A Logic Programming Approach to Reaction Systems

Reaction systems (RS) are a computational framework inspired by the functioning of living cells, suitable to model the main mechanisms of biochemical reactions. RS have shown to be useful also for computer science applications, e.g. to model circuits or transition systems. Since their introduction about 10 years ago, RS matured into a fruitful and dynamically evolving research area. They have become a popular novel model of interactive computation. RS can be seen as a rewriting system interacting with the environment represented by the context. RS pose some problems of implementation, as it is a relatively recent computation model, and several extensions of the basic model have been designed. In this paper we present some preliminary work on how to implement this formalism in a logic programming language (Prolog). To the best of our knowledge this is the first approach to RS in logic programming. Our prototypical implementation does not aim to be highly performing, but has the advantage of being high level and easily modifiable. So it is suitable as a rapid prototyping tool for implementing several extensions of reaction systems in the literature as well as new ones. We also make a preliminary implementation of a kind of memoization mechanism for stopping potentially infinite and repetitive computations. Then we show how to implement in our interpreter an extension of RS for modeling a nondeterministic context and interaction between components of a (biological) system. We then present an extension of the interpreter for implementing the recently introduced networks of RS

Abstract Interpretation of Temporal Concurrent Constraint Programs

International audienceTimed Concurrent Constraint Programming (tcc) is a declarative model for concurrency offering a logic for specifying reactive systems, i.e. systems that continuously interact with the environment. The universal tcc formalism (utcc) is an extension of tcc with the abil- ity to express mobility. Here mobility is understood as communication of private names as typically done for mobile systems and security protocols. In this paper we consider the denotational semantics for tcc, and we extend it to a "collecting" semantics for utcc based on closure operators over sequences of constraints. Relying on this semantics, we formalize a general framework for data flow analyses of tcc and utcc programs by abstract inter- pretation techniques. The concrete and abstract semantics we propose are compositional, thus allowing us to reduce the complexity of data flow analyses. We show that our method is sound and parametric with respect to the abstract domain. Thus, different analyses can be performed by instantiating the framework. We illustrate how it is possible to reuse abstract domains previously defined for logic programming to perform, for instance, a groundness analysis for tcc programs. We show the applicability of this analysis in the context of reactive systems. Furthermore, we make also use of the abstract semantics to exhibit a secrecy flaw in a security protocol. We also show how it is possible to make an analysis which may show that tcc programs are suspension free. This can be useful for several purposes, such as for optimizing compilation or for debugging

SOS Rules for Equivalences of Reaction Systems

Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by reactions. Entities can also be provided by an external context. RS semantics is defined in terms of an (unlabelled) rewrite system: given the current set of entities, a rewrite step consists of the application of all and only the enabled reactions. In this paper we define, for the first time, a labelled transition system for RSs in the structural operational semantics (SOS) style. This is achieved by distilling a signature whose operators directly correspond to the ingredients of RSs and by defining some simple SOS inference rules for any such operator to define the behaviour of the RS in a compositional way. The rich information recorded in the labels allows us to define an assertion language to tailor behavioural equivalences on some specific properties or entities. The SOS approach is suited to drive additional enhancements of RSs along features such as quantitative measurements of entities and communication between RSs. The SOS rules have been also exploited to design a prototype implementation in logic programming.Comment: Part of WFLP 2020 pre-proceeding

Derivation of Constraints from Machine Learning Models and Applications to Security and Privacy

This paper shows how we can combine the power of machine learning with the flexibility of constraints. More specifically, we show how machine learning models can be represented by first-order logic theories, and how to derive these theories. The advantage of this representation is that it can be augmented with additional formulae, representing constraints of some kind on the data domain. For instance, new knowledge, or potential attackers, or fairness desiderata. We consider various kinds of learning algorithms (neural networks, k-nearest-neighbours, decision trees, support vector machines) and for each of them we show how to infer the FOL formulae. Then we focus on one particular application domain, namely the field of security and privacy. The idea is to represent the potentialities and goals of the attacker as a set of constraints, then use a constraint solver (more precisely, a solver modulo theories) to verify the satisfiability. If a solution exists, then it means that an attack is possible, otherwise, the system is safe. We show various examples from different areas of security and privacy; specifically, we consider a side-channel attack on a password checker, a malware attack on smart health systems, and a model-inversion attack on a neural network

Compositional modelling of signalling pathways in timed concurrent constraint programming

International audienceThe biological data regarding the signalling pathways often consider single pathways or a small number of them. We propose a methodology for composing this kind of data in a coherent framework, in order to be able to investigate a bigger number of signalling pathways. We specify a biological system by means of a set of stoichiometric-like equations resembling the essential features of molecular interactions. We represent these equations by a timed concurrent constraint (ntcc) language, which can deal with partial information and the time for a reaction to occur. We describe a freely available prototypical implementation of our framework

Verification of Spatial and Temporal Modalities in Biochemical Systems

AbstractBiochemical systems such as metabolic and signaling pathways tend to be arranged in a physical space: the product of one reaction must be in the right place to become the reactant for the subsequent reaction in the pathway. Moreover, in some cases, the behavior of the systems can depend on both, the location of the reactants as well as on the time needed for the reaction to occur. We address the problem of specifying and verifying properties of biochemical systems that exhibit both temporal and spatial modalities at the same time. For that, we use as specification language a fragment of intuitionistic linear logic with subexponentials (SELL). The subexponential signature allows us to capture the spatial relations among the different components of the system and the timed constraints for reactions to occur. We show that our framework is general enough to give a declarative semantics to P-Systems and we show that such logical characterization has a strong level of adequacy. Hence, derivations in SELL follow exactly the behavior of the modeled system

On Unfolding Completeness for Rewriting Logic Theories

Many transformation systems for program optimization, program synthesis, and program specialization are based on fold/unfold transformations. In this paper, we investigate the semantic properties of a narrowing-based unfolding transformation that is useful to transform rewriting logic theories. We also present a transformation methodology that is able to determine whether an unfolding transformation step would cause incompleteness and avoid this problem by completing the transformed rewrite theory with suitable extra rules. More precisely, our methodology identifies the sources of incompleteness and derives a set of rules that are added to the transformed rewrite theory in order to preserve the semantics of the original theory.Alpuente Frasnedo, M.; Baggi, M.; Ballis, D.; Falaschi, M. (2010). On Unfolding Completeness for Rewriting Logic Theories. http://hdl.handle.net/10251/863