Abstract Analysis of Universal Properties for tccp

[EN] The Timed Concurrent Constraint Language (tccp) is a time extension of the concurrent constraint paradigm of Saraswat. tccp was defined to model reactive systems, where infinite behaviors arise naturally. In previous works, a semantic framework and abstract diagnosis method for the language has been defined. On the basis of that semantic framework, this paper proposes an abstract semantics that, together with a widening operator, is suitable for the definition of different analyses for tccp programs. The abstract semantics is correct and can be represented as a finite graph where each node represents a hypothetical computational step of the program containing approximated information for the variables. The widening operator allows us to guarantee the convergence of the abstract fixpoint computation.This work has been supported by the Andalusian Excellence Project P11-TIC7659. This work has been partially supported by the EU (FEDER) and the Spanish MINECO under grant TIN 2013-45732-C4-1-P (DAMAS) and by Generalitat Valenciana PROMETEOII/2015/013Comini, M.; Gallardo Melgarejo, MDM.; Titolo, L.; Villanueva, A. (2015). Abstract Analysis of Universal Properties for tccp. Lecture Notes in Computer Science. 163-178. https://doi.org/10.1007/978-3-319-27436-2_10S163178Alpuente, M., Gallardo, M.M., Pimentel, E., Villanueva, A.: A semantic framework for the abstract model checking of tccp programs. Theor. Comput. Sci. 346(1), 58–95 (2005)Bagnara, R., Hill, P.M., Ricci, E., Zaffanella, E.: Precise widening operators for convex polyhedra. Sci Comput. Program. 58(1–2), 28–56 (2005)Comini, M., Titolo, L., Villanueva, A.: Abstract diagnosis for timed concurrent constraint programs. Theor. Pract. Log. Program. 11(4–5), 487–502 (2011)Comini, M., Titolo, L., Villanueva, A.: A condensed goal-independent bottom-up fixpoint modeling the behavior of tccp. Technical report, DSIC, Universitat Politècnica de València (2013). http://riunet.upv.es/handle/10251/34328Cousot, P., Cousot, R.: Abstract Interpretation: a unified lattice model for static analysis of programs by construction or approximation of fixpoints. In: Proceedings of the 4th ACM SIGACT-SIGPLAN Symposium on Principles of Programming Languages, Los Angeles, California, January 17–19, pp. 238–252. ACM Press, New York (1977)de Boer, F.S., Gabbrielli, M., Meo, M.C.: A timed concurrent constraint language. Inf. Comput. 161(1), 45–83 (2000)Falaschi, M. Gabbrielli, M., Marriott, K., Palamidessi, C.: Compositional analysis for concurrent constraint programming. In: Proceedings of the Eighth Annual IEEE Symposium on Logic in Computer Science, pp. 210–221. IEEE Computer Society Press, Los Alamitos (1993)Falaschi, M., Olarte, C., Palamidessi, C.: Abstract interpretation of temporal concurrent constraint programs. Theor. Pract. Log. Program. (TPLP) 15(3), 312–357 (2015)Falaschi, M., Villanueva, A.: Automatic verification of timed concurrent constraint programs. Theor. Pract. Log. Program. 6(3), 265–300 (2006)Saraswat, V.A.: Concurrent Constraint Programming. The MIT Press, Cambridge (1993)Zaffanella, E., Giacobazzi, R., Levi, G.: Abstracting synchronization in concurrent constraint programming. J. Funct. Log. Program. 6, 1997 (1997

Modelling concurrent systems specified in a temporal concurrent constraint language -I

In this paper we present an approach to model concurrent systems specified in a temporal concurrent constraint language. Our goal is to construct a framework in which it is possible to apply the Model Checking technique to programs specified in such language. This work is the first step to the framework construction. We present a formalism to transform a specification into a tcc Structure. This structure is a graph representation of the program behavior. Our basic tool is the Timed Concurrent Constraint Programming (tcc) framework defined by Saraswat et al. to describe reactive systems. With this language we take advantage of both the natural properties of the declarative paradigm and of the fact that the notion of time is built into the semantics of the programming language. In fact, on this ground it becomes reasonable to introduce the idea of applying the technique of Model Checking to a finite time interval (introduced by the user). With this restriction we naturally force the space representing the behavior of the program to be finite and hence Model Checking algorithms to be applicable. The graph construction is a completely automatic process that takes as input the tcc specification

Modeling and Analyzing Reaction Systems in Maude

Reaction Systems (RSs) are a successful computational framework for modeling systems inspired by biochemistry. An RS defines a set of rules (reactions) over a finite set of entities (e.g., molecules, proteins, genes, etc.). A computation in this system is performed by rewriting a finite set of entities (a computation state) using all the enabled reactions in the RS, thereby producing a new set of entities (a new computation state). The number of entities in the reactions and in the computation states can be large, making the analysis of RS behavior difficult without a proper automated support. In this paper, we use the Maude language—a programming language based on rewriting logic—to define a formal executable semantics for RSs, which can be used to precisely simulate the system behavior as well as to perform reachability analysis over the system computation space. Then, by enriching the proposed semantics, we formalize a forward slicer algorithm for RSs that allows us to observe the evolution of the system on both the initial input and a fragment of it (the slicing criterion), thus facilitating the detection of forward causality and influence relations due to the absence/presence of some entities in the slicing criterion. The pursued approach is illustrated by a biological reaction system that models a gene regulation network for controlling the process of differentiation of T helper lymphocytes

Modeling Concurrent systems specified in a Temporal Concurrent Constraint language-I

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A program analysis framework for tccp based on abstract interpretation

[EN] The timed concurrent constraint language (tccp) is a timed extension of the concurrent constraint paradigm. tccp was defined to model reactive systems, where infinite behaviors arise naturally. In previous works, a semantic framework and abstract diagnosis method for the language have been defined. On the basis of that semantic framework, this paper proposes an abstract semantics that, together with a widening operator, is suitable for the definition of different analyses for tccp programs. The abstract semantics is correct and can be represented as a finite graph where each node represents a hypothetical (abstract) computational step of the program. The widening operator allows us to guarantee the convergence of the abstract fixpoint computation.This author has been supported by the Andalusian Excellence Project P11-TIC-7659. This work has been partially supported by the EU (FEDER) and the Spanish MINECO under grants TIN 2015-69175-C4-1-R and TIN 2013-45732-C4-1-P and by Generalitat Valenciana PROMETEOII/2015/013Comini, M.; Gallardo, M.; Titolo, L.; Villanueva, A. (2017). A program analysis framework for tccp based on abstract interpretation. Formal Aspects of Computing. 29(3):531-557. https://doi.org/10.1007/s00165-016-0409-8S531557293Alpuente M, Gallardo MM, Pimentel E, Villanueva A (2006) A semantic framework for the abstract model checking of tccp programs. Theor Comput Scie 346(1): 58–95Bagnara R, Hill PM., Ricci E, Zaffanella E (2005) Precise widening operators for convex polyhedra. Sci Comput Program 58(1–2):28–56Cousot P, Cousot R (1977) Abstract interpretation: a unified lattice model for static analysis of programs by construction or approximation of fixpoints. In: Proceedings of the 4th ACM SIGACT-SIGPLAN symposium on principles of programming languages, Los Angeles, California, January 17–19. ACM Press, New York, pp 238–252Clarke EM, Grumberg O, Jha S, Lu Y, Veith H (2000) Counterexample-guided abstraction refinement. In: CAV, Lecture Notes in Computer Science, vol 1855. Springer, pp 154–169Comini M, Gallardo MM, Titolo L, Villanueva A (2015) Abstract Analysis of Universal Properties for tccp. In: Falaschi M (ed) Logic-based Program Synthesis and Transformation, 25th International Symposium, LOPSTR 2015. Revised Selected Papers, Lecture Notes in Computer Science, vol 9527. Springer, pp 163–178Comini M, Titolo L, Villanueva A (2011) Abstract diagnosis for timed concurrent constraint programs. Theory Pract Logic Programm 11(4-5):487–502Comini M, Titolo L, Villanueva A (2013) A condensed goal-independent bottom-up fixpoint modeling the behavior of tccp. Technical report, DSIC, Universitat Politècnica de València. http://riunet.upv.es/handle/10251/34328de Boer FS, Gabbrielli M, Meo MC (2000) A timed concurrent constraint language. Inf Comput 161(1): 45–83Falaschi M, Gabbrielli M, Marriott K, Palamidessi C (1993) Compositional analysis for concurrent constraint programming. In: Proceedings of the eighth annual IEEE symposium on logic in computer science, Los Alamitos, CA, USA, IEEE Computer Society Press, pp 210–221Falaschi M, Olarte C, Palamidessi C (2015) Abstract interpretation of temporal concurrent constraint programs. Theory and Pract Logic Program (TPLP) 15(3): 312–357Falaschi M, Villanueva A (2006) Automatic verification of timed concurrent constraint programs. Theory Pract Logic Program 6(3): 265–300Gallardo MM, Merino P, Pimentel E (2002) Refinement of LTL formulas for abstract model checking. In: Static analysis, 9th international symposium, SAS 2002, Madrid, Spain, September 17–20, 2002, Proceedings, pp 395–410Saraswat VA (1993) Concurrent constraint programming. The MIT Press, CambridgeSaraswat VA, Rinard M, Panangaden P (1991) The semantic foundations of concurrent constraint programming. In: Proceedings of the 18th ACM SIGPLAN-SIGACT symposium on principles of programming languages. ACM, New York, pp 333–352Zaffanella E, Giacobazzi R, Levi G (1997) Abstracting synchronization in concurrent constraint programming. J Funct Logic Program (6

Semantics of Input-Consuming Logic Programs

Input-consuming programs are logic programs with an additional restriction on the selectability (actually, on the resolvability) of atoms. this class of programs arguably allows to model logic programs employing a dynamic selection rule and constructs such as delay declarations: as shown also in [5], a large number of them are actually input-consuming. \ud in this paper we show that - under some syntactic restrictions - the tex2html_wrap_inline117-semantics of a program is correct and fully abstract also for input-consuming programs. this allows us to conclude that for a large class of programs employing delay declarations there exists a model-theoretic semantics which is equivalent to the operational one

Thirty years of invasion: the distribution of the invasive crayfish Procambarus clarkii in Italy

The presence of the red swamp crayfish Procambarus clarkii in Italy is documented since 1989, but no comprehensive data are available on its spread through time at the national scale. New confirmed records for Procambarus clarkii are continuously arising in recent years across the country. By reviewing the scientific and grey literature, we obtained an up-to-date map of the species invasion in Italy. This information can help to monitor and understand the spread of this highly invasive crayfish and to implement more effective management measures

Network-scale effects of invasive species on spatially-structured amphibian populations

Understanding the factors affecting the dynamics of spatially-structured populations (SSP) is a central topic of conservation and landscape ecology. Invasive alien species are increasingly important drivers of the dynamics of native species. However, the impacts of invasives are often assessed at the patch scale, while their effects on SSP dynamics are rarely considered. We used long-term abundance data to test whether the impact of invasive crayfish on subpopulations can also affect the whole SSP dynamics, through their influence on source populations. From 2010 to 2018, we surveyed a network of 58 ponds and recorded the abundance of Italian agile frog clutches, the occurrence of an invasive crayfish, and environmental features. Using Bayesian hierarchical models, we assessed relationhips between frog abundance in ponds and a) environmental features; b) connectivity within the SSP; c) occurrence of invasive species at both the patch- and the SSP-levels. If spatial relationships between ponds were overlooked, we did not detect effects of crayfish presence on frog abundance or trends. When we jointly considered habitat, subpopulation and SSP features, processes acting at all these levels affected frog abundance. At the subpopulation scale, frog abundance in a year was related to habitat features, but was unrelated to crayfish occurrence at that site during the previous year. However, when we considered the SSP level, we found a strong negative relationship between frog abundance in a given site and crayfish frequency in surrounding wetlands during the previous year. Hence, SSP-level analyses can identify effects that would remain unnoticed when focussing on single patches. Invasive species can affect population dynamics even in not invaded patches, through the degradation of subpopulation networks. Patch-scale assessments of the impact of invasive species can thus be insufficient: predicting the long-term interplay between invasive and native populations requires landscape-level approaches accounting for the complexity of spatial interactions

A Computational Model of the Secondary Hemostasis Pathway in Reaction Systems

Reaction Systems (RSs) are a computational framework inspired by biochemical mechanisms. An RS defines a finite set of reactions over a finite set of entities (molecules, proteins, etc). Starting from an initial set of entities (the initial state), a computation is performed by applying all reactions to a state in order to produce the following state, giving rise to a sequence of sets of entities. RSs have shown to be a general computational framework whose application ranges from the modeling of biological phenomena to molecular chemistry and computer science. In this paper, we contribute to research on the application of RSs for modeling biological systems. We consider the problem of modeling hemostasis, for which several models have been defined, starting from the 1960s. Previous models are based on sets of ordinary differential equations, while we develop a discrete model in RSs for pathways of the secondary hemostasis. Then, we implement our model in BioReSolve, a computational framework for RSs that we have previously defined which provides tools for the specification and verification of properties. By using the tools in BioReSolve we derive important observations on the model behaviour for hemostasis, and in particular, we study the role of three important inhibitors, verifying that their presence or absence leads to phenomena such as thrombophilia, or thromboembolism, or excessive coagulation, etc. We can also study computationally the causality relations between the molecules involved in the reactions showing which entities play a fundamental role, thus contributing to the design of more effective and specialized drugs. Our work can hence help to show how to model complex biological systems in RSs and derive computationally and biologically relevant properties of the systems

Quantitative extensions of reaction systems based on SOS semantics

Reaction systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reaction and are produced by reactions or provided by the environment. In this paper, we define two quantitative variants of RSs: the first one is along the time dimension, to specify delays for making available reactions products and durations to protract their permanency, while the second deals with the possibility to specify different concentration levels of a substance in order to enable or inhibit a reaction. Technically, both extensions are obtained by modifying in a modular way the Structural Operational Semantics (SOS) for RSs that was already defined in the literature. Our approach maintains several advantages of the original semantics definition that were: (1) providing a formal specification of the RS dynamics that enables the reuse of many formal analysis techniques and favours the implementation of tools, and (2) making the RS framework extensible, by adding or changing some of the SOS rules in a compositional way. We provide a prototype logic programming implementation and apply our tool to three different case studies: the tumour growth, the Th cell differentiation in the immune system and neural communication