François Fages

Theor. Comput. Sci., 2024

On Teaching Constraint-based Modeling and Algorithms for Decision Support in Prolog.

[BibT_eX]

[DOI]

Proceedings of the Workshop Proceedings of the 40th International Conference on Logic Programming (ICLP-WS 2024) co-located with the 40th International Conference on Logic Programming (ICLP 2024), 2024

A Constraint-Based Mathematical Modeling Library in Prolog with Answer Constraint Semantics.

[BibT_eX]

[DOI]

Proceedings of the Functional and Logic Programming - 17th International Symposium, 2024

Graphical Conditions Ensuring Equality Between Differential and Mean Stochastic Dynamics.

[BibT_eX]

[DOI]

Hugo Buscemi

Proceedings of the Computational Methods in Systems Biology, 2024

2023

Neural-based classification rule learning for sequential data.

[BibT_eX]

[DOI]

Proceedings of the Eleventh International Conference on Learning Representations, 2023

On Estimating Derivatives of Input Signals in Biochemistry.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2023

2022

Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design.

[BibT_eX]

[DOI]

Jean-Philippe Stephan

Thierry Dorval

PLoS Comput. Biol., 2022

Algebraic Biochemistry: A Framework for Analog Online Computation in Cells.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2022

Stability Versus Meta-stability in a Skin Microbiome Model.

[BibT_eX]

[DOI]

Eléa Thibault Greugny

Georgios N. Stamatas

Proceedings of the Computational Methods in Systems Biology, 2022

2021

Model learning to identify systemic regulators of the peripheral circadian clock.

[BibT_eX]

[DOI]

Bioinform., 2021

Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2021

2020

On the Complexity of Quadratization for Polynomial Differential Equations.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2020

Graphical Conditions for Rate Independence in Chemical Reaction Networks.

[BibT_eX]

[DOI]

Elisabeth Degrand

Proceedings of the Computational Methods in Systems Biology, 2020

Artificial Intelligence in Biological Modelling.

[BibT_eX]

[DOI]

Proceedings of the A Guided Tour of Artificial Intelligence Research: Volume III: Interfaces and Applications of Artificial Intelligence, 2020

2019

Formal methods for the synthesis of biomolecular circuits (NII Shonan Meeting 157).

[BibT_eX]

[DOI]

NII Shonan Meet. Rep., 2019

On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2019

On Chemical Reaction Network Design by a Nested Evolution Algorithm.

[BibT_eX]

[DOI]

Elisabeth Degrand

Proceedings of the Computational Methods in Systems Biology, 2019

Biochemical Threshold Function Implementation with Zero-Order Ultrasensitivity.

[BibT_eX]

[DOI]

Wei-Chih Huang

Jie-Hong Roland Jiang

Franck Molina

Proceedings of the 2019 IEEE Biomedical Circuits and Systems Conference, 2019

2018

Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels.

[BibT_eX]

[DOI]

Adrien Baudier

CoRR, 2018

The SYMBIONT project: symbolic methods for biological networks.

[BibT_eX]

[DOI]

ACM Commun. Comput. Algebra, 2018

On Robustness Computation and Optimization in BIOCHAM-4.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2018

2017

Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2017

Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data.

[BibT_eX]

[DOI]

Arthur Carcano

Proceedings of the Computational Methods in Systems Biology, 2017

Recombinase-based genetic circuit optimization.

[BibT_eX]

[DOI]

Chun-Ning Lai

Proceedings of the IEEE Biomedical Circuits and Systems Conference, 2017

2016

Packing with Complex Shapes

[BibT_eX]

[DOI]

ERCIM News, 2016

On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity.

[BibT_eX]

[DOI]

Constraints An Int. J., 2016

Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis.

[BibT_eX]

[DOI]

Biosyst., 2016

Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation.

[BibT_eX]

[DOI]

Bioinform., 2016

Panorama of real-life applications in logistics embedding bin packing optimization algorithms, robotics and cloud computing technologies.

[BibT_eX]

[DOI]

Abderrahmane Aggoun

Ahmed Rhiat

Proceedings of the 3rd International Conference on Logistics Operations Management, 2016

A Stochastic Continuous Optimization Backend for MiniZinc with Applications to Geometrical Placement Problems.

[BibT_eX]

[DOI]

Thierry Martinez

Abder Aggoun

Proceedings of the Integration of AI and OR Techniques in Constraint Programming, 2016

Influence Systems vs Reaction Systems.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 2016

2015

Hybrid Simulations of Heterogeneous Biochemical Models in SBML.

[BibT_eX]

[DOI]

Jie-Hong Roland Jiang

ACM Trans. Model. Comput. Simul., 2015

Inferring reaction systems from ordinary differential equations.

[BibT_eX]

[DOI]

Steven Gay

Theor. Comput. Sci., 2015

Search by constraint propagation.

[BibT_eX]

[DOI]

Thierry Martinez

Proceedings of the 17th International Symposium on Principles and Practice of Declarative Programming, 2015

Reconfigurable neuromorphic computation in biochemical systems.

[BibT_eX]

[DOI]

Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2015

Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis.

[BibT_eX]

[DOI]

Pauline Traynard

Proceedings of the Computational Methods in Systems Biology, 2015

2014

On the subgraph epimorphism problem.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2014

A constraint solving approach to model reduction by tropical equilibration.

[BibT_eX]

[DOI]

Ovidiu Radulescu

Algorithms Mol. Biol., 2014

Cells as Machines: Towards Deciphering Biochemical Programs in the Cell.

[BibT_eX]

[DOI]

Proceedings of the Distributed Computing and Internet Technology, 2014

Trace Simplifications Preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock.

[BibT_eX]

[DOI]

Pauline Traynard

Proceedings of the Computational Methods in Systems Biology, 2014

Building reconfigurable circuitry in a biochemical world.

[BibT_eX]

[DOI]

Proceedings of the IEEE Biomedical Circuits and Systems Conference, 2014

2013

Guest Editors' Introduction to the Special Section on Computational Methods in Systems Biology.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Preface.

[BibT_eX]

[DOI]

Simon de Givry

Christine Solnon

RAIRO Oper. Res., 2013

Un modèle booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri

[BibT_eX]

[DOI]

CoRR, 2013

On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models.

[BibT_eX]

[DOI]

Anthony José da Cunha Carneiro Lins

Proceedings of the Computational Methods in Systems Biology, 2013

2012

A Comparative Analysis of FSS with CMA-ES and S-PSO in Ill-Conditioned Problems.

[BibT_eX]

[DOI]

Fernando Buarque de Lima Neto

Carmelo J. A. Bastos Filho

Proceedings of the Intelligent Data Engineering and Automated Learning - IDEAL 2012, 2012

A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets.

[BibT_eX]

[DOI]

Proceedings of the Principles and Practice of Constraint Programming, 2012

Inferring Reaction Models from ODEs.

[BibT_eX]

[DOI]

Steven Gay

Proceedings of the Computational Methods in Systems Biology, 2012

2011

Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2011

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.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2011

Towards Real-Time Control of Gene Expression: Controlling the Hog Signaling Cascade.

[BibT_eX]

[DOI]

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2010

Computational Systems Biology in BIOCHAM.

[BibT_eX]

[DOI]

ERCIM News, 2010

Integrating Rule-Based Modelling and Constraint Programming for Solving Industrial Packing Problems.

[BibT_eX]

[DOI]

ERCIM News, 2010

A graphical method for reducing and relating models in systems biology.

[BibT_eX]

[DOI]

Steven Gay

Bioinform., 2010

A Logical Paradigm for Systems Biology (Invited Talk).

[BibT_eX]

[DOI]

Proceedings of the Technical Communications of the 26th International Conference on Logic Programming, 2010

2009

A general computational method for robustness analysis with applications to synthetic gene networks.

[BibT_eX]

[DOI]

Bioinform., 2009

Procedural Code Generation <i>vs</i> Static Expansion in Modelling Languages for Constraint Programming.

[BibT_eX]

[DOI]

Julien Martin

Thierry Martinez

Proceedings of the Recent Advances in Constraints, 2009

Modelling Search Strategies in Rules2CP.

[BibT_eX]

[DOI]

Julien Martin

Proceedings of the Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, 2009

From Model-Checking to Temporal Logic Constraint Solving.

[BibT_eX]

[DOI]

Aurélien Rizk

Proceedings of the Principles and Practice of Constraint Programming, 2009

On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle.

[BibT_eX]

[DOI]

Elisabetta De Maria

Proceedings of the Computational Methods in Systems Biology, 7th International Conference, 2009

2008

Abstract interpretation and types for systems biology.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2008

On temporal logic constraint solving for analyzing numerical data time series.

[BibT_eX]

[DOI]

Aurélien Rizk

Theor. Comput. Sci., 2008

Formal Cell Biology in Biocham.

[BibT_eX]

[DOI]

Proceedings of the Formal Methods for Computational Systems Biology, 2008

Model Revision from Temporal Logic Properties in Computational Systems Biology.

[BibT_eX]

[DOI]

Proceedings of the Probabilistic Inductive Logic Programming - Theory and Applications, 2008

From Reaction Models to Influence Graphs and Back: A Theorem.

[BibT_eX]

[DOI]

Proceedings of the Formal Methods in Systems Biology, First International Workshop, 2008

From Rules to Constraint Programs with the Rules2CP Modelling Language.

[BibT_eX]

[DOI]

Julien Martin

Proceedings of the Recent Advances in Constraints, 2008

On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

2007

Langages formels dans la machine abstraite biochimique BIOCHAM.

[BibT_eX]

[DOI]

Laurence Calzone

L. Fosse

Tech. Sci. Informatiques, 2007

Net-WMS - A New Generation of Warehouse Management Systems Networked Services.

[BibT_eX]

[DOI]

Abder Aggoun

ERCIM News, 2007

Patient-Tailored Cancer Therapeutics - The Tempo Project.

[BibT_eX]

[DOI]

Jean Clairambault

ERCIM News, 2007

Abstract Critical Pairs and Confluence of Arbitrary Binary Relations.

[BibT_eX]

[DOI]

Rémy Haemmerlé

Proceedings of the Term Rewriting and Applications, 18th International Conference, 2007

Closures and Modules Within Linear Logic Concurrent Constraint Programming.

[BibT_eX]

[DOI]

Rémy Haemmerlé

Proceedings of the FSTTCS 2007: Foundations of Software Technology and Theoretical Computer Science, 2007

On the Analysis of Numerical Data Time Series in Temporal Logic.

[BibT_eX]

[DOI]

Aurélien Rizk

Proceedings of the Computational Methods in Systems Biology, International Conference, 2007

2006

From Syntax to Semantics in Systems Biology Towards Automated Reasoning Tools.

[BibT_eX]

[DOI]

Trans. Comp. Sys. Biology, 2006

Machine Learning Biochemical Networks from Temporal Logic Properties.

[BibT_eX]

[DOI]

Laurence Calzone

Trans. Comp. Sys. Biology, 2006

Editorial.

[BibT_eX]

[DOI]

Narendra Jussien

Christine Solnon

RAIRO Oper. Res., 2006

A constraint programming approach to cutset problems.

[BibT_eX]

[DOI]

Akash Lal

Comput. Oper. Res., 2006

BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge.

[BibT_eX]

[DOI]

Laurence Calzone

Bioinform., 2006

Modules for Prolog Revisited.

[BibT_eX]

[DOI]

Rémy Haemmerlé

Proceedings of the Logic Programming, 22nd International Conference, 2006

06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification.

[BibT_eX]

[DOI]

Adelinde M. Uhrmacher

Proceedings of the Simulation and Verification of Dynamic Systems, 17.04. - 22.04.2006, 2006

Type Inference in Systems Biology.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, International Conference, 2006

2005

Temporal Logic Constraints in the Biochemical Abstract Machine BIOCHAM.

[BibT_eX]

[DOI]

Proceedings of the Logic Based Program Synthesis and Transformation, 2005

A Type System for CHR.

[BibT_eX]

[DOI]

Proceedings of the Logic Programming, 21st International Conference, 2005

05371 Abstracts Collection - Principles and Practices of Semantic Web Reasoning.

[BibT_eX]

[DOI]

Proceedings of the Principles and Practices of Semantic Web Reasoning, 2005

2004

Modeling and querying biomolecular interaction networks.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2004

Invited talks.

[BibT_eX]

[DOI]

Künstliche Intell., 2004

CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming.

[BibT_eX]

[DOI]

Rémi Coolen

Constraints An Int. J., 2004

Automated Reasoning Tools for Molecular Biology.

[BibT_eX]

[DOI]

Proceedings of the KI 2004: Advances in Artificial Intelligence, 2004

CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, International Conference, 2004

The Biochemical Abstract Machine BIOCHAM.

[BibT_eX]

[DOI]

Proceedings of the Computational Methods in Systems Biology, International Conference, 2004

2003

Contraintes de sous-typage dans les quasi-treillis.

[BibT_eX]

[DOI]

Tech. Sci. Informatiques, 2003

"Model Checking" symbolique de réseaux biochimiques.

[BibT_eX]

[DOI]

Nathalie Chabrier

Tech. Sci. Informatiques, 2003

"Model Checking" symbolique de réseaux bio-chimiques.

[BibT_eX]

Nathalie Chabrier

Proceedings of the Journées Francophones de Programmation en Logique avec Contraintes (JFPLC 2003), 2003

Symbolic Model-Checking for Biochemical Systems.

[BibT_eX]

[DOI]

Proceedings of the Logic Programming, 19th International Conference, 2003

Subtyping Constraints in Quasi-lattices.

[BibT_eX]

[DOI]

Proceedings of the FST TCS 2003: Foundations of Software Technology and Theoretical Computer Science, 2003

Symbolic Model Checking of Biochemical Networks.

[BibT_eX]

[DOI]

Nathalie Chabrier

Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003

2002

CLPGUI: a generic graphical user interface for constraint logic programming over finite domains.

[BibT_eX]

[DOI]

Proceedings of the 12th International Workshop on Logic Programming Environments, 2002

Surcharge et sous-typage dans TCLP.

[BibT_eX]

Proceedings of the Programmation en logique avec contraintes, 2002

TCLP: Overloading, Subtyping and Parametric Polymorphism Made Practical for CLP.

[BibT_eX]

[DOI]

Proceedings of the Logic Programming, 18th International Conference, 2002

2001

Typing constraint logic programs.

[BibT_eX]

[DOI]

Theory Pract. Log. Program., 2001

Linear Concurrent Constraint Programming: Operational and Phase Semantics.

[BibT_eX]

[DOI]

Inf. Comput., 2001

CLP versus LS on Log-based Reconciliation Problems

[BibT_eX]

[DOI]

CoRR, 2001

Programmes logiques avec contraintes typés.

[BibT_eX]

Proceedings of the Programmation en logique avec contraintes, Actes des JFPLC'2001, 24 avril, 2001

2000

Concurrent constraint programming and linear logic (abstract).

[BibT_eX]

[DOI]

Proceedings of the 2nd international ACM SIGPLAN conference on on Principles and practice of declarative programming, 2000

Using Modes to Ensure Subject Reduction for Typed Logic Programs with Subtyping.

[BibT_eX]

[DOI]

Jan-Georg Smaus

Pierre Deransart

Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 2000

1998

Experiments in Reactive Constraint Logic Programming.

[BibT_eX]

[DOI]

J. Log. Program., 1998

Analysis of Normal Logic Programs.

[BibT_eX]

[DOI]

Roberta Gori

Proceedings of the Static Analysis, 5th International Symposium, 1998

Phase Semantics and Verification of Concurrent Constraint Programs.

[BibT_eX]

[DOI]

Proceedings of the Thirteenth Annual IEEE Symposium on Logic in Computer Science, 1998

A Generic Type System for CLP(chi).

[BibT_eX]

Massimo Paltrinieri

Proceedings of the 1998 Joint International Conference and Symposium on Logic Programming, 1998

1997

Combining Explicit Negation and Negation by Failure Via Belnap's Logic.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1997

Constructive Negation by Pruning.

[BibT_eX]

[DOI]

J. Log. Program., 1997

Concurrent Constraint Programming and Non-commutative Logic.

[BibT_eX]

[DOI]

Proceedings of the Computer Science Logic, 11th International Workshop, 1997

1996

From Constraint Minimization to Goal Optimization in CLP Languages.

[BibT_eX]

[DOI]

Proceedings of the Second International Conference on Principles and Practice of Constraint Programming, 1996

A Hierarchy of Semantics for Normal Constraint Logic Programs.

[BibT_eX]

[DOI]

Roberta Gori

Proceedings of the Algebraic and Logic Programming, 5th International Conference, 1996

1995

Un modèle d'exécution réactif et interactif pour la programmation logique avec contraintes.

[BibT_eX]

Proceedings of the JFPLC'95, 1995

A Reactive Constraint Logic Programming Scheme.

[BibT_eX]

Proceedings of the Logic Programming, 1995

Data Alignment and Task Scheduling on Parallel Machines Using Concurrent Model-based Programming.

[BibT_eX]

Proceedings of the First International Workshop on Concurrent Constraint Programming, 1995

1994

Consistency of Clark's completion and existence of stable models.

[BibT_eX]

Methods Log. Comput. Sci., 1994

Constructive Negation by Pruning and Optimizing Higher-Order Predicates for CLP and CC Languages

[BibT_eX]

[DOI]

Proceedings of the Constraint Programming: Basics and Trends, Châtillon Spring School, 1994

Data Alignment and Task Scheduling On Parallel Machines Using Concurrent Constraint Model-based Programming.

[BibT_eX]

Proceedings of the Logic Programming, 1994

Handling Preferences in Constraint Logic Programming with Relational Optimization.

[BibT_eX]

[DOI]

Proceedings of the Programming Language Implementation and Logic Programming, 1994

1993

Average-Case Analysis of Unification Algorithms.

[BibT_eX]

[DOI]

Luc Albert

Rafael Casas

Theor. Comput. Sci., 1993

On the Semantics of Optimization Predicates in CLP languages.

[BibT_eX]

Proceedings of the Principles and Practice of Constraint Programming, 1993

1991

A New Fixpoint Semantics for General Logic Programs Compared with the Well-Founded and the Stable Model Semantics.

[BibT_eX]

[DOI]

New Gener. Comput., 1991

A Metalevel Compiler of CLP(FD) and Its Combination with Intelligent Backtracking.

[BibT_eX]

Philippe Codognet

Proceedings of the Constraint Logic Programming, 1991

Average Case Analysis of Unification Algorithms.

[BibT_eX]

[DOI]

Proceedings of the STACS 91, 1991

1988

Average Case Complexity Analysis of the Rete Multi-Pattern Match Algorithm.

[BibT_eX]

[DOI]

Luc Albert

Proceedings of the Automata, Languages and Programming, 15th International Colloquium, 1988

1987

Associative-Commutative Unification.

[BibT_eX]

[DOI]

J. Symb. Comput., 1987

1986

Complete Sets of Unifiers and Matchers in Equational Theories.

[BibT_eX]

[DOI]

Gérard P. Huet

Theor. Comput. Sci., 1986

1983

Note sur l'unification des termes de premier ordre finis et infinis.

[BibT_eX]