Causal analysis of positive Reaction Systems
Authors: 
Linda Brodo, Roberto Bruni, Moreno Falaschi, Roberta Gori, Paolo Milazzo, Valeria Montagna, Pasquale PulieriAuthors Info & Claims
Linda Brodo, Roberto Bruni, Moreno Falaschi, Roberta Gori, Paolo Milazzo, Valeria Montagna, Pasquale PulieriAuthors Info & ClaimsPages 509 - 526
Abstract
Cause/effect analysis of complex systems is instrumental in better understanding many natural phenomena. Moreover, formal analysis requires the availability of suitable abstract computational models that somehow preserve the features of interest. Our contribution focuses on the analysis of Reaction Systems (RSs), a qualitative computational formalism inspired by biochemical reactions in living cells. The primary challenge lies in dealing with inhibition mechanisms. On the one hand, inhibitors enhance the expressiveness of the computational abstraction; on the other hand, they can introduce nonmonotonic behaviors that can be computationally hard to deal with in the analysis. We propose an encoding of RSs into an equivalent formulation without inhibitors (called Positive RSs, PRSs for short) that is easier to handle, because PRSs exhibit monotonic behaviors. The effectiveness of our transformation is witnessed by its impact on two different techniques for cause/effect analysis. The first, called slicing, allows detecting the causes of some unforeseen phenomenon by reasoning backward along a given computation. Here, PRSs can be exploited to improve the quality of the analysis. The second technique, predictor analysis, is addressed by introducing a novel tool called MuMa, which is based on must/maybe sets, whence the tool name, an original abstraction for approximating ancestor formulas. MuMa exploits PRSs to improve the performance of the analysis.
References
[1]
Alpuente M., Ballis D., Espert J., and Romero D. Backward trace slicing for rewriting logic theories Proc. of CADE’11 2011 Berlin Springer 34-48
[2]
Alpuente M., Ballis D., Frechina F., and Romero D. Using conditional trace slicing for improving Maude programs Sci. Comput. Program. 2014 80 385-415
[3]
Alpuente M., Ballis D., Frechina F., and Sapiña J. Debugging Maude programs via runtime assertion checking and trace slicing J. Log. Algebraic Methods Program. 2016 85 707-736
[4]
Azimi S. Steady states of constrained Reaction Systems Theor. Comput. Sci. 2017 701 C 20-26
[5]
Azimi S., Iancu B., and Petre I. Reaction System models for the heat shock response Fundam. Inform. 2014 131 3–4 299-312
[6]
Barbuti R., Gori R., Levi F., and Milazzo P. Investigating dynamic causalities in Reaction Systems Theor. Comput. Sci. 2016 623 114-145
[7]
Barbuti R., Bernasconi A., Gori R., and Milazzo P. Computing preimages and ancestors in Reaction Systems Proc. of TPNC 2018 2018 Berlin Springer 23-35
[8]
Barbuti R., Gori R., Levi F., and Milazzo P. Generalized contexts for Reaction Systems: definition and study of dynamic causalities Acta Inform. 2018 55 3 227-267
[9]
Barbuti R., Gori R., Milazzo P., and Nasti L. A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models J. Membr. Comput. 2020 2 207-226
[10]
Barbuti R., Bernasconi A., Gori R., and Milazzo P. Characterization and computation of ancestors in Reaction Systems Soft Comput. 2021 25 3 1683-1698
[11]
Barbuti R., Gori R., and Milazzo P. Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation Theor. Comput. Sci. 2021 881 3-24
[12]
Bodei C., Gori R., and Levi F. Causal static analysis for Brane Calculi Theor. Comput. Sci. 2015 587 73-103
[13]
Brijder, R., Ehrenfeucht, A., Rozenberg, G.: A note on causalities in Reaction Systems. ECEASST 30 (2010)
[14]
Brijder R., Ehrenfeucht A., Main M.G., and Rozenberg G. A tour of Reaction Systems Int. J. Found. Comput. Sci. 2011 22 7 1499-1517
[15]
Brodo L., Bruni R., and Falaschi M. Alvim M., Chatzikokolakis K., Olarte C., and Valencia F. Enhancing reaction systems: a process algebraic approach The Art of Modelling Computational Systems 2019 Berlin Springer 68-85
[16]
Brodo L., Bruni R., and Falaschi M. A logical and graphical framework for Reaction Systems Theor. Comput. Sci. 2021 875 1-27
[17]
Brodo L., Bruni R., Falaschi M., Gori R., Levi F., and Milazzo P. Exploiting modularity of SOS semantics to define quantitative extensions of Reaction Systems Proc. of TPNC 2021 2021 Berlin Springer 15-32
[18]
Brodo L., Bruni R., and Falaschi M. Dynamic slicing of Reaction Systems based on assertions and monitors Proc. of PADL 2023 2023 Berlin Springer 107-124
[19]
Brodo, L., Bruni, R., Falaschi, M., Gori, R., Milazzo, P.: Attractor and slicing analysis of a T Cell differentiation model based on reaction systems Proceedings of DataMod 2023 Springer, Berlin, LNCS. (In press)
[20]
Busi N. Causality in membrane systems Proc. of WMC 2007 2007 160-171
[21]
CellCollective Org: CD4+ T cell differentiation model webpage on the CellCollective platform (2018). https://cellcollective.org/#module/2901:1/t-cell-differentiation/1. Last accessed: 18 Sept. 2023
[22]
Corolli L., Maj C., Marinia F., Besozzi D., and Mauri G. An excursion in Reaction Systems: from computer science to biology Theor. Comput. Sci. 2012 454 95-108
[23]
Cousot P. Principles of Abstract Interpretation 2021 Cambridge MIT Press
[24]
Cousot P. and Cousot R. Abstract interpretation: a unified lattice model for static analysis of programs by construction or approximation of fixpoints Proc. of POPL 1977 1977 New York ACM Press 238-252
[25]
Cousot P. and Cousot R. Systematic design of program analysis frameworks Proc. of POPL 1979 1979 New York ACM Press 269-282
[26]
Deng C. and Cousot P. The systematic design of responsibility analysis by abstract interpretation ACM Trans. Program. Lang. Syst. 2022 44 1 3:1-3:90
[27]
Dennunzio A., Formenti E., Manzoni L., and Porreca A.E. Ancestors, descendants, and gardens of Eden in Reaction Systems Theor. Comput. Sci. 2015 608 16-26
[28]
Dennunzio A., Formenti E., Manzoni L., and Porreca A.E. Dediu A., Formenti E., Martín-Vide C., and Truthe B. Preimage problems for Reaction Systems Proc. of LATA 2015 2015 Berlin Springer 537-548
[29]
Ehrenfeucht A. and Rozenberg G. Reaction Systems Fundam. Inform. 2007 75 1–4 263-280 http://content.iospress.com/articles/fundamenta-informaticae/fi75-1-4-15
[30]
Falaschi M., Gabbrielli M., Olarte C., and Palamidessi C. Dynamic slicing for concurrent constraint languages Fundam. Inform. 2020 177 3–4 331-357
[31]
Formenti E., Manzoni L., and Porreca A.E. Fixed points and attractors of Reaction Systems Proc. of CiE 2014 2014 Berlin Springer 194-203
[32]
Gori R. and Levi F. Abstract interpretation based verification of temporal properties for BioAmbients Inf. Comput. 2010 208 8 869-921
[33]
Korel B. and Laski J. Dynamic program slicing Inf. Process. Lett. 1988 29 3 155-163
[34]
Mendoza, L., Xenarios, I.: A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor. Biol. Med. Model. 3(13) (2006).
[35]
Ochoa C., Silva J., and Vidal G. Dynamic slicing of lazy functional programs based on redex trails High.-Order Symb. Comput. 2008 21 1–2 147-192
[36]
Okubo F. and Yokomori T. The computational capability of chemical reaction automata Nat. Comput. 2016 15 2 215-224
[37]
Salomaa A. Functional constructions between Reaction Systems and propositional logic Int. J. Found. Comput. Sci. 2013 24 1 147-160
[38]
Salomaa A. Minimal and almost minimal Reaction Systems Nat. Comput. 2013 12 3 369-376
[39]
Silva J. A vocabulary of program slicing-based techniques ACM Comput. Surv. 2012 44 3 12:1-12:41
[40]
Weiser M. Program slicing IEEE Trans. Softw. Eng. 1984 10 4 352-357
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Publication History
Published: 19 June 2024
Accepted: 04 June 2024
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