Two Decades of Maude

This paper is a tribute to José Meseguer, from the rest of us in the Maude team, reviewing the past, the present, and the future of the language and system with which we have been working for around two decades under his leadership. After reviewing the origins and the language's main features, we present the latest additions to the language and some features currently under development. This paper is not an introduction to Maude, and some familiarity with it and with rewriting logic are indeed assumed.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Improving the efficiency of AC matching and unification

This report consists of three independent parts that each study important steps in the matching and unification process for AC theories. In the first part we consider the problem of AC matching where there is just a single (variadic) AC symbol and no free function symbols in the pattern and subject. We show that even this restricted problem is NP-complete. We give some search methods and empirical results. In the second part we consider the full AC matching problem where there is no restriction on AC and free functions symbols allowed in the pattern and subject. Our approach is to build a hierarchy of bipartite graph matching problems which encodes all the possible solutions of subproblems. Certain sets of solutions to the graph problems are then used to construct simplified AC systems which are solved by a constrained search. In the final part we focus on one of the computationally intensive steps in current AC unification algorithms : the extraction of potential unifiers from a diophantine basis. We show that certain sub-problems are NP-complete and derive a new search algorithm which is shown to be at worst equivalent to the best published algorithm and which is potentially much better

Built-in Variant Generation and Unification, and Their Applications in Maude 2.7

This paper introduces some novel features of Maude 2.7. We have added support for: (i) built-in order-sorted unification modulo associativity, commutativity, and identity, (ii) built-in variant generation, (iii) built-in order-sorted unification modulo a finite variant theory, and (iv) symbolic reachability modulo a finite variant theory.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Programming and symbolic computation in Maude

[EN] Rewriting logic is both a flexible semantic framework within which widely different concurrent systems can be naturally specified and a logical framework in which widely different logics can be specified. Maude programs are exactly rewrite theories. Maude has also a formal environment of verification tools. Symbolic computation is a powerful technique for reasoning about the correctness of concurrent systems and for increasing the power of formal tools. We present several new symbolic features of Maude that enhance formal reasoning about Maude programs and the effectiveness of formal tools. They include: (i) very general unification modulo user-definable equational theories, and (ii) symbolic reachability analysis of concurrent systems using narrowing. The paper does not focus just on symbolic features: it also describes several other new Maude features, including: (iii) Maude's strategy language for controlling rewriting, and (iv) external objects that allow flexible interaction of Maude object-based concurrent systems with the external world. In particular, meta-interpreters are external objects encapsulating Maude interpreters that can interact with many other objects. To make the paper self-contained and give a reasonably complete language overview, we also review the basic Maude features for equational rewriting and rewriting with rules, Maude programming of concurrent object systems, and reflection. Furthermore, we include many examples illustrating all the Maude notions and features described in the paper.Duran has been partially supported by MINECO/FEDER project TIN2014-52034-R. Escobar has been partially supported by the EU (FEDER) and the MCIU under grant RTI2018-094403-B-C32, by the Spanish Generalitat Valenciana under grant PROMETE0/2019/098, and by the US Air Force Office of Scientific Research under award number FA9550-17-1-0286. MartiOliet and Rubio have been partially supported by MCIU Spanish project TRACES (TIN2015-67522-C3-3-R). Rubio has also been partially supported by a MCIU grant FPU17/02319. Meseguer and Talcott have been partially supported by NRL Grant N00173 -17-1-G002. Talcott has also been partially supported by ONR Grant N00014-15-1-2202.Durán, F.; Eker, S.; Escobar Román, S.; NARCISO MARTÍ OLIET; José Meseguer; Rubén Rubio; Talcott, C. (2020). Programming and symbolic computation in Maude. Journal of Logical and Algebraic Methods in Programming. 110:1-58. https://doi.org/10.1016/j.jlamp.2019.100497S158110Alpuente, M., Escobar, S., Espert, J., & Meseguer, J. (2014). A modular order-sorted equational generalization algorithm. Information and Computation, 235, 98-136. doi:10.1016/j.ic.2014.01.006K. Bae, J. Meseguer, Predicate abstraction of rewrite theories, in: [36], 2014, pp. 61–76.Bae, K., & Meseguer, J. (2015). Model checking linear temporal logic of rewriting formulas under localized fairness. Science of Computer Programming, 99, 193-234. doi:10.1016/j.scico.2014.02.006Bae, K., Meseguer, J., & Ölveczky, P. C. (2014). Formal patterns for multirate distributed real-time systems. Science of Computer Programming, 91, 3-44. doi:10.1016/j.scico.2013.09.010P. Borovanský, C. Kirchner, H. Kirchner, P.E. Moreau, C. Ringeissen, An overview of ELAN, in: [77], 1998, pp. 55–70.Bouhoula, A., Jouannaud, J.-P., & Meseguer, J. (2000). Specification and proof in membership equational logic. Theoretical Computer Science, 236(1-2), 35-132. doi:10.1016/s0304-3975(99)00206-6Bravenboer, M., Kalleberg, K. T., Vermaas, R., & Visser, E. (2008). Stratego/XT 0.17. A language and toolset for program transformation. Science of Computer Programming, 72(1-2), 52-70. doi:10.1016/j.scico.2007.11.003Bruni, R., & Meseguer, J. (2006). Semantic foundations for generalized rewrite theories. Theoretical Computer Science, 360(1-3), 386-414. doi:10.1016/j.tcs.2006.04.012M. Clavel, F. Durán, S. Eker, S. Escobar, P. Lincoln, N. Martí-Oliet, C.L. Talcott, Two decades of Maude, in: [86], 2015, pp. 232–254.Clavel, M., Durán, F., Eker, S., Lincoln, P., Martı́-Oliet, N., Meseguer, J., & Quesada, J. F. (2002). Maude: specification and programming in rewriting logic. Theoretical Computer Science, 285(2), 187-243. doi:10.1016/s0304-3975(01)00359-0Clavel, M., & Meseguer, J. (2002). Reflection in conditional rewriting logic. Theoretical Computer Science, 285(2), 245-288. doi:10.1016/s0304-3975(01)00360-7F. Durán, S. Eker, S. Escobar, N. Martí-Oliet, J. Meseguer, C.L. Talcott, Associative unification and symbolic reasoning modulo associativity in Maude, in: [121], 2018, pp. 98–114.Durán, F., Lucas, S., Marché, C., Meseguer, J., & Urbain, X. (2008). Proving operational termination of membership equational programs. Higher-Order and Symbolic Computation, 21(1-2), 59-88. doi:10.1007/s10990-008-9028-2F. Durán, J. Meseguer, An extensible module algebra for Maude, in: [77], 1998, pp. 174–195.Durán, F., & Meseguer, J. (2003). Structured theories and institutions. Theoretical Computer Science, 309(1-3), 357-380. doi:10.1016/s0304-3975(03)00312-8Durán, F., & Meseguer, J. (2007). Maude’s module algebra. Science of Computer Programming, 66(2), 125-153. doi:10.1016/j.scico.2006.07.002Durán, F., & Meseguer, J. (2012). On the Church-Rosser and coherence properties of conditional order-sorted rewrite theories. The Journal of Logic and Algebraic Programming, 81(7-8), 816-850. doi:10.1016/j.jlap.2011.12.004F. Durán, P.C. Ölveczky, A guide to extending Full Maude illustrated with the implementation of Real-Time Maude, in: [116], 2009, pp. 83–102.S. Escobar, Multi-paradigm programming in Maude, in: [121], 2018, pp. 26–44.Escobar, S., Meadows, C., Meseguer, J., & Santiago, S. (2014). State space reduction in the Maude-NRL Protocol Analyzer. Information and Computation, 238, 157-186. doi:10.1016/j.ic.2014.07.007Escobar, S., Sasse, R., & Meseguer, J. (2012). Folding variant narrowing and optimal variant termination. The Journal of Logic and Algebraic Programming, 81(7-8), 898-928. doi:10.1016/j.jlap.2012.01.002H. Garavel, M. Tabikh, I. Arrada, Benchmarking implementations of term rewriting and pattern matching in algebraic, functional, and object-oriented languages – the 4th rewrite engines competition, in: [121], 2018, pp. 1–25.Goguen, J. A., & Burstall, R. M. (1992). Institutions: abstract model theory for specification and programming. Journal of the ACM, 39(1), 95-146. doi:10.1145/147508.147524Goguen, J. A., & Meseguer, J. (1984). Equality, types, modules, and (why not?) generics for logic programming. The Journal of Logic Programming, 1(2), 179-210. doi:10.1016/0743-1066(84)90004-9Goguen, J. A., & Meseguer, J. (1992). Order-sorted algebra I: equational deduction for multiple inheritance, overloading, exceptions and partial operations. Theoretical Computer Science, 105(2), 217-273. doi:10.1016/0304-3975(92)90302-vR. Gutiérrez, J. Meseguer, Variant-based decidable satisfiability in initial algebras with predicates, in: [61], 2018, pp. 306–322.Gutiérrez, R., Meseguer, J., & Rocha, C. (2015). Order-sorted equality enrichments modulo axioms. Science of Computer Programming, 99, 235-261. doi:10.1016/j.scico.2014.07.003Horn, A. (1951). On sentences which are true of direct unions of algebras. Journal of Symbolic Logic, 16(1), 14-21. doi:10.2307/2268661Katelman, M., Keller, S., & Meseguer, J. (2012). Rewriting semantics of production rule sets. The Journal of Logic and Algebraic Programming, 81(7-8), 929-956. doi:10.1016/j.jlap.2012.06.002Kowalski, R. (1979). Algorithm = logic + control. Communications of the ACM, 22(7), 424-436. doi:10.1145/359131.359136Lucanu, D., Rusu, V., & Arusoaie, A. (2017). A generic framework for symbolic execution: A coinductive approach. Journal of Symbolic Computation, 80, 125-163. doi:10.1016/j.jsc.2016.07.012D. Lucanu, V. Rusu, A. Arusoaie, D. Nowak, Verifying reachability-logic properties on rewriting-logic specifications, in: [86], 2015, pp. 451–474.Lucas, S., & Meseguer, J. (2016). Normal forms and normal theories in conditional rewriting. Journal of Logical and Algebraic Methods in Programming, 85(1), 67-97. doi:10.1016/j.jlamp.2015.06.001N. Martí-Oliet, J. Meseguer, A. Verdejo, A rewriting semantics for Maude strategies, in: [116], 2009, pp. 227–247.Martí-Oliet, N., Palomino, M., & Verdejo, A. (2007). Strategies and simulations in a semantic framework. Journal of Algorithms, 62(3-4), 95-116. doi:10.1016/j.jalgor.2007.04.002Meseguer, J. (1992). Conditional rewriting logic as a unified model of concurrency. Theoretical Computer Science, 96(1), 73-155. doi:10.1016/0304-3975(92)90182-fMeseguer, J. (2012). Twenty years of rewriting logic. The Journal of Logic and Algebraic Programming, 81(7-8), 721-781. doi:10.1016/j.jlap.2012.06.003Meseguer, J. (2017). Strict coherence of conditional rewriting modulo axioms. Theoretical Computer Science, 672, 1-35. doi:10.1016/j.tcs.2016.12.026J. Meseguer, Generalized rewrite theories and coherence completion, in: [121], 2018, pp. 164–183.Meseguer, J. (2018). Variant-based satisfiability in initial algebras. Science of Computer Programming, 154, 3-41. doi:10.1016/j.scico.2017.09.001Meseguer, J., Goguen, J. A., & Smolka, G. (1989). Order-sorted unification. Journal of Symbolic Computation, 8(4), 383-413. doi:10.1016/s0747-7171(89)80036-7Meseguer, J., & Ölveczky, P. C. (2012). Formalization and correctness of the PALS architectural pattern for distributed real-time systems. Theoretical Computer Science, 451, 1-37. doi:10.1016/j.tcs.2012.05.040Meseguer, J., Palomino, M., & Martí-Oliet, N. (2008). Equational abstractions. Theoretical Computer Science, 403(2-3), 239-264. doi:10.1016/j.tcs.2008.04.040Meseguer, J., & Roşu, G. (2007). The rewriting logic semantics project. Theoretical Computer Science, 373(3), 213-237. doi:10.1016/j.tcs.2006.12.018Meseguer, J., & Roşu, G. (2013). The rewriting logic semantics project: A progress report. Information and Computation, 231, 38-69. doi:10.1016/j.ic.2013.08.004Meseguer, J., & Skeirik, S. (2017). Equational formulas and pattern operations in initial order-sorted algebras. Formal Aspects of Computing, 29(3), 423-452. doi:10.1007/s00165-017-0415-5Meseguer, J., & Thati, P. (2007). Symbolic reachability analysis using narrowing and its application to verification of cryptographic protocols. Higher-Order and Symbolic Computation, 20(1-2), 123-160. doi:10.1007/s10990-007-9000-6C. Olarte, E. Pimentel, C. Rocha, Proving structural properties of sequent systems in rewriting logic, in: [121], 2018, pp. 115–135.Ölveczky, P. C., & Meseguer, J. (2007). Semantics and pragmatics of Real-Time Maude. Higher-Order and Symbolic Computation, 20(1-2), 161-196. doi:10.1007/s10990-007-9001-5Ölveczky, P. C., & Thorvaldsen, S. (2009). Formal modeling, performance estimation, and model checking of wireless sensor network algorithms in Real-Time Maude. Theoretical Computer Science, 410(2-3), 254-280. doi:10.1016/j.tcs.2008.09.022Rocha, C., Meseguer, J., & Muñoz, C. (2017). Rewriting modulo SMT and open system analysis. Journal of Logical and Algebraic Methods in Programming, 86(1), 269-297. doi:10.1016/j.jlamp.2016.10.001Şerbănuţă, T. F., Roşu, G., & Meseguer, J. (2009). A rewriting logic approach to operational semantics. Information and Computation, 207(2), 305-340. doi:10.1016/j.ic.2008.03.026Skeirik, S., & Meseguer, J. (2018). Metalevel algorithms for variant satisfiability. Journal of Logical and Algebraic Methods in Programming, 96, 81-110. doi:10.1016/j.jlamp.2017.12.006S. Skeirik, A. Ştefănescu, J. Meseguer, A constructor-based reachability logic for rewrite theories, in: [61], 2018, pp. 201–217.Strachey, C. (2000). Higher-Order and Symbolic Computation, 13(1/2), 11-49. doi:10.1023/a:1010000313106A. Ştefănescu, S. Ciobâcă, R. Mereuta, B.M. Moore, T. Serbanuta, G. Roşu, All-path reachability logic, in: [36], 2014, pp. 425–440.Tushkanova, E., Giorgetti, A., Ringeissen, C., & Kouchnarenko, O. (2015). A rule-based system for automatic decidability and combinability. Science of Computer Programming, 99, 3-23. doi:10.1016/j.scico.2014.02.00

Extensional and Intensional Strategies

This paper is a contribution to the theoretical foundations of strategies. We first present a general definition of abstract strategies which is extensional in the sense that a strategy is defined explicitly as a set of derivations of an abstract reduction system. We then move to a more intensional definition supporting the abstract view but more operational in the sense that it describes a means for determining such a set. We characterize the class of extensional strategies that can be defined intensionally. We also give some hints towards a logical characterization of intensional strategies and propose a few challenging perspectives

Basic completion strategies as another application of the Maude strategy language

The two levels of data and actions on those data provided by the separation between equations and rules in rewriting logic are completed by a third level of strategies to control the application of those actions. This level is implemented on top of Maude as a strategy language, which has been successfully used in a wide range of applications. First we summarize the Maude strategy language design and review some of its applications; then, we describe a new case study, namely the description of completion procedures as transition rules + control, as proposed by Lescanne.Comment: In Proceedings WRS 2011, arXiv:1204.531

Nationwide oncological networks for resection of colorectal liver metastases in the Netherlands:Differences and postoperative outcomes

INTRODUCTION: Widespread differences in patient demographics and disease burden between hospitals for resection of colorectal liver metastases (CRLM) have been described. In the Netherlands, networks consisting of at least one tertiary referral centre and several regional hospitals have been established to optimize treatment and outcomes. The aim of this study was to assess variation in case-mix, and outcomes between these networks. METHODS: This was a population-based study including all patients who underwent CRLM resection in the Netherlands between 2014 and 2019. Variation in case-mix and outcomes between seven networks covering the whole country was evaluated. Differences in case-mix, expected 30-day major morbidity (Clavien-Dindo ≥3a) and 30-day mortality between networks were assessed. RESULTS: In total 5383 patients were included. Thirty-day major morbidity was 5.7% and 30-day mortality was 1.5%. Significant differences between networks were observed for Charlson Comorbidity Index, ASA 3+, previous liver resection, liver disease, preoperative MRI, preoperative chemotherapy, ≥3 CRLM, diameter of largest CRLM ≥55 mm, major resection, combined resection and ablation, rectal primary tumour, bilobar and extrahepatic disease. Uncorrected 30-day major morbidity ranged between 3.3% and 13.1% for hospitals, 30-day mortality ranged between 0.0% and 4.5%. Uncorrected 30-day major morbidity ranged between 4.4% and 6.0% for networks, 30-day mortality ranged between 0.0% and 2.5%. No negative outliers were observed after case-mix correction. CONCLUSION: Variation in case-mix and outcomes are considerably smaller on a network level as compared to a hospital level. Therefore, auditing is more meaningful at a network level and collaboration of hospitals within networks should be pursued

Case-mix adjustment to compare nationwide hospital performances after resection of colorectal liver metastases

Background: Differences in patient demographics and disease burden can influence comparison of hospital performances. This study aimed to provide a case-mix model to compare short-term postoperative outcomes for patients undergoing liver resection for colorectal liver metastases (CRLM). Methods: This retrospective, population-based study included all patients who underwent liver resection for CRLM between 2014 and 2018 in the Netherlands. Variation in case-mix variables between hospitals and influence on postoperative outcomes was assessed using multivariable logistic regression. Primary outcomes were 30-day major morbidity and 30-day mortality. Validation of results was performed on the data from 2019. Results: In total, 4639 patients were included in 28 hospitals. Major morbidity was 6.2% and mortality was 1.4%. Uncorrected major morbidity ranged from 3.3% to 13.7% and mortality ranged from 0.0% to 5.0%. between hospitals. Significant differences between hospitals were observed for age higher than 80 (0.0%-17.1%, p <0.001), ASA 3 or higher (3.3%-36.3%, p <0.001), histopathological parenchymal liver disease (0.0%-47.1%, p <0.001), history of liver resection (8.1%-36.3%, p <0.001), major liver resection (6.7%-38.0%, p <0.001) and synchronous metastases (35.5%-62.1%, p <0.001). Expected 30-day major morbidity between hospitals ranged from 6.4% to 11.9% and expected 30-day mortality ranged from 0.6% to 2.9%. After case-mix correction no significant outliers concerning major morbidity and mortality remained. Validation on patients who underwent liver resection for CRLM in 2019 affirmed these outcomes. Conclusion: Case-mix adjustment is a prerequisite to allow for institutional comparison of short-term postoperative outcomes after liver resection for CRLM. (C) 2020 University Medical Center Groningen. Published by Elsevier Ltd

Early indicators of exposure to biological threat agents using host gene profiles in peripheral blood mononuclear cells

<p>Abstract</p> <p>Background</p> <p>Effective prophylaxis and treatment for infections caused by biological threat agents (BTA) rely upon early diagnosis and rapid initiation of therapy. Most methods for identifying pathogens in body fluids and tissues require that the pathogen proliferate to detectable and dangerous levels, thereby delaying diagnosis and treatment, especially during the prelatent stages when symptoms for most BTA are indistinguishable flu-like signs.</p> <p>Methods</p> <p>To detect exposures to the various pathogens more rapidly, especially during these early stages, we evaluated a suite of host responses to biological threat agents using global gene expression profiling on complementary DNA arrays.</p> <p>Results</p> <p>We found that certain gene expression patterns were unique to each pathogen and that other gene changes occurred in response to multiple agents, perhaps relating to the eventual course of illness. Nonhuman primates were exposed to some pathogens and the <it>in vitro</it> and <it>in vivo</it> findings were compared. We found major gene expression changes at the earliest times tested post exposure to aerosolized <it>B. anthracis </it>spores and 30 min post exposure to a bacterial toxin.</p> <p>Conclusion</p> <p>Host gene expression patterns have the potential to serve as diagnostic markers or predict the course of impending illness and may lead to new stage-appropriate therapeutic strategies to ameliorate the devastating effects of exposure to biothreat agents.</p