Selected publications
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2025
Fages, François, Hemery, Mathieu, Soliman, Sylvain. On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry. ACM Commun. Comput. Algebra, 58(2):15–22, 2025. [ preprint ]
2024
Buscemi, Hugo, Fages, François. Graphical Conditions ensuring Equality between Differential and Mean Stochastic Dynamics. In CMSB 2024 - 22nd International Conference on Computational Methods in Systems Biology,, volume LNCS-14971 of Lecture Notes in Computer Science. Springer Nature Switzerland, 2024. [ preprint ]
François Fages. A Constraint-based Mathematical Modeling Library in Prolog with Answer Constraint Semantics. In 17th International Symposium on Functional and Logic Programming, FLOPS 2024, pages 135–150, volume 14659 of LNCS. Springer-Verlag, 2024. [ preprint ]
Fages, François. On Teaching Constraint-based Modeling and Algorithms for Decision Support in Prolog. In Worskhop Proc. of the 40th Int. Conf. on Logic Programming, ICLP-WS 2024., 2024. [ preprint ]
Fages, François, Hemery, Mathieu, Soliman, Sylvain. On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry. In 49th International Symposium on Symbolic and Algebraic Computation (ISSAC 2024), 2024. [ preprint ]
Hemery, Mathieu, Fages, François. On a model of online analog computation in the cell with absolute functional robustness: algebraic characterization, function compiler and error control. Theoretical Computer Science, 991:114432, 2024. [ preprint ]
Trinh, Van-Giang, Benhamou, Belaid, Soliman, Sylvain, Fages, François. Graphical conditions for the existence, unicity and number of regular models. In ICLP 2024 - 40th International Conference on Logic Programming, 2024. [ preprint ]
2023
Collery, Marine, Bonnard, Philippe, Fages, François, Kusters, Remy. Neural-based classification rule learning for sequential data. In ICLR 2023 - The Eleventh International Conference on Learning Representations, 2023. [ preprint ]
Fages, François, Molina, Franck. The Cell, a Chemical Analog Calculator. In Symbolic Approaches to Modeling and Analysis of Biological Systems, pages 235–254. John Wiley Sons, Ltd, 2023. [ preprint ]
Hemery, Mathieu, Fages, François. On Estimating Derivatives of Input Signals in Biochemistry. In CMSB 2023 - 21st International Conference on Computational Methods in Systems Biology, volume 14137 of LNCS. Springer-Verlag, 2023. [ preprint ]
Thibault Greugny, Eléa, Fages, François and Radulescu, Ovidiu, Szmolyan, Peter, Stamatas, Georgios. A Skin Microbiome Model with AMP interactions and Analysis of Quasi-Stability vs Stability in Population Dynamics. Theoretical Computer Science, 983:114294, 2023. [ preprint ]
2022
François Fages, Franck Molina. La cellule, un calculateur analogique chimique. In Approches symboliques de la modélisation et de l'analyse des systèmes biologiques, pages 255–273. ISTE group, Ed Ltd, London, 2022. [ preprint ] [ video ]
E. Greugny, J. Bensaci, F. Fages, G. Stamatas. Computational modeling predicts impaired barrier function and higher sensitivity to skin inflammation following pH elevation. Journal of Experimental Dermatology, 2022. [ preprint ]
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 Computational Biology, 18(6), 2022.
Eléa Thibault Greugny, Georgios N Stamatas and François Fages. Stability versus Meta-stability in a Skin Microbiome Model. In CMSB'22: Proceedings of the twentieth international conference on Computational Methods in Systems Biology, volume 13447 of LNCS. Springer-Verlag, 2022. [ preprint ] [ slides ]
Mathieu Hemery, François Fages. Algebraic Biochemistry: a Framework for Analog Online Computation in Cells. In CMSB'22: Proceedings of the twentieth international conference on Computational Methods in Systems Biology, volume 13447 of LNCS. Springer-Verlag, 2022. [ preprint ] [ slides ] [ video ]
Lüders, Christoph, Bellot, Eléonore and Fages, François, Radulescu, Ovidiu, Soliman, Sylvain. Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2). . Inria Saclay, 2022. [ preprint ]
2021
Collery, Marine, Bonnard, Philippe, Fages, François. Apprentissage de règles pour la détection de fraudes. In RJCIA 2021 - Dix-neuvièmes Rencontres des Jeunes Chercheurs en Intelligence Artificielle, pages 77–78, 2021. [ preprint ]
Mathieu Hemery, François Fages, Sylvain Soliman. Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs. In CMSB'21: Proceedings of the nineteenth international conference on Computational Methods in Systems Biology, volume 12881 of LNCS. Springer-Verlag, 2021. [ preprint ]
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. Bioinformatics, 37:i401-i409, 2021. [ preprint ] [ slides ] [ video ]
Julien Martinelli, Sandrine Dulong, Xiao-Mei Li , Michèle Teboul, Sylvain Soliman, Francis Lévi, François Fages, Annabelle Ballesta. Apprentissage de modèles mécanistiques du système circadien, vers la personnalisation de la chronothérapie des cancers. Médecine du Sommeil, 18(4):190, 2021. [ preprint ]
2020
Elisabeth Degrand, François Fages, Sylvain Soliman. Graphical Conditions for Rate Independence in Chemical Reaction Networks. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, volume 12314 of LNCS. Springer-Verlag, 2020. [ preprint ] [ slides ] [ video ]
François Fages. Artificial Intelligence in Biological Modeling. In A Guided Tour of Artificial Intelligence Research, Volume III: Interfaces and Applications of AI. Springer-Verlag, 2020. [ preprint ]
Mathieu Hemery, François Fages, Sylvain Soliman. On the Complexity of Quadratization for Polynomial Differential Equations. In CMSB'20: Proceedings of the eighteenth international conference on Computational Methods in Systems Biology, LNCS. Springer-Verlag, 2020. [ preprint ]
Francisco Santos Schneider, Patrick Amar, Asma Bahri, Julien Espeut, Julie Baptiste, Mellis Alali, François Fages, Franck Molina. Biomachines for Medical Diagnosis. Advanced Materials Letters, 11(4):1535–1558, 2020.
2019
Elisabeth Degrand, Mathieu Hemery, François Fages. On Chemical Reaction Network Design by a Nested Evolution Algorithm. In CMSB'19: Proceedings of the seventeenth international conference on Computational Methods in Systems Biology, volume 11773 of LNCS. Springer-Verlag, 2019. [ preprint ]
François Fages. Information Leakage in a Music Score. In The Art of Modeling Computational Systems - A Journey from Logic and Concurrency Theory to Security and Privacy - Essays Dedicated to Catuscia Palamidessi on the Occasion of Her 60th Birthday. Springer-Verlag, 2019. [ preprint ]
Huang, Wei-Chih, Jiang, Jie-Hong, Fages, François, Molina, Franck. Biochemical Threshold Function Implementation with Zero-Order Ultrasensitivity. In 15th IEEE Biomedical Circuits and Systems Conference, 2019. [ preprint ]
Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages. On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics. In CMSB'19: Proceedings of the seventeenth international conference on Computational Methods in Systems Biology, volume 11773 of LNCS. Springer-Verlag, 2019. [ preprint ]
Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages. A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data. In ICML Workshop on Computational Biology, 2019. [ preprint ]
2018
Boulier, François, Fages, François and Radulescu, Ovidiu, Samal, Satya S, Schuppert, Andreas, Seiler, Werner M., Sturm, Thomas and Walcher, Sebastian, Weber, Andreas. The SYMBIONT Project: Symbolic Methods for Biological Networks. ACM Communications in Computer Algebra, 52(3), 2018.
Adrien Baudier, François Fages, Sylvain Soliman. Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. Journal of Theoretical Biology, 459:79–89, 2018. [ preprint ]
Alexis Courbet, Patrick Amar, François Fages, Eric Renard, Franck Molina. Computer-aided biochemical programming of synthetic microreactors as diagnostic devices. Molecular Systems Biology, 14(4), 2018. [ preprint ]
François Fages, Le Guludec, Guillaume. Biochemical Programs and Analog-Digital Mixed Algorithms in the Cell. In Life Sciences, Information Sciences, pages 201–216. Wiley, 2018.
François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman. Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018. [ preprint ]
Fages, François, Soliman, Sylvain. On Robustness Computation and Optimization in BIOCHAM-4. In CMSB'18: Proceedings of the sixteenth international conference on Computational Methods in Systems Biology, LNCS. Springer-Verlag, 2018. [ preprint ]
2017
Carcano, Arthur, Fages, François, Soliman, Sylvain. Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. In CMSB'17: Proceedings of the fifteenth international conference on Computational Methods in Systems Biology, pages 74–90, volume 10545 of , 2017. [ preprint ]
François Fages, Le Guludec, Guillaume. Programmation biochimique et algorithmes mixtes analogiques-digitaux dans la cellule. In Sciences du vivant, sciences de l'information. ISTE Ed. Ltd, London, 2017. [ preprint ]
Fages, François, Le Guludec, Guillaume and Bournez, Olivier, Pouly, Amaury. Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs. In CMSB'17: Proceedings of the fiveteen international conference on Computational Methods in Systems Biology, pages 108–127, volume 10545 of LNCS. Springer-Verlag, 2017. [ preprint ]
Lai, Chun-Ning, Jiang, Jie-Hong, Fages, François. Recombinase-Based Genetic Circuit Optimization. In 13th IEEE Biomedical Circuits and Systems Conference, 2017. [ preprint ] [ preprint ]
2016
Abderrahmane Aggoun, Nicolas Beldiceanu, Gilles Chabert, François Fages. Packing with Complex Shapes. ERCIM News, 2016(105), 2016. [ preprint ]
Abder Aggoun, Ahmed Rhiat, François Fages. Panorama of real-life applications in logistics embedding bin packing optimization algorithms, robotics and cloud computing technologies. In Proc. 3rd IEEE International Conference on Logistics Operations Management, GOL'16, 2016. [ preprint ]
Fournier, David, Martinez, Thierry, Fages, François, Mulard, Denis. Metro Energy Optimization through Rescheduling: Mathematical Models and Heuristic Algorithm Compared to MILP and CMA-ES. . Inria Saclay Ile de France, 2016. [ preprint ]
François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman. Influence Systems vs Reaction Systems. In CMSB'16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology, pages 98–115, volume 9859 of LNCS. Springer-Verlag, 2016. [ preprint ]
Thierry Martinez, François Fages, Abder Aggoun. A Stochastic Continuous Optimization Backend for MiniZinc with Applications to Geometrical Placement Problems. In Proceedings of the 13th International Conference on Integration of Artificial Intelligence and Operations Research Techniques in Constraint Programming, CPAIOR'16, 2016. [ preprint ]
Thierry Martinez, François Fages, Abder Aggoun. Un solveur d'optmization stochastique pour MiniZinc avec des applications à des problèmes de placements géométriques. In Douzièmes Journées Francophones de Programmation par Contraintes JFPC'16, 2016. [ preprint ]
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, 21(2):251–276, 2016. [ preprint ]
Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry. Logical model specification aided by model- checking techniques: application to the mammalian cell cycle regulation. Bioinformatics, 32(17):i772-i780, 2016. [ preprint ]
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-alpha Up-Regulation during Mitosis. Biosystems, 149:59–69, 2016. [ preprint ]
2015
Tai-Yin Chiu, Hui-Ju K. Chiang, Ruei-Yang Huang , Jie-Hong R. Jiang, François Fages. Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications. PLoS ONE, 10(9):e0137442, 2015.
Hui-Ju Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman. Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Transactions on Modeling and Computer Simulation (TOMACS), 25(2):14:1–14:22, 2015. [ preprint ]
Hui-Ju Chiang, Jie-Hong Jiang, François Fages. Reconfigurable Neuromorphic Computation in Biochemical Systems. In Proc. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBC, 2015. [ preprint ]
François Fages. Machinerie cellulaire et programmation biochimique: vers une informatique de la cellule (exposé invité). In Actes 11ièmes Journèes Francophones de Programmation par Contraintes JFPC'15, 2015.
François Fages, Steven Gay, Sylvain Soliman. Inferring Reaction Systems from Ordinary Differential Equations. Theoretical Computer Science, 599:64–78, 2015. [ preprint ]
Thierry Martinez, François Fages, Sylvain Soliman. Search by Constraint Propagation. In Proceedings of the 17th International Conference on Principles and Practice of Declarative Programming, PPDP'15, pages 173–183. ACM, 2015. [ preprint ]
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. In CMSB'15: Proceedings of the thirteenth international conference on Computational Methods in Systems Biology, pages 208–221, volume 9308 of LNCS. Springer-Verlag, 2015. [ preprint ]
2014
Katherine Chiang, Jie-Hong Jiang, François Fages. Building Reconfigurable Circuitry in a Biochemical World. In BioCAS'14: IEEE Biomedical Circuits and Systems Conference. IEEE, 2014. [ preprint ]
François Fages. Cells as Machines: towards Deciphering Biochemical Programs in the Cell (Keynote Talk). In 21st European Conference on Artificial Intelligence ECAI'14, 2014. [ slides ]
François Fages. Cells as Machines: towards Deciphering Biochemical Programs in the Cell (Invited Talk). In Proc. 10th International Conference on Distributed Computing and Internet Technology ICDCIT'14, pages 50–67, volume 8337 of Lecture Notes in Computer Science. Springer-Verlag, 2014. [ preprint ] [ video ]
David Fournier, François Fages, Denis Mulard. A Greedy Heuristic for Optimizing Metro Regenerative Energy Usage. In Proceedings of the second international conference on railway technology: research, development and maintenance. Civil-Comp Press, 2014. [ preprint ]
François Fages, Pauline Traynard. Temporal Logic Modeling of Dynamical Behaviors: First-Order Patterns and Solvers. In Logical Modeling of Biological Systems, pages 291–323. John Wiley Sons, Inc., 2014. [ preprint ]
Steven Gay, François Fages, Thierry Martinez, Sylvain Soliman, Christine Solnon. On the subgraph Epimorphism Problem. Discrete Applied Mathematics, 162:214–228, 2014. [ preprint ]
Sylvain Soliman, François Fages, Ovidiu Radulescu. A constraint solving approach to model reduction by tropical equilibration. Algorithms for Molecular Biology, 9(24), 2014.
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. In CMSB'14: Proceedings of the twelth international conference on Computational Methods in Systems Biology, pages 114–128, LNCS. Springer-Verlag, 2014. [ preprint ] [ slides ]
J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages, S. Bottani, P. Hersen, G. Batt. In silico control of biomolecular processes. In Computational Methods in Synthetic Biology. Humana Press, Springer, 2014. [ preprint ]
2013
Katherine Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman. On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models. In CMSB'13: Proceedings of the eleventh international conference on Computational Methods in Systems Biology, pages 192–205, volume 8130 of LNCS. Springer-Verlag, 2013. [ preprint ]
Steven Gay, François Fages, Francesco Santini, Sylvain Soliman. Solving Subgraph Epimorphism Problems using CLP and SAT. In Proceedings of the ninth Workshop on Constraint Based Methods for Bioinformatics WCB'13, colocated with CP 2013, pages 67–74, 2013. [ preprint ]
Ruei-Yang Huang, De-An Huang, Hui-Ju Katherine Chiang, Jie-Hong Jiang, François Fages. Species Minimization in Computation with Biochemical Reactions. In IWBDA'13: Proceedings of the fifth International Workshop on Bio-Design Automation, 2013. [ preprint ]
Thierry Martinez, Lumadaiara Vitorino, François Fages, Abderrahmane Aggoun. On Solving Mixed Shapes Packing Problems by Continuous Optimization with the CMA Evolution Strategy. In Proceedings of the first Computational Intelligence BRICS Congress BRICS-CCI'13, pages 515–521. IEEE Press, 2013. [ preprint ]
Sylvain Soliman, François Fages, Ovidiu Radulescu. A Constraint Solving Approach to Tropical Equilibration and Model Reduction. In Proceedings of the ninth Workshop on Constraint Based Methods for Bioinformatics WCB'13, colocated with CP 2013, pages 27–36, 2013. [ preprint ]
2012
François Fages, Steven Gay, Sylvain Soliman. Inferring Reaction Models from ODEs. In CMSB'12: Proceedings of the tenth international conference on Computational Methods in Systems Biology, pages 370–373, volume 7605 of LNCS. Springer-Verlag, 2012. [ preprint ]
David Fournier, Denis Mulard, François Fages. Energy optimization of metro timetables: a hybrid approach. In Doctoral Programme Proceedings of the 18th International Conference on Principles and Practive of Constraint Programming CP'12, pages 7–12, 2012.
David Fournier, Denis Mulard, François Fages. Optimisation énergétique de tables horaires de métros: une approche hybride. In Actes de Journées Francophones de Programmation par Contraintes JFPC'12, pages 127–130, 2012.
Domitille Heitzler, Guillaume Durand, Nathalie Gallay, Aurélien Rizk, Seungkirl Ahn, Jihee Kim, Jonathan D. Violin, Laurence Dupuy and Christophe Gauthier et al. Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling. Molecular Systems Biology, 8(590), 2012.
Anthony Lins, Fernando Buarque, François Fages, Carmelo Filho. A Comparative Analysis of FSS with CMA-ES and S-PSO in Ill-Conditioned Problems. In Intelligent Data Engineering and Automated Learning - 13th International Conference IDEAL, pages 416–422, volume 7435 of Lecture Notes in Computer Science. Springer, 2012. [ preprint ]
Faten Nabli, François Fages, Thierry Martinez, Sylvain Soliman. A Boolean Model for Enumerating Minimal Siphons and Traps in Petri-nets. In Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, pages 798–814, volume 7514 of LNCS. Springer-Verlag, 2012. [ preprint ] [ slides ] [ poster ]
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. In Actes de Journées Francophones de Programmation par Contraintes JFPC'12, 2012. [ preprint ]
Jannis Uhlendorf, Agnés Miermont, Thierry Delaveau, Gilles Charvin, François Fages and Samuel Bottani, Gregory Batt, Pascal Hersen. Long-term model predictive control of gene expression at the population and single-cell levels. Proceedings of the National Academy of Sciences USA, 109(35):14271–14276, 2012.
2011
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. Theoretical Computer Science, 412(21):2108–2127, 2011. [ preprint ]
Steven Gay, Thierry Martinez, Sylvain Soliman, François Fages. A Constraint Program For Subgraph Epimorphisms with Application to Identifying Model Reductions in Systems Biology. In Proceedings of the seventh Workshop on Constraint Based Methods for Bioinformatics WCB'11, colocated with CP 2011, pages 59–66, 2011. [ preprint ]
Julien Martin, Thierry Martinez, François Fages. Static Expansion vs Procedural Code Generation in Rule-based Modeling Languages. In Recent Advances in Constraints, pages 38–58, LNAI. Springer-Verlag, 2011. [ preprint ]
Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. Continuous Valuations of Temporal Logic Specifications with applications to Parameter Optimization and Robustness Measures. Theoretical Computer Science, 412(26):2827–2839, 2011. [ preprint ]
Jannis Uhlendorf, Samuel Bottani, François Fages, Pascal Hersen, Grégory Batt. Towards real-time control of gene experession: controlling the HOG signaling cascade. In Proceedings of the 16th Pacific Symposium on Biocomputing (PSB 2011), pages 338–349, 2011. [ preprint ]
2010
Abder Aggoun, Nicolas Beldiceanu, Mats Carlsson , François Fages. Integrating Rule-Based Modelling and Constraint Programming for Solving Industrial Packing Problems. ERCIM News, 81, 2010. [ preprint ]
François Fages. A Logical Paradigm for Systems Biology (Invited Talk). In Technical Communications of the 26th International Conference on Logic Programming, pages 2–3, volume 7 of Leibniz International Proceedings in Informatics (LIPIcs). Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2010. [ preprint ]
François Fages. A graphical method for reducing and relating models in systems biology (invited talk). In ICSB'10 11th International Conference on Systems Biology. University of Edinburgh, UK, 2010. [ preprint ]
François Fages, Grégory Batt, Elisabetta De Maria, Dragana Jovanovska, Aurélien Rizk, Sylvain Soliman. Computational Systems Biology in BIOCHAM. ERCIM News, 82, 2010. [ preprint ]
François Fages, Sylvain Soliman. New Computational Methods for Systems Biology (tutorial). In ICSB'10 11th International Conference on Systems Biology: abstract of tutorials. University of Edinburgh, UK, 2010.
Steven Gay, Sylvain Soliman, François Fages. A Graphical Method for Reducing and Relating Models in Systems Biology. Bioinformatics, 26(18):i575–i581, 2010.
Dragana Jovanovska, François Fages, Sylvain Soliman. SBGN support in BIOCHAM. Nature Precedings, 2010. [ preprint ]
2009
Elisabetta De Maria, François Fages, Sylvain Soliman. On Coupling Models using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle. In CMSB'09: Proceedings of the seventh international conference on Computational Methods in Systems Biology, pages 142–157, volume 5688 of LNCS. Springer-Verlag, 2009. [ preprint ]
François Fages, Julien Martin. Modelling search strategies in Rules2CP. In Proceedings of CPAIOR'09, pages 321–322, volume 5547 of LNCS. Springer-Verlag, 2009. [ preprint ]
François Fages, Julien Martin. From Rules to Constraint Programs with the Rules2CP Modelling language. In Recent Advances in Constraints, Revised Selected Papers of the 13th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP'08, pages 66–83, volume 5655 of LNAI. Springer-Verlag, 2009. [ preprint ]
François Fages, Thierry Martinez, Cleyton Mario de Oliveira Rodrigues. CHR modulaire avec ask et tell. In Actes de Journées Francophones de Programmation par Contraintes JFPC'09, 2009. [ preprint ]
François Fages, Aurélien Rizk. From Model-Checking to Temporal Logic Constraint Solving. In Proceedings of CP'2009, 15th International Conference on Principles and Practice of Constraint Programming, pages 319–334, LNCS. Springer-Verlag, 2009. [ preprint ]
Domitille Heitzler, Pascale Crépieux, Anne Poupon, Frédérique Clément, François Fages, Eric Reiter. Towards a systems biology approach to G protein-coupled receptor signalling: challenges and expectations. C.R. Biologies, 332:947–957, 2009.
Sriram Krishnamachari, Sylvain Soliman, François Fages. Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans. Journal of Theoretical Biology, 258(1):71–88, 2009. [ preprint ]
Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics, 12(25):il69–il78, 2009.
2008
François Fages, Julien Martin. Des règles aux contraintes avec le langage de modélisation Rules2CP. In Actes de Journées Francophones de Programmation par Contraintes JFPC'08, 2008.
François Fages, Aurélien Rizk. Analyse de Séries Temporelles par Résolution de Contraintes de Logique Temporelle. In Actes de Journées Francophones de Programmation par Contraintes JFPC'08, 2008.
François Fages, Aurélien Rizk. On Temporal Logic Constraint Solving for the Analysis of Numerical Data Time series. Theoretical Computer Science, 408(1):55–65, 2008. [ preprint ]
François Fages, Sylvain Soliman. From reaction models to influence graphs and back: a theorem. In Proceedings of Formal Methods in Systems Biology FMSB'08, LNCS. Springer-Verlag, 2008. [ preprint ]
François Fages, Sylvain Soliman. Model Revision from Temporal Logic Properties in Systems Biology. In Probabilistic Inductive Logic Programming, pages 287–304, volume 4911 of LNCS. Springer-Verlag, 2008. [ preprint ]
François Fages, Sylvain Soliman. Formal Cell Biology in BIOCHAM. In 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, pages 54–80, volume 5016 of LNCS. Springer-Verlag, 2008. [ preprint ]
François Fages, Sylvain Soliman. Abstract Interpretation and Types for Systems Biology. Theoretical Computer Science, 403(1):52–70, 2008. [ preprint ]
Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman. On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology. In CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology, pages 251–268, volume 5307 of LNCS. Springer-Verlag, 2008. [ preprint ]
2007
Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. Langages formels dans la machine abstraite biochimique BIOCHAM. Techniques et Sciences Informatiques, 26(1–2):47–72, 2007. [ preprint ]
Jean Clairambault, François Fages, Sylvain Soliman. Patient-tailored cancer therapeutics - The TEMPO Project. ERCIM News, 69:24–25, 2007. [ preprint ]
Alessandro Dal Palu, Agostino Dovier, François Fages, Sebastian Will. Constraint-based Methods in Bioinformatics. In Future and trends of Constraint Programming: the next ten years. Hermès, 2007. [ preprint ]
François Fages. Des contraintes au programme. Revue littéraire de l'Institut Universitaire de France, Actes de Savoirs, PUF, 2007. [ preprint ]
François Fages, Aurélien Rizk. On the Analysis of Numerical Data Time Series in Temporal Logic. In CMSB'07: Proceedings of the fifth international conference on Computational Methods in Systems Biology, pages 48–63, volume 4695 of LNCS. Springer-Verlag, 2007. [ preprint ]
Rémy Haemmerlé, François Fages. Abstract Critical Pairs and Confluence of Arbitrary Binary Relations. In Proceedings of th 18th International Conference on Rewriting Techniques and Applications, RTA'07, LNCS. Springer-Verlag, 2007. [ preprint ]
Rémy Haemmerlé, François Fages, Sylvain Soliman. Closures and Modules within Linear Logic Concurrent Constraint Programming. In Proceedings of FSTTCS 2007, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, pages 544–556, volume 4855 of LNCS. Springer-Verlag, 2007. [ preprint ]
2006
Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. Machine learning biochemical networks from temporal logic properties. In Transactions on Computational Systems Biology VI, pages 68–94, volume 4220 of LNBI. Springer-Verlag, 2006. [ preprint ]
Emmanuel Coquery, François Fages. A type system for CHR. In Recent Advances in Constraints, revised selected papers from CSCLP'05, pages 100–117, LNAI. Springer-Verlag, 2006. [ preprint ]
Laurence Calzone, François Fages, Sylvain Soliman. BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge. Bioinformatics, 22(14):1805–1807, 2006. [ preprint ]
François Fages. From Syntax to Semantics in Systems Biology - Towards Automated Reasoning Tools. Transactions on Computational Systems Biology IV, 3939:68–70, 2006. [ preprint ]
François Fages. Programmation logique et contraintes. In Encyclopédie d'informatique, pages 151–162. Vuibert, 2006. [ preprint ]
François Fages, Akash Lal. A Constraint Programming Approach to Cutset Problems. Journal Computers and Operations Research, 33:10:2852–2865, 2006. [ preprint ]
François Fages, Sylvain Soliman. Type Inference in Systems Biology. In CMSB'06: Proceedings of the fourth international conference on Computational Methods in Systems Biology, volume 4210 of LNCS. Springer-Verlag, 2006. [ preprint ]
Rémy Haemmerlé, François Fages. Modules for Prolog Revisited. In Proceedings of International Conference on Logic Programming ICLP 2006, pages 41–55, LNCS. Springer-Verlag, 2006. [ preprint ]
2005
Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Lucie Gentils, Sylvain Soliman. Machine learning bio-molecular interactions from temporal logic properties. In CMSB'05: Proceedings of the third international conference on Computational Methods in Systems Biology, 2005. [ preprint ]
Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. A Machine Learning approach to Biochemical Reaction Rules Discovery. In Proceedings of Foundations of Systems Biology and Engineering FOSBE'05, pages 375–379, 2005. [ preprint ]
Laurence Calzone, Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle. In Actes de JOBIM'05, pages 183–192, 2005.
Emmanuel Coquery, François Fages. A prescriptive type system for CHR (short paper). In Proceedings of International Conference on Logic Programming ICLP 2005, pages 402–403, volume 3668 of LNCS. Springer-Verlag, 2005.
Emmanuel Coquery, François Fages. Un système de types pour CHR. In Actes de Journées Francophones de Programmation par Contraintes JFPC'05, 2005. [ preprint ]
François Fages. Temporal logic constraints in the biochemical abstract machine BIOCHAM (invited talk). In Proceedings of Logic Based Program Synthesis and Transformation, LOPSTR'05, LNCS, 2005. [ preprint ]
Rémy Haemmerlé, François Fages. Un système de modules fermé pour la PLC. In Actes de Journées Francophones de Programmation par Contraintes JFPC'05, 2005.
2004
Nathalie Chabrier-Rivier, Marc Chiaverini, Vincent Danos, François Fages, Vincent Schächter. Modeling and querying biochemical interaction networks. Theoretical Computer Science, 325(1):25–44, 2004. [ preprint ]
Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman. The Biochemical Abstract Machine BIOCHAM. In CMSB'04: Proceedings of the second international workshop on Computational Methods in Systems Biology, pages 172–191, volume 3082 of LNCS. Springer-Verlag, 2004. [ preprint ]
François Fages. Automated reasoning tools for molecular biology (invited talk). In Proceedings of the 27th Annual German Conference on AI, KI'04, pages 1–2, volume 3238 of LNAI. Springer-Verlag, 2004.
François Fages, Sylvain Soliman, Rémi Coolen. CLPGUI: a Generic Graphical User Interface for Constraint Logic Programming. Journal of Constraints, Special Issue on User-Interaction in Constraint Satisfaction, 9(4):241–262, 2004. [ preprint ]
François Fages, Sylvain Soliman, Nathalie Chabrier-Rivier. Modelling and Querying Interaction Networks in the Biochemical Abstract Machine BIOCHAM. Journal of Biological Physics and Chemistry, 4(2):64–73, 2004. [ preprint ]
Sylvain Soliman, François Fages. CMBSlib: a Library for Comparing Formalisms and Models of Biological Systems. In CMSB'04: Proceedings of the second international workshop on Computational Methods in Systems Biology, pages 231–235, volume 3082 of LNCS. Springer-Verlag, 2004. [ preprint ]
2003
Nathalie Chabrier, François Fages. Symbolic model checking of biochemical networks. In CMSB'03: Proceedings of the first workshop on Computational Methods in Systems Biology, pages 149–162, volume 2602 of LNCS. Springer-Verlag, 2003. [ preprint ]
Emmanuel Coquery, François Fages. Subtyping constraints in quasi-lattices. In Proceedings of the 23rd conference on foundations of software technology and theoretical computer science, FSTTCS'2003, pages 136–148, volume 2914 of LNCS. Springer-Verlag, 2003. [ preprint ]
Emmanuel Coquery, François Fages. Contraintes de sous-typage dans les quasi-treillis. In Actes des Journées Francophones de la Programmation en Logique avec Contraintes JFPLC'2003, pages 253–266, special issue of RSTI. Hermès, 2003. [ preprint ]
Nathalie Chabrier, François Fages. "Model-checking" symbolique de réseaux biochimiques. In Actes des Journées Francophones de la Programmation en Logique avec Contraintes JFPLC'2003, pages 155–168, special issue of RSTI. Hermès, 2003. [ preprint ]
François Fages. Symbolic model checking for biochemical systems (invited talk). In Proceedings of International Conference on Logic Programming ICLP'03, pages 102, volume 2916 of LNCS. Springer-Verlag, 2003. [ preprint ]
François Fages, Akash Lal. A Global Constraint for Cutset Problems. In Proceedings of Fifth International Workshop on Integration of AI and OR techniques in constraint programming for combinatorial optimization problems CPAIOR'03, 2003. [ preprint ]
2002
Emmanuel Coquery, François Fages. TCLP: overloading, subtyping and parametric polymorphism made practical for constraint logic programming. In Proceedings of International Conference on Logic Programming ICLP 2002, pages 480, volume 2401 of LNCS. Springer-Verlag, 2002. [ preprint ]
Emmanuel Coquery, François Fages. Surcharge et sous-typage dans TCLP. In Actes des Journées Francophones de Programmation en Logique et programmation par Contraintes, JFPLC'2002. Hermès, 2002.
2001
Emmanuel Coquery, François Fages. Programmes logiques avec contraintes typés. In Actes des Journées Francophones de la Programmation en Logique avec Contraintes JFPLC'2001, pages 223–237, 2001. [ preprint ]
François Fages, Emmanuel Coquery. Typing Constraint Logic Programs. Journal of Theory and Practice of Logic Programming, 1(6):751–777, 2001. [ preprint ]
François Fages, Paul Ruet, Sylvain Soliman. Linear concurrent constraint programming: operational and phase semantics. Information and Computation, 165(1):14–41, 2001. [ preprint ]
2000
François Fages. Concurrent constraint programming and linear logic (invited talk). In Proceedings of ACM Sigplan conference on Principles and Practice of Declarative Programming PPDP'2000. ACM Publishing Company, 2000. [ preprint ]
Jan-Georg Smaus, François Fages, Pierre Deransart. Using Modes to Ensure Subject Reduction for Typed Logic Programs with Subtyping. In Proceedings of FSTTCS '2000, LNCS. Springer-Verlag, 2000. [ preprint ]
1999
François Fages. Dossier spécial sur les méthodes formelles en génie logiciel: survol des concepts formels. Syseca Magazine (19), 1999.
1998
François Fages, Julian Fowler, Thierry Sola. Experiments in Reactive Constraint Logic Programming. Journal of Logic Programming, 37:1-3:185–212, 1998. [ preprint ]
François Fages, Roberta Gori. Analysis of normal logic programs. In Proc. Static Analysis SAS'98, pages 82–98, LNCS 1503. Springer-Verlag, 1998. [ preprint ]
François Fages, Massimo Paltrinieri. A generic type system for CLP(X). In Proc. JICSLP'98, Poster paper. MIT Press, 1998. [ preprint ]
François Fages, Paul Ruet, Sylvain Soliman. Phase Semantics and Verification of Concurrent Constraint Programs. In Proceedings of the 13thAnnual IEEE Symposium on Logic In Computer Science, pages 141–152. IEEE Computer Society, 1998. [ preprint ]
1997
François Fages. Constructive negation by pruning. Journal of Logic Programming, 32(2):85–118, 1997. [ preprint ]
Paul Ruet, François Fages. Concurrent constraint programming and mixed non-commutative linear logic. In Proc. of Computer Science Logic CSL'97, pages 406–423, volume 1414 of LNCS. Springer-Verlag, 1997. [ preprint ]
Paul Ruet, François Fages. Combining explicit negation and negation by failure via Belnap's logic. Theoretical Computer Science, 171:61–75, 1997. [ preprint ]
1996
François Fages. Programmation Logique par Contraintes. In , Collection Cours de l'Ecole Polytechnique. Ed. Ellipses, Paris (192p), 1996. [ preprint ]
François Fages, Roberta Gori. A Hierarchy of Operational and Denotational Semantics for General Constraint Logic Programming Languages. In Proc. International Conference on Algebraic and Logic Programming, ALP'96, LNCS. Springer-Verlag, 1996. [ preprint ]
1995
Philippe Codognet, Radhia Cousot, François Fages, Roberto Giacobazzi, Jean-Louis Imbert and Jean-François Pique, Antoine Rauzy. Langages Logiques concurrents avec contraintes. . Ecole Normale Supérieure, Rapport final de l'action inter-PRC Informatique MESR 93S0051, "Opérations de recherches coordonnées en calcul parallèle et distribuée", 1995.
François Fages. Constructive negation by pruning and optimization higher-order predicates for CLP and CC languages. In Constraint Programming: Basics and Trends, pages 68–89, LNCS 910. Springer-Verlag, 1995. [ preprint ]
François Fages, Julian Fowler, Thierry Sola. A Reactive Constraint Logic Programming Scheme. In Proc. International Conference on Logic Programming ICLP'95. MIT Press, 1995. [ preprint ]
Julian Fowler, Thierry Sola, François Fages. Un modèle d'exécution réactif et interactif pour la programmation logique avec contraintes. In Actes des Journées francophones de programmation logique, JFPL'95. Hermès, 1995. [ preprint ]
Jean Jourdan, François Fages, Didier Rozzonelli, Alain Demeure. Data alignment and task scheduling on parallel machine using concurrent model-based programming. In Proc. of Concurrent Constraint Programming, CCP'95, 1995. [ preprint ]
1994
François Fages. Consistency of Clark's Completion and Existence of Stable Models. Methods of Logic in Computer Science, 1:51–60, 1994. [ preprint ]
François Fages, Julian Fowler, Thierry Sola. Handling preferences in constraint logic programming with relational optimization. In Proc. Programming Language Implementation and Logic Programming, PLILP'94, pages 261–276, LNCS 844. Springer-Verlag, 1994. [ preprint ]
Paul Ruet, François Fages. Combining explicit negation and negation by failure via Belnap's logic. In Proc. Workshop on Uncertainty in Logic Programming, International Symposium on Logic Programming, ILPS'94, 1994. [ preprint ]
1993
Luc Albert, Rafael Casas, François Fages. Average case analysis of unification algorithms. Theoretical Computer Science, 113:3–34, 1993. [ preprint ]
Philippe Codognet, François Fages, Thierry Sola. A meta-level compiler for CLP(FD) and its combination with intelligent backtracking. In Constraint Logic Programming : Selected Research, pages 437–456. MIT Press, 1993. [ preprint ]
François Fages. On the semantics of optimization predicates in CLP languages. In Proc. 13th Conference Foundations of Software Technology and Theoretical Computer Science FSTTCS'93, pages 193–204, LNCS 761. Springer-Verlag, 1993. [ preprint ]
1992
P. Albert, François Fages. XRete: un générateur de systèmes experts temps-réel. Revue de Génie Logiciel, 1992. [ preprint ]
Philippe Codognet, François Fages, Jean Jourdan, Rémi Lissajoux, Thierry Sola. On the design of Meta(F) and its applications in Air Traffic Control. In Proc. of the Constraints Workshop of International Conference and Symposium on Logic Programming, ICSLP'92, 1992. [ preprint ]
François Fages. Aspects sémantiques et algorithmiques de la déduction automatique. Habilitation à diriger des Recherches, Univ. Paris VII. Jury composé de Gérard Huet (Président), Krzyzstof Apt, Rapporteur, Jean Gallier, Rapporteur, Jean-Pierre Jouannaud, Rapporteur, Alain Colmerauer, Guy Cousineau, Claude Puech, 1992.
François Fages, Rémi Lissajoux. Sémantique opérationnelle et compilation des systèmes de production. Revue d'Intelligence Artificielle, 6(4):431–456, 1992. [ preprint ]
1991
Luc Albert, Rafael Casas, François Fages, Paul Zimmermann. Average case analysis of unification algorithm. In Proc. Symposium on Theoretical Aspects of Computer Science, STACS'91, LNCS. Springer-Verlag, 1991. [ preprint ]
François Fages. A new fixpoint semantics for general logic programs compared with the well-founded and the stable model semantics. New Generation Computing, 9:425–443, 1991. [ preprint ]
1990
François Fages. A new fixpoint semantics for general logic programs compared with the well-founded and the stable model semantics. In Proc. Seventh International Conference on Logic Programming, ICLP'90, 1990. [ preprint ]
François Fages, Rémi Lissajoux. Systèmes experts temps réel: une introduction au langage XRete. Revue technique Thomson-CSF, 23, 1990. [ preprint ]
1989
François Fages. Optimizations of Rete Algorithm, and Implementation of Logical Dependencies. In Proc. AAAI Spring Symposium, 1989. [ preprint ]
1988
Luc Albert, François Fages. Average Case Complexity Analysis of the Rete Multi-Pattern Match Algorithm. In Proc. International Conference on Automata, Languages and Programming ICALP'88. Springer-Verlag, 1988. [ preprint ]
François Fages. Rule-Based Extensions of Programming Languages: a Proposal to Integrate Expert Systems into Applications at the Target Language Level. In Proc. 8èmes journèes sur les Systèmes Experts et leurs Applications, 1988. [ preprint ]
François Fages. On the Proceduralization of Rules in Expert Systems. In Programming of Future Generation Computers. North-Holland, 1988. [ preprint ]
Thierry Shang, François Fages. Real-Time Expert System for On-Board Radar Identification. In Proc. 55th Symposium AVP-AGARD on Software Engineering and its Applications, 1988. [ preprint ]
1987
François Fages. Associative-Commutative Unification. Journal of Symbolic Computation, 3:257–275, 1987. [ preprint ]
1986
François Fages, Gérard Huet. Complete Sets of Unifiers and Matchers in Equational Theories. Theoretical Computer Science, 43:189–200, 1986. [ preprint ]
1984
François Fages. Associative-Commutative Unification. In Proc. of seventh Conference on Automated Deduction CADE'84, LNCS. Springer-Verlag, 1984. [ preprint ]
1983
François Fages. Formes canoniques dans les algèbres booléennes, et application à la démonstration automatique en logique du premier ordre. Thèse de troisième cycle, Univ. Paris VI. Jury composé de Bernard Robinet, Président, Gérard Huet, Jean-Pierre Jouannaud, Guy Cousineau, Alain Colmerauer, Maurice Nivat, Jean-François Perrot, 1983.
François Fages, Gérard Huet. Unification and Matching in Equational Theories. In Proc. of CAAP'83, 8th Colloquium on Trees in Algebra and Programming, pages 205–220, LNCS. Springer-Verlag, 1983. [ preprint ]