Constraints are a natural way to represent knowledge, and constraint programming is a declarative programming paradigm that has been successfully used to express and solve many practical combinatorial optimization problems. Examples of application domains are scheduling, production planning, resource allocation, communication networks, robotics, and bioinformatics. These proceedings contain the research papers presented at the 12th International Workshop on Constraint Solving and Constraint Logic Programming (CSCLP'07), held on June 7th and 8th 2007, at INRIA Rocquencourt, France […]
Sat, Dec 1, 2007
Le développement de langages formels pour modéliser les systèmes biologiques ouvre la voie à la conception de nouveaux outils de raisonnement automatique destinés au biologiste modélisateur. La machine abstraite biochimique BIOCHAM est un environnement logiciel qui offre un langage simple de règles pour modéliser des interactions biomoléculaires, et un lan-gage puissant fondé sur la logique temporelle pour formaliser les propriétés biologiques du sys-tème. En s'appuyant sur ces deux langages formels, il devient possible d'utiliser des techniques d'apprentissage automatique pour inférer de nouvelles règles de réaction, estimer les valeurs des paramètres cinétiques, et corriger ou compléter les modèles semi-automatiquement […]
Sat, Dec 1, 2007
There are two somewhat contradictory ways of looking at modules in a given programming language. On the one hand, module systems are largely independent of the particulars of programming languages. On the other hand, the module constructs may interfere with the programming constructs, and may be redundant with the other scope mechanisms of a specific programming language, such as closures for instance […]
Sat, Dec 1, 2007
Module systems are an essential feature of programming languages as they facilitate the re-use of existing code and the development of general purpose libraries. There are however two somewhat contradictory ways of looking at modules in a given programming language. On the one hand, module systems are largely independent of the particulars of programming languages, and several examples of module systems have indeed been adapted to different programming languages […]
Fri, Dec 1, 2006
One central issue in systems biology is the definition of formal languages for describing complex biochemical systems and their behavior at different levels. The biochemical abstract machine BIOCHAM is based on two formal languages, one rule-based language used for modeling biochemical networks, at three abstraction levels corresponding to three semantics: boolean, concentration and population; and one temporal logic language used for formalizing the biological properties of the system. In this paper, we show how the temporal logic language can be turned into a specification language […]
Fri, Dec 1, 2006
Cancer treatments based on the administration of medicines at different times of the day have been shown to be more efficient against malign cells and less damaging towards healthy ones. These results might be related to the recent discovery of links between the circadian clock, (controlled by the light/dark cycle of a day), and the cell cycle. However, if many models have been developed to describe both of these cycles, to our knowledge none has described a real interaction between them […]
Fri, Dec 1, 2006
BIOCHAM (the BIOCHemical Abstract Machine) is a software environment for modeling biochemical systems. It is based on two aspects: (1) the analysis and simulation of boolean, kinetic and stoch-astic models and (2) the formalization of biological properties in temporal logic. BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model […]
Sat, Apr 1, 2006
Most of the work on temporal representation issues in Machine Learning deals with the problem of learning/mining temporal patterns from a large set of temporal data. In this paper we investigate the somewhat different problem of learning the behavioral rules of a system from its observed temporal properties formalized in temporal logic. Our interest in this problem arose from Systems Biology and the development of machine learning techniques for learning biochemical reaction rules and kinetic parameters in the Biochemical Abstract Machine BIOCHAM […]
Thu, Dec 1, 2005
Beyond numerical simulation, the possibility of performing symbolic computation on bio-molecular interaction networks opens the way to the design of new automated reasoning tools for biologists/modelers. The Biochemical Abstract machine BIOCHAM provides a precise semantics to biomolecular interaction maps as concurrent transition systems. Based on this formal semantics, BIOCHAM offers a compositional rule-based language for modeling biochemical systems, and an original query language based on temporal logic for expressing biological queries about reachability, checkpoints, oscillations or stability […]
Thu, Dec 1, 2005
Fri, Jul 1, 2005
With the advent of formal languages for modeling bio-molecu-lar interaction systems, the design of automated reasoning tools to assist the biologist becomes possible. The biochemical abstract machine BIOCHAM software environment offers a rule-based language to model bio-molecular interactions and an original temporal logic based language to formalize the biological properties of the system. Building on these two formal languages, machine learning techniques can be used to infer new molecular interaction rules from temporal properties […]
Fri, Apr 1, 2005
In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning to ols for querying the temporal properties of the system under all its possible behavi ors […]
Wed, Dec 1, 2004
Recent progress in high-throughput data-production technologies pushes research towardsystems biology, focusing on the global interaction between the components ofbiomolecular processes. In this article we present a formal modelling environment fornetwork biology, called the Biochemical Abstract Machine (BIOCHAM). Biochamdelivers precise semantics to biomolecular interaction maps […]
Fri, Oct 1, 2004
CLPGUI is a generic graphical user interface for visualizing and controlling the execution of constraint logic programs. CLPGUI has been designed to be used in different contexts: initially for teaching purposes, then for debugging complex programs of real-world scale, and recently for developing end-user interfaces. The challenge of developing a tool which is generic w.r.t […]
Fri, Oct 1, 2004
Sun, Feb 1, 2004
We present a translation of the asynchronous pi-calculus into linear concurrent constraint languages (LCC), and use that translation and the recent advances in the logical semantics of LCC to give an account of the restriction operator in Intuitionistic Linear Logic. This allows us to express as a Linear Logic theory, a notion of space similar to what has recently been introduced by Gabbay and Pitts in modal logics. It also permits to relate more closely the pi-calculus and CC paradigms that people have wanted to compare for a long time […]
Mon, Dec 1, 2003
In this thesis, we study the close links between linear logic and on current constraint programming, from the angle of semantics and more precisely of program verification. We refine the observables that can be characterized in linear logic and extend existing results to obtain a more precise and more general semantics. These results are only based on a more faithful translationfrom agents into logic formulae and on an enrichment of the theory […]
Sun, Apr 1, 2001
In this paper we give a logical semantics for the class CC of concurrent constraint programming languages and for its extension LCC based on linear constraint systems. Besides the characterization in intuitionistic logic of the stores of CC computations, we show that both the stores and the successes of LCC computations can be characterized in intuitionistic linear logic. We illustrate the usefulness of these results by showing with examples how the phase semantics of linear logic can be used to give simple semantical" proofs of safety properties of LCC programs […]
Thu, Feb 1, 2001