. CSCLP 2005: 100-117 - [c36]Emmanuel Coquery, François Fages:
A Type System for CHR. ICLP 2005: 402-403 - [c35]François Fages:
Temporal Logic Constraints in the Biochemical Abstract Machine BIOCHAM. LOPSTR 2005: 1-5 - [e4]Boi Faltings, Adrian Petcu, François Fages, Francesca Rossi:
Recent Advances in Constraints, Joint ERCIM/CoLogNet International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2004, Lausanne, Switzerland, June 23-25, 2004, Revised Selected and Invited Papers. Lecture Notes in Computer Science 3419, Springer 2005, ISBN 3-540-25176-6 [contents] - [e3]François Fages, Sylvain Soliman:
Principles and Practice of Semantic Web Reasoning, Third International Workshop, PPSWR 2005, Dagstuhl Castle, Germany, September 11-16, 2005, Proceedings. Lecture Notes in Computer Science 3703, Springer 2005, ISBN 3-540-28793-0 [contents] - [i4]François Bry, François Fages, Massimo Marchiori, Hans Jürgen Ohlbach:
05371 Abstracts Collection - Principles and Practices of Semantic Web Reasoning. Principles and Practices of Semantic Web Reasoning 2005 - 2004
- [j15]François Fages, Sylvain Soliman, Rémi Coolen:
CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming. Constraints An Int. J. 9(4): 241-262 (2004) - [j14]Martin A. Riedmiller, François Fages, Malik Ghallab, Wolfgang Wahlster, Jörg H. Siekmann:
Invited talks. Künstliche Intell. 18(3): 44- (2004) - [j13]Nathalie Chabrier-Rivier, Marc Chiaverini, Vincent Danos, François Fages, Vincent Schächter:
Modeling and querying biomolecular interaction networks. Theor. Comput. Sci. 325(1): 25-44 (2004) - [c34]Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman:
The Biochemical Abstract Machine BIOCHAM. CMSB 2004: 172-191 - [c33]Sylvain Soliman, François Fages:
CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems. CMSB 2004: 231-235 - [c32]François Fages:
Automated Reasoning Tools for Molecular Biology. KI 2004: 1-2 - [e2]Krzysztof R. Apt, François Fages, Francesca Rossi, Péter Szeredi, József Váncza:
Recent Advances in Constraints, Joint ERCIM/CoLogNET International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP 2003, Budapest, Hungary, June 30 - July 2, 2003, Selected Papers. Lecture Notes in Computer Science 3010, Springer 2004, ISBN 3-540-21834-3 [contents] - [i3]François Fages, Emmanuel Coquery:
Typing constraint logic programs. CoRR cs.PL/0405100 (2004) - 2003
- [j12]Nathalie Chabrier, François Fages:
"Model Checking" symbolique de réseaux biochimiques. Tech. Sci. Informatiques 22(1): 155-168 (2003) - [j11]Emmanuel Coquery, François Fages:
Contraintes de sous-typage dans les quasi-treillis. Tech. Sci. Informatiques 22(1): 253-266 (2003) - [c31]Nathalie Chabrier, François Fages:
Symbolic Model Checking of Biochemical Networks. CMSB 2003: 149-162 - [c30]Emmanuel Coquery, François Fages:
Subtyping Constraints in Quasi-lattices. FSTTCS 2003: 136-148 - [c29]François Fages:
Symbolic Model-Checking for Biochemical Systems. ICLP 2003: 102 - [c28]Nathalie Chabrier, François Fages:
"Model Checking" symbolique de réseaux bio-chimiques. JFPLC 2003: 155-168 - [c27]Emmanuel Coquery, François Fages:
Contraintes de sous-typage dans les quasi-treillis. JFPLC 2003: 253-266 - 2002
- [c26]Emmanuel Coquery, François Fages:
TCLP: Overloading, Subtyping and Parametric Polymorphism Made Practical for CLP. ICLP 2002: 480 - [c25]Emmanuel Coquery, François Fages:
Surcharge et sous-typage dans TCLP. JFPLC 2002: 273- - [c24]François Fages:
CLPGUI: a generic graphical user interface for constraint logic programming over finite domains. WLPE 2002: 47-62 - 2001
- [j10]François Fages, Paul Ruet, Sylvain Soliman:
Linear Concurrent Constraint Programming: Operational and Phase Semantics. Inf. Comput. 165(1): 14-41 (2001) - [j9]François Fages, Emmanuel Coquery:
Typing constraint logic programs. Theory Pract. Log. Program. 1(6): 751-777 (2001) - [c23]Emmanuel Coquery, François Fages:
Programmes logiques avec contraintes typés. JFPLC 2001: 223-238 - [i2]François Fages:
CLP versus LS on Log-based Reconciliation Problems. CoRR cs.PL/0109033 (2001) - 2000
- [c22]