Some recent papers of François Fages


Computational Systems Biology


A Graphical Method for Reducing and Relating Models in Systems Biology by Steven Gay, Sylvain Soliman and François Fages. European Conference on Computational Biology, ECCB'10, Ghent, Belgium. Bioinformatics 2010 26:i575-i581. (pdf, slides)

A Logical Paradigm for Systems Biology (invited talk) by François Fages. International Conference on Logic Programming, ICLP Edinburgh, FLOC'10. July 2010. (text in pdf, slides in ppt)

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 by Elisabetta de Maria, François Fages and Sylvain Soliman. Theoretical Computer Science 412(21):2108-2127,  March 2011 (pdf)
Extended version of:
On Coupling Models using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle by Elisabetta de Maria, François Fages and Sylvain Soliman. Proc of the 6th International Conference on Computational Methods in Systems Biology CMSB'09. Springer-Verlag, LNBI 5688:142-157. 2009.(pdf).

A General Computational Method for Robustness Analysis with Applications to Synthetic Gene Networks by Aurélien Rizk, Grégory Batt, François Fages and Sylvain Soliman. 17th Annual International Conference on Itelligent Systems for Molecular Biology. Bioinformatics 25:169-178. 2009. (pdf)

Dynamics of the interlocked positive feedback loops explaining the robust  epigenetic switching in Candida albicans by K. Sriram, Sylvain Soliman, Francois Fages. Journal of Theoretical Biology 258(1):71, May 2009.

Continuous Valuations of Temporal Logic Speci cations with applicationsto Parameter Optimization and Robustness Measures by Aurélien Rizk, Grégory Batt, François Fages, Aurélien Rizk and Sylvain Soliman. Theoretical Computer Science, 2011 (pdf)
Extended version of:
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology by Aurélien Rizk, Grégory Batt, François Fages and Sylvain Soliman. Computational Methods in Systems Biology CMSB'08. Springer-Verlag, LNBI 5307:251-268. May. 2008.(pdf)

Formal Cell Biology in BIOCHAM (tutorial) by François Fages and Sylvain Soliman. 8th International School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology. In memory of Nadia Busi. Bertinoro, Italy. Springer-Verlag, LNCS 5016. Mar. 2008.(pdf)

From reaction models to influence graphs and back: a theorem by François Fages and Sylvain Soliman. Formal Methods in Systems Biology. Springer-Verlag LNBI 5054:90-102. Feb. 2008.(pdf).

On Temporal Logic Constraint Solving for the Analysis of Numerical Data Time series by François Fages and Aurélien Rizk.Theoretical Computer Science 408, pp. 55-65, 2009. (pdf)

Model Revision from Temporal Logic Properties in Computational Systems Biology by François Fages and Sylvain Soliman. Book's chapter in Probabilistic Inductive Logic, Eds. L. de Raedt, P. Frasconi, K. Kersting, S. Muggleton. Springer-Verlag LNAI 4911:287-304. 2008. preprint.

Semantical and Algorithmic Aspects of the Living. Talk by François Fages at INRIA Paris-Rocquencourt, Séminaire Modèles et Algorithmes. slides and video.

Abstract Interpretation and Types for Systems Biology. by François Fages and Sylvain Soliman. Theoretical Computer Science 403, p.52-70. 2008. pdf.

On the Analysis of Numerical Data Time Series in Temporal Logic. by François Fages and Aurélien Rizk. Computational Methods in Systems Biology, CMSB'07 Edinbirgh. Springer-Verlag LNBI 4695:48-63, 2007. pdf.

Formal validation of dynamical models and application to cell cycle control. by François Fages. Ecole thématique: Dynamical modelling of biological regulatory networks. Les Houches, France. April 2007. slides.

Type inference in Systems Biology. by François Fages and Sylvain Soliman. Computational Methods in Systems Biology, CMSB'06 Trento. Springer-Verlag LNBI 4210, pp. 48-62, 2006. pdf. slides.

BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge. by Laurence Calzone, François Fages and Sylvain Soliman. Bioinformatics 22:1805-1807, July 2006. pdf.

Machine Learning Biochemical Networks from Temporal Logic Properties. by Laurence Calzone, Nathalie Chabrier-Rivier, François Fages and Sylvain Soliman. Transactions on Computational Systems Biology VI. Springer-Verlag. LNBI 4220 pp. 68-94, 2006. pdf. (Slides presented at WCB'06 pps).

Langages formels dans la machine abstraite biochimique BIOCHAM. by Laurence Calzone, Nathalie Chabrier-Rivier, François Fages and Sylvain Soliman. Technique et Science Informatique. A paraître 2006. pdf.

From Syntax to Semantics in Systems Biology, Towards Automated Reasoning Tools. Invited Talk at the Converging Sciences meeting, Trento, Italy, December 2004. Transactions on Computational Systems Biology IV, LNBI 3939 pp. 68-70. 2006. pdf.

Temporal Logic Constraints in the Biochemical Abstract Machine BIOCHAM. Invited Talk at SAS/LOPSTR September 2005 London, by François Fages. Springer-Verlag LNCS 3901 pp. 1-5. 2005. Paper pdf. Slides ppt.

Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM by François Fages, Sylvain Soliman and Nathalie Chabrier-Rivier. Journal of Biological Physics and Chemistry 4(2), pp.64-73. October 2004. Preprint available as pdf.

The Biochemical Abstract Machine BIOCHAM by Nathalie Chabrier-Rivier, François Fages and Sylvain Soliman.
Proceedings of the Second International Workshop on Computational Methods in Systems Biology CMSB'04, Springer-Verlag LNCS. 2004. Preprint available as ps.gz.

CMBSlib: a Library for Comparinng Formalisms and Models of Biological Systems by Sylvain Soliman and François Fages.
Proceedings of the Second International Workshop on Computational Methods in Systems Biology CMSB'04, Springer-Verlag LNCS. 2004. Available as ps.gz.

Constraint-based Model Checking of  Non-deterministic Hybrid Systems: A First Experiment in Systems Biology by François Fages. Workshop on Constraint Programming and Constriants for Verification CP+CV'04 associated to ETAPS'04.  Slides pps

Symbolic model-checking for biochemical systems: logic programming steps towards formal biology (invited tutorial) by François Fages. International Conference on Logic Programming ICLP'03, Mumbai, India. December 2003. MIT Press. Slides available as ppt.

The Biochemical Abstract Machine BIOCHAM (short presentation) by Nathalie Chabrier and François Fages.
European Conference on Computational Biology ECCB'03. Paris. September 2003.  Available as ps.

Modeling and querying biomolecular interaction networks by Nathalie Chabrier, Marc Chiaverini, Vincent Danos, François Fages. and Vincent Schächter. Theoretical Computer Science 325(1), pp.25-44.  September 2004. Available as pdf. 

Symbolic model checking of biochemical networks by Nathalie Chabrier and François Fages.
Proceedings of the First International Workshop on Computational Methods in Systems Biology CMSB'03, Springer-Verlag LNCS 2602, pp.149-162, Rivereto, Italy, March 2003. Available as ps. 

Slides (invited talk) presented at the Workshop  on Formal Methods and Biological Reasoning associated to the 3rd International Conference on Systems Biology ICSB'02, Stockohlm, December 2002.
 

Concurrent Constraint Programming and Linear Logic


Closures and Modules within Linear Logic Concurrent Constraint Programming by Rémy Haemmerlé, François  Fages and Sylvain Soliman. FSTTCS, Dec. 2007, New Delhi. Springer-Verlag LNCS. 2007. pdf

On internalizing modules as agents in Linear logic concurrent constraint languages by Rémy Haemmerlé, François  Fages and Sylvain Soliman. INRIA Research Report 5981. 2006.

A precise semantics of concurrent constraint programs by François  Fages and Sylvain Soliman. Submitted to publication. February 2001. ( ps).

Concurrent constraint programming and linear logic by François  Fages. Invited talk at the ACM conference on Principles and Practice of Declarative Programming, PPDP'2000, Montreal. (   ps, dvi  , slides.ps  , slides.ps.gz ).

Linear concurrent constraint programming: operational and phase semantics by François Fages, Paul Ruet and Sylvain Soliman. Journal of Information and Computation 165(1) pp.14-41. February 2001. (preprint ps.gz,ps , dvi ).

Expressiveness and complexity of concurrent constraint programming: a finite model theoretic approach by François Fages, Sylvain Soliman and Victor Vianu. This is a LIENS research report Liens-98-14. December 1998. It is available as ps and dvi.

Phase Semantics and Verification of Concurrent Constraint Programs (extended abstract) by François Fages, Paul Ruet and Sylvain Soliman. This is a paper that will be presented at LICS'98, Indianapolis. It is available as ps.

Concurrent Constraint Programming and Mixed Non-Commutative Linear Logic, by Paul Ruet and François Fages. This is a paper presented at CSL'97, Springer-Verlag LNCS 1414, 1997. It is available as ps.
 
 

Constraint Logic Programming


Static Expansion vs Procedural Code Generation in Rule-based Modeling Languages. Julien Martin, Thierry Martinez, François Fages. In Recent Advances in Constraints. Springer-Verlag LNAI 6384:38-58, 2011. pdf.

From Model-Checking to Temporal Logic Constraint Solving by François Fages and Aurélien Rizk. Proc of 15th International Conference on Principles and Practice of Constraint Programming, CP'09. LNCS, Springer-Verlag. 2009 (preprint)

Modelling Search Strategies in Rules2CP. François Fages and Julien Martin. Proc. of the 6th International Conferenceon the integration of AI and OR techniques in constraint programming for combinatoiral optimization problems, CPAIOR'09. Springer-Verlag LNCS 5547:321-322, 2009. pdf.

Abstract Context Operators for Proving Commutation and Confluence without Termination by Rémy Haemmerlé and François Fages. Research Report. January 2009, pdf.

Modular CHR with ask and tell. François Fages, Cleyton Mario de Oliveira Rodrigues and Thierry Martinez. Workshop CHR. July2008. pdf.

From Rules to Constraint Programs with the Rules2CP Modelling Language. François Fages and Julien Martin. INRIA Research Report RR-6495, April 2008. pdf . 13th Workshop on Constraint Solving and Constraint Logic Programming, CSCLP’08, Rome, Juin 2008. Recent Advances in Constraints, Springer-Verlag LNAI 5655:66-83, 2009. pdf.

Des contraintes au programme. François Fages. Revue littéraire Actes de Savoirs, PUF. 2007. pdf.

From Business Rules to Constraint Programs in Wharehouse Management Systems by Julien Martin and François Fages. Doctoral Programme, 13th International Conference on Logic Programming CP'07, Providence, USA.  2007, pdf.

Abstract Critical Pairs and Confluence of Arbitrary Binary Relations by Rémy Haemmerlé and François Fages. 18th International Conference on Rewriting Techniques and Applications, RTA'07, Paris, France. Springer Verlag, LNCS 4533, pp. 214-228,  2007, pdf.

Modules for Prolog Revisited by Rémy Haemmerlé and François Fages. 22nd International Conference on Logic Programming ICLP'06. Seattle, USA. Springer Verlag, LNCS 4079, pp. 41-55,  2006, pdf.

A Type System for CHR by Emmanuel Coquery and François Fages. ERCIM/Colognet Workshop on Constraint Solving and Constraint Logic Programming CSCLP'05. Springer-Verlag LNAI 3978, 2006. Preprint pdf.

Allocation distirubée de ressources dans le système CONSENSUS by Sylvain Sécherre and François Fages. Rapport Technique INRIA RT0308.

Programmation Logique et Contraintes. by François Fages. Encylopédie de l'informatique et des systèmes d'information. pp.1038-1049. Vuibert. preprint.

A Constraint Programming Approach to Cutset Problems by François Fages and Akash Lal. Computers and Operations Research 33:10:2852-2865. October 2006. Preprint available as ps.

CLPGUI: a Generic Graphical User Interface for Constraint Logic Programming  by François Fages, Sylvain Soliman and Rémi Coolen. Journal of Constraints 9(4) 2004. Preprint available at ps.gz and pdf.

Recent Advances in Constraints, 2003. Edited by K.R. Apt, F. Fages, F. Rossi, P. Szeredi and J. Vancza. Selected papers of the Joint ERCIM/CoLogNET International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP'03, Budapest, Hungary, June 30-July 2, 2003. Publisher Springer-Verlag, Lectures Notes in Artificial Intelligence, LNAI 3010, May 2004.

Subtyping Constraints in Quasi-lattices by Emmanuel Coquery and François Fages. To appear in Foundations of Software Tehcnology and Theoretical Computer Science, FSTTCS'03. Springer-Verlag. Lecture Notes in Computer Science. December 2003. Complete version available as INRIA research report RR4926 ps.

A Global Constraint for Cutset Problems by François Fages and Akash Lal. Fifth International Workshop on Integration of AI and OR techniques in constraint programming for combinatorial optimization problems CPAIOR'03, Montreal, Canada. April 2003. Available as ps or pdf (slides.ps).

3D Visualization and Control in CLPGUI by François Fages. Workshop on User Interaction in Constraint Satisfaction UICS'02 associated to Principles and Practice of Constraint Programming CP'02, Ithaca, September 2002. Available as ps.gz.

CLPGUI: a generic graphical user interface for constraint logic programming over finite domains by François Fages. Workshop on Logic Programming Environments WLPE'02 associated to ICLP'02 and FLOC'02. Copenhague, Août 2002. Available at ps.gz.

TCLP: overloading, subtyping and parametric polymorphism made practical for constraint logic programming by Emmanuel Coquery and François Fages. Poster at the International Conference on Logic Programming ICLP 2002, Copenhagen, LNCS 2401, Springer-Verlag. Complete version in INRIA Research Report. May 2002. Available as ps.

Surcharge et sous-typage dans TCLP by Emmanuel Coquery and François Fages. Journées Francophones de Programmation en Logique et programmation par Contraintes  JFPLC'2002, Nice. Ed; M. Rueher, Hermes Paris, May 2002.

From Typing Constraints to Typed Constraint Systems in CHR by Emmanuel Coquery and François Fages. Third workshop on Rule-based Constraint Reasoning and Programming, CP'01, Cyprus. December 2001. Available as ps.gz. (slides ps.gz].

Typing Constraint Logic Programs by François Fages and Emmanuel  Coquery. Journal of Theory and Practice of Logic Programming TPLP 1(6)., pp. 751-777. November 2001. Available as   ps.

A Constraint Programming Approach to Log-based Reconciliation Problems for Nomadic Applications by François Fages.  Revised August 2001. Available as ps or ps.gz.

CLP versus LS on Log-based Reconciliation Problems by François Fages. 6th ERCIM workshop of the Constraint Group, Prague, Czech Rep. May 2001. Available as ps.gz.

ESSLLI'01 course notes on Constraint Logic Programming by François Fages, (revised version of Ecole Jeunes Chercheurs du GDR Programmation du CNRS, and of ESSLLI'97, Aix-en-Provence), Helsinki, Finland, August 2001, available as ps

Using Modes to Ensure Subject Reduction for Typed Logic Programs with Subtyping by Jan Smaus, François Fages et Pierre Deransart. This is the complete version of an article to be presented at FSTTCS'2000 New Dehli, December 2000, Springer-Verlag LNCS. It is available as ps and ps.gz.

Experiments in Reactive Constraint Logic Programming by François Fages, Julian Fowler and Thierry Sola. This is an article which has appeared in the Journal of Logic Programming 37:1-3:185-212. July 1998. It is available as ps.

A Generic Type System for CLP(X) by François Fages and Massimo Paltrinieri.This is a LIENS research report R97-16, presented as a poster at JICSLP'98, MIT Press, 1998. It is available as ps and dvi .

Programmation Logique par Contraintes by François Fages, Collection Cours de l'Ecole Polytechnique, Ed. Ellipses, Paris, Mai 1996. book

A Reactive Constraint Logic Programming Scheme by François Fages, Julian Fowler and Thierry Sola. This is the paper presented at the International Conference on Logic Programming, ICLP'95, Japan, June 1995, MIT Press. It is available as ps.

Un modele d'execution interactif et reactif pour la programmation logique avec contraintes by François Fages, Julian Fowler and Thierry Sola. This is the paper presented at the Journees Francophones de Programmation Logique, JFPL'95, Dijon, Mai 1995. It is available as ps.

A Metalevel compiler of CLP(FD) and its combination with intelligent backtracking by Philippe Codognet, François Fages and Thierry Sola. This paper is part of the book entitled "Constraint Logic Programming: selected research", edited by F. Benhamou and A. Colmerauer, MIT Press, 1993. It is available as ps .
 
 

Constructive Negation and Optimization

Analysis of normal logic programs by François Fages and Roberta Gori. This is a paper that will be presented at SAS'98, SPringer-Verlag LNCS. It is available as ps and dvi .

Constructive negation by pruning by François Fages. This is a version of a paper published in the Journal of Logic Programming 32(2) 1997 . It is available as dvi and as ps .

A hierarchy of semantics for normal constraint logic programs, by François Fages and Roberta Gori. This is an article presented at ALP'96. Springer-Verlag LNCS 1139, 1996. It is available as ps.

Negation constructive en programmation logique avec contraintes by François Fages. This is a paper presented at the Journees du GDR Programmation, CNRS, Grenoble, Novembre 1995. It is available as ps.

Constructive negation by pruning and optimization higher-order predicates for CLP and CC languages by François Fages. This is the paper presented at the Ecole de Printemps d'Informatique Théorique, 1994, LNCS 910. It is available as dvi.

From constraint minimization to goal optimization in CLP languages, by François Fages. This is a paper presented at the International Logic Programming Symposium ILPS'95, Post-conference Workshop on Constraints, Databases and Logic Programming, Portland, Oregon, 1995. A revised version of it is available as dvi.

Handling Preferences in Constraint Logic Programming with Relational Optimization by François Fages, Julian Fowler and Thierry Sola. This is the paper presented at the 6th International Symposium PLILP'94, Madrid, Sept. 1994, LNCS 844, Springer-Verlag. It is available as ps.

On the semantics of optimization predicates in CLP languages. by François Fages. This is the paper presented at the 13th FSTTCS conference in Bombay, Springer-Verlag LNCS 761, 1993. It is available as ps.
 
 

Negation by default

Default Reasoning in CHRv by Marcos Aurélio, François Fages and Jacques Robin. Workshop Constraint Handling Rules CHR'08. Linz, Austria. 2008. pdf.

Combining explicit negation and negation by failure via Belnap's logic by Paul Ruet and François Fages. This is the paper presented at the Workshop on Uncertainty and Deductive Databases associated to 7th International Symposium on Logic Programming ILPS'94, Ithaca, Nov. 1994. A revised version appeared in Theoretical Computer Science 171:61-75, 1997. It is available as ps.

Consistency of Clark's Completion and Existence of Stable Models by François Fages. This is an electronic version of an article published in Methods of Logic in Computer Science, 1:51-60, 1994. It is available as ps.
 
 
 

Some older papers from 1982 to 1999 are listed in my Curriculum Vitae.