Propositional Dynamic Logic with Converse and Repeat for Message-Passing Systems

The model checking problem for propositional dynamic logic (PDL) over message sequence charts (MSCs) and communicating finite state machines (CFMs) asks, given a channel bound $B$, a PDL formula $\varphi$ and a CFM $\mathcal{C}$, whether every existentially $B$-bounded MSC $M$ accepted by $\mathcal{C}$ satisfies $\varphi$. Recently, it was shown that this problem is PSPACE-complete. In the present work, we consider CRPDL over MSCs which is PDL equipped with the operators converse and repeat. The former enables one to walk back and forth within an MSC using a single path expression whereas the latter allows to express that a path expression can be repeated infinitely often. To solve the model checking problem for this logic, we define message sequence chart automata (MSCAs) which are multi-way alternating parity automata walking on MSCs. By exploiting a new concept called concatenation states, we are able to inductively construct, for every CRPDL formula $\varphi$, an MSCA precisely accepting the set of models of $\varphi$. As a result, we obtain that the model checking problem for CRPDL and CFMs is still in PSPACE

Unification in the Description Logic EL

The Description Logic EL has recently drawn considerable attention since, on the one hand, important inference problems such as the subsumption problem are polynomial. On the other hand, EL is used to define large biomedical ontologies. Unification in Description Logics has been proposed as a novel inference service that can, for example, be used to detect redundancies in ontologies. The main result of this paper is that unification in EL is decidable. More precisely, EL-unification is NP-complete, and thus has the same complexity as EL-matching. We also show that, w.r.t. the unification type, EL is less well-behaved: it is of type zero, which in particular implies that there are unification problems that have no finite complete set of unifiers.Comment: 31page

An Optimizing Protocol Transformation for Constructor Finite Variant Theories in Maude-NPA

[EN] Maude-NPA is an analysis tool for cryptographic security protocols that takes into account the algebraic properties of the cryptosystem. Maude-NPA can reason about a wide range of cryptographic properties. However, some algebraic properties, and protocols using them, have been beyond Maude-NPA capabilities, either because the cryptographic properties cannot be expressed using its equational unification features or because the state space is unmanageable. In this paper, we provide a protocol transformation that can safely get rid of cryptographic properties under some conditions. The time and space difference between verifying the protocol with all the crypto properties and verifying the protocol with a minimal set of the crypto properties is remarkable. We also provide, for the first time, an encoding of the theory of bilinear pairing into Maude-NPA that goes beyond the encoding of bilinear pairing available in the Tamarin toolPartially supported by the EU (FEDER) and the Spanish MCIU under grant RTI2018-094403-B-C32, by the Spanish Generalitat Valenciana under grant PROMETEO/2019/098, and by the US Air Force Office of Scientific Research under award number FA9550-17-1-0286. Julia Sapiña has been supported by the Generalitat Valenciana APOSTD/2019/127 grantAparicio-Sánchez, D.; Escobar Román, S.; Gutiérrez Gil, R.; Sapiña-Sanchis, J. (2020). An Optimizing Protocol Transformation for Constructor Finite Variant Theories in Maude-NPA. Springer Nature. 230-250. https://doi.org/10.1007/978-3-030-59013-0_12S230250Maude-NPA manual v3.1. http://maude.cs.illinois.edu/w/index.php/Maude_Tools:_Maude-NPAThe Tamarin-Prover Manual, 4 June 2019. https://tamarin-prover.github.io/manual/tex/tamarin-manual.pdfAl-Riyami, S.S., Paterson, K.G.: Tripartite authenticated key agreement protocols from pairings. In: Paterson, K.G. (ed.) Cryptography and Coding 2003. LNCS, vol. 2898, pp. 332–359. Springer, Heidelberg (2003). https://doi.org/10.1007/978-3-540-40974-8_27Baader, F., Snyder, W.: Unification theory. In: Robinson, J.A., Voronkov, A. (eds.) Handbook of Automated Reasoning, vol. 1, pp. 447–533. Elsevier Science (2001)Baelde, D., Delaune, S., Gazeau, I., Kremer, S.: Symbolic verification of privacy-type properties for security protocols with XOR. In: 30th IEEE Computer Security Foundations Symposium, CSF 2017, pp. 234–248. IEEE Computer Society (2017)Blanchet, B.: Modeling and verifying security protocols with the applied pi calculus and ProVerif. Found. Trends Privacy Secur. 1(1–2), 1–135 (2016)Clavel, M., et al.: Maude manual (version 3.0). Technical report, SRI International, Computer Science Laboratory (2020). http://maude.cs.uiuc.eduComon-Lundh, H., Delaune, S.: The finite variant property: how to get rid of some algebraic properties. In: Giesl, J. (ed.) RTA 2005. LNCS, vol. 3467, pp. 294–307. Springer, Heidelberg (2005). https://doi.org/10.1007/978-3-540-32033-3_22Cremers, C.J.F.: The scyther tool: verification, falsification, and analysis of security protocols. In: Gupta, A., Malik, S. (eds.) CAV 2008. LNCS, vol. 5123, pp. 414–418. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-70545-1_38Dreier, J., Duménil, C., Kremer, S., Sasse, R.: Beyond subterm-convergent equational theories in automated verification of stateful protocols. In: Maffei, M., Ryan, M. (eds.) POST 2017. LNCS, vol. 10204, pp. 117–140. Springer, Heidelberg (2017). https://doi.org/10.1007/978-3-662-54455-6_6Escobar, S., Hendrix, J., Meadows, C., Meseguer, J.: Diffie-Hellman cryptographic reasoning in the Maude-NRL protocol analyzer. In: Proceedings of 2nd International Workshop on Security and Rewriting Techniques (SecReT 2007) (2007)Escobar, S., Meadows, C., Meseguer, J.: A rewriting-based inference system for the NRL protocol analyzer and its meta-logical properties. Theor. Comput. Sci. 367(1–2), 162–202 (2006)Escobar, S., Meadows, C., Meseguer, J.: Maude-NPA: cryptographic protocol analysis modulo equational properties. In: Aldini, A., Barthe, G., Gorrieri, R. (eds.) FOSAD 2007-2009. LNCS, vol. 5705, pp. 1–50. Springer, Heidelberg (2009). https://doi.org/10.1007/978-3-642-03829-7_1Escobar, S., et al.: Protocol analysis in Maude-NPA using unification modulo homomorphic encryption. In: Proceedings of PPDP 2011, pp. 65–76. ACM (2011)Escobar, S., Meadows, C.A., Meseguer, J., Santiago, S.: State space reduction in the Maude-NRL protocol analyzer. Inf. Comput. 238, 157–186 (2014)Escobar, S., Sasse, R., Meseguer, J.: Folding variant narrowing and optimal variant termination. J. Log. Algebr. Program. 81(7–8), 898–928 (2012)Fabrega, F.J.T., Herzog, J.C., Guttman, J.D.: Strand spaces: why is a security protocol correct? In: Proceedings of IEEE Symposium on Security and Privacy, pp. 160–171 (1998)Guttman, J.D.: Security goals and protocol transformations. In: Mödersheim, S., Palamidessi, C. (eds.) TOSCA 2011. LNCS, vol. 6993, pp. 130–147. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-27375-9_8Joux, A.: A one round protocol for tripartite Diffie-Hellman. In: Bosma, W. (ed.) ANTS 2000. LNCS, vol. 1838, pp. 385–393. Springer, Heidelberg (2000). https://doi.org/10.1007/10722028_23Kim, Y., Perrig, A., Tsudik, G.: Communication-efficient group key agreement. In: Dupuy, M., Paradinas, P. (eds.) SEC 2001. IIFIP, vol. 65, pp. 229–244. Springer, Boston, MA (2002). https://doi.org/10.1007/0-306-46998-7_16Küsters, R., Truderung, T.: Using ProVerif to analyze protocols with Diffie-Hellman exponentiation. In: IEEE Computer Security Foundations, pp. 157–171 (2009)Küsters, R., Truderung, T.: Reducing protocol analysis with XOR to the XOR-free case in the horn theory based approach. J. Autom. Reason. 46(3–4), 325–352 (2011)Meadows, C.: The NRL protocol analyzer: an overview. J. Logic Program. 26(2), 113–131 (1996)Meier, S., Cremers, C., Basin, D.: Strong invariants for the efficient construction of machine-checked protocol security proofs. In: 2010 23rd IEEE Computer Security Foundations Symposium, pp. 231–245 (2010)Meseguer, J.: Conditional rewriting logic as a united model of concurrency. Theoret. Comput. Sci. 96(1), 73–155 (1992)Meseguer, J.: Variant-based satisfiability in initial algebras. Sci. Comput. Program. 154, 3–41 (2018)Meseguer, J.: Generalized rewrite theories, coherence completion, and symbolic methods. J. Log. Algebr. Meth. Program. 110, 100483 (2020)Mödersheim, S., Viganò, L.: The open-source fixed-point model checker for symbolic analysis of security protocols. In: Aldini, A., Barthe, G., Gorrieri, R. (eds.) FOSAD 2007-2009. LNCS, vol. 5705, pp. 166–194. Springer, Heidelberg (2009). https://doi.org/10.1007/978-3-642-03829-7_6Sasse, R., Escobar, S., Meadows, C., Meseguer, J.: Protocol analysis modulo combination of theories: a case study in Maude-NPA. In: Cuellar, J., Lopez, J., Barthe, G., Pretschner, A. (eds.) STM 2010. LNCS, vol. 6710, pp. 163–178. Springer, Heidelberg (2011). https://doi.org/10.1007/978-3-642-22444-7_11Schmidt, B., Sasse, R., Cremers, C., Basin, D.A.: Automated verification of group key agreement protocols. In: 2014 IEEE Symposium on Security and Privacy, SP 2014, pp. 179–194. IEEE Computer Society (2014)Skeirik, S., Meseguer, J.: Metalevel algorithms for variant satisfiability. J. Log. Algebraic Methods Program. 96, 81–110 (2018)TeReSe: Term Rewriting Systems. Cambridge University Press, Cambridge (2003)Yang, F., Escobar, S., Meadows, C.A., Meseguer, J., Narendran, P.: Theories of homomorphic encryption, unification, and the finite variant property. In: Proceedings of PPDP 2014, pp. 123–133. ACM (2014

Brain tumour diagnostics using a DNA methylation-based classifier as a diagnostic support tool

Aims: Methylation profiling (MP) is increasingly incorporated in the diagnostic process of central nervous system (CNS) tumours at our centres in The Netherlands and Scandinavia. We aimed to identify the benefits and challenges of MP as a support tool for CNS tumour diagnostics. Methods: About 502 CNS tumour samples were analysed using (850 k) MP. Profiles were matched with the DKFZ/Heidelberg CNS Tumour Classifier. For each case, the final pathological diagnosis was compared to the diagnosis before MP. Results: In 54.4% (273/502) of all analysed cases, the suggested methylation class (calibrated score ≥0.9) corresponded with the initial pathological diagnosis. The diagnosis of 24.5% of these cases (67/273) was more refined after incorporation of the MP result. In 9.8% of cases (49/502), the MP result led to a new diagnosis, resulting in an altered WHO grade in 71.4% of these cases (35/49). In 1% of cases (5/502), the suggested class based on MP was initially disregarded/interpreted as misleading, but in retrospect, the MP result predicted the right diagnosis for three of these cases. In six cases, the suggested class was interpreted as ‘discrepant but noncontributory’. The remaining 33.7% of cases (169/502) had a calibrated score <0.9, including 7.8% (39/502) for which no class indication was given at all (calibrated score <0.3). Conclusions: MP is a powerful tool to confirm and fine-tune the pathological diagnosis of CNS tumours, and to avoid misdiagnoses. However, it is crucial to interpret the results in the context of clinical, radiological, histopathological and other molecular information

Protocol analysis modulo combination of theories: A case study in Maude-NPA

There is a growing interest in formal methods and tools to analyze cryptographic protocols modulo algebraic properties of their underlying cryptographic functions. It is well-known that an intruder who uses algebraic equivalences of such functions can mount attacks that would be impossible if the cryptographic functions did not satisfy such equivalences. In practice, however, protocols use a collection of well-known functions, whose algebraic properties can naturally be grouped together as a union of theories E 1... ¿ n. Reasoning symbolically modulo the algebraic properties E 1... ¿ n requires performing (E 1... ¿ n)-unification. However, even if a unification algorithm for each individual E i is available, this requires combining the existing algorithms by methods that are highly non-deterministic and have high computational cost. In this work we present an alternative method to obtain unification algorithms for combined theories based on variant narrowing. Although variant narrowing is less efficient at the level of a single theory E i, it does not use any costly combination method. Furthermore, it does not require that each E i has a dedicated unification algorithm in a tool implementation. We illustrate the use of this method in the Maude-NPA tool by means of a well-known protocol requiring the combination of three distinct equational theories. © 2011 Springer-Verlag.R. Sasse and J. Meseguer have been partially supported by NSF Grants CNS0716638, CNS-0831064 and CNS-0904749. S. Escobar has been partially supported by the EU (FEDER) and the Spanish MEC/MICINN under grant TIN 2007-68093- C02-02. C. Meadows has been partially supported by NSF Grant CNS-0904749National Science Foundation, EEUUSasse, R.; Escobar Román, S.; Meadows, C.; Meseguer, J. (2011). Protocol analysis modulo combination of theories: A case study in Maude-NPA. En Security and Trust Management. Springer Verlag (Germany). 6710:163-178. doi:10.1007/978-3-642-22444-7_11S1631786710Abadi, M., Cortier, V.: Deciding knowledge in security protocols under equational theories. Theoretical Computer Science 367(1-2), 2–32 (2006)Armando, A., Basin, D.A., Boichut, Y., Chevalier, Y., Compagna, L., Cuéllar, J., Drielsma, P.H., Héam, P.-C., Kouchnarenko, O., Mantovani, J., Mödersheim, S., von Oheimb, D., Rusinowitch, M., Santiago, J., Turuani, M., Viganò, L., Vigneron, L.: The avispa tool for the automated validation of internet security protocols and applications. In: Etessami, K., Rajamani, S.K. (eds.) CAV 2005. LNCS, vol. 3576, pp. 281–285. Springer, Heidelberg (2005)Baader, F., Schulz, K.U.: Unification in the union of disjoint equational theories: Combining decision procedures. In: Kapur, D. (ed.) CADE 1992. LNCS, vol. 607, pp. 50–65. Springer, Heidelberg (1992)Basin, D.A., Mödersheim, S., Viganò, L.: An on-the-fly model-checker for security protocol analysis. In: Snekkenes, E., Gollmann, D. (eds.) ESORICS 2003. LNCS, vol. 2808, pp. 253–270. Springer, Heidelberg (2003)Baudet, M., Cortier, V., Delaune, S.: YAPA: A generic tool for computing intruder knowledge. In: Treinen, R. (ed.) RTA 2009. LNCS, vol. 5595, pp. 148–163. Springer, Heidelberg (2009)Blanchet, B.: An efficient cryptographic protocol verifier based on prolog rules. In: CSFW, pp. 82–96. IEEE Computer Society, Los Alamitos (2001)Bursuc, S., Comon-Lundh, H.: Protocol security and algebraic properties: Decision results for a bounded number of sessions. In: Treinen, R. (ed.) RTA 2009. LNCS, vol. 5595, pp. 133–147. Springer, Heidelberg (2009)Chevalier, Y., Küsters, R., Rusinowitch, M., Turuani, M.: An NP decision procedure for protocol insecurity with XOR. In: LICS, pp. 261–270. IEEE Computer Society, Los Alamitos (2003)Chevalier, Y., Rusinowitch, M.: Hierarchical combination of intruder theories. Inf. Comput. 206(2-4), 352–377 (2008)Chevalier, Y., Rusinowitch, M.: Symbolic protocol analysis in the union of disjoint intruder theories: Combining decision procedures. Theor. Comput. Sci. 411(10), 1261–1282 (2010)Ciobâcă, Ş., Delaune, S., Kremer, S.: Computing knowledge in security protocols under convergent equational theories. In: Schmidt, R.A. (ed.) CADE-22. LNCS, vol. 5663, pp. 355–370. Springer, Heidelberg (2009)Comon-Lundh, H., Delaune, S.: The finite variant property: How to get rid of some algebraic properties. In: Giesl, J. (ed.) RTA 2005. LNCS, vol. 3467, pp. 294–307. Springer, Heidelberg (2005)Cortier, V., Delaitre, J., Delaune, S.: Safely composing security protocols. In: Arvind, V., Prasad, S. (eds.) FSTTCS 2007. LNCS, vol. 4855, pp. 352–363. Springer, Heidelberg (2007)Cremers, C.J.F.: The scyther tool: Verification, falsification, and analysis of security protocols. In: Gupta, A., Malik, S. (eds.) CAV 2008. LNCS, vol. 5123, pp. 414–418. Springer, Heidelberg (2008)Escobar, S., Meadows, C., Meseguer, J.: A rewriting-based inference system for the NRL protocol analyzer and its meta-logical properties. Theoretical Computer Science 367(1-2), 162–202 (2006)Escobar, S., Meadows, C., Meseguer, J.: Maude-NPA: Cryptographic protocol analysis modulo equational properties. In: Aldini, A., Barthe, G., Gorrieri, R. (eds.) FOSAD 2007/2008/2009 Tutorial Lectures. LNCS, vol. 5705, pp. 1–50. Springer, Heidelberg (2009)Escobar, S., Meseguer, J., Sasse, R.: Effectively checking or disproving the finite variant property. Technical Report UIUCDCS-R-2008-2960, Department of Computer Science - University of Illinois at Urbana-Champaign (April 2008)Escobar, S., Meseguer, J., Sasse, R.: Effectively checking the finite variant property. In: Voronkov, A. (ed.) RTA 2008. LNCS, vol. 5117, pp. 79–93. Springer, Heidelberg (2008)Escobar, S., Meseguer, J., Sasse, R.: Variant narrowing and equational unification. Electr. Notes Theor. Comput. Sci. 238(3), 103–119 (2009)Escobar, S., Sasse, R., Meseguer, J.: Folding variant narrowing and optimal variant termination. In: Ölveczky, P.C. (ed.) WRLA 2010. LNCS, vol. 6381, pp. 52–68. Springer, Heidelberg (2010)Fabrega, F.J.T., Herzog, J., Guttman, J.: Strand Spaces: What Makes a Security Protocol Correct? Journal of Computer Security 7, 191–230 (1999)Guo, Q., Narendran, P.: Unification and matching modulo nilpotence. In: CADE-13. LNCS, vol. 1104, pp. 261–274. Springer, Heidelberg (1996)Harkins, D., Carrel, D.: The Internet Key Exchange (IKE), IETF RFC 2409, (November 1998)Jouannaud, J.-P., Kirchner, C., Kirchner, H.: Incremental construction of unification algorithms in equational theories. In: Díaz, J. (ed.) ICALP 1983. LNCS, vol. 154, pp. 361–373. Springer, Heidelberg (1983)Küsters, R., Truderung, T.: Reducing protocol analysis with xor to the xor-free case in the Horn theory based approach. In: ACM Conference on Computer and Communications Security, pp. 129–138 (2008)Küsters, R., Truderung, T.: Using ProVerif to analyze protocols with Diffie-Hellman exponentiation. In: CSF, pp. 157–171. IEEE Computer Society, Los Alamitos (2009)Lafourcade, P., Terrade, V., Vigier, S.: Comparison of cryptographic verification tools dealing with algebraic properties. In: Degano, P., Guttman, J.D. (eds.) FAST 2009. LNCS, vol. 5983, pp. 173–185. Springer, Heidelberg (2010)Lowe, G.: Breaking and fixing the Needham-Schroeder public-key protocol using FDR. In: Margaria, T., Steffen, B. (eds.) TACAS 1996. LNCS, vol. 1055, pp. 147–166. Springer, Heidelberg (1996)Meadows, C.: The NRL protocol analyzer: An overview. J. Log. Program. 26(2), 113–131 (1996)Meseguer, J.: Conditional rewriting logic as a united model of concurrency. Theor. Comput. Sci. 96(1), 73–155 (1992)Meseguer, J.: Membership algebra as a logical framework for equational specification. In: Parisi-Presicce, F. (ed.) WADT 1997. LNCS, vol. 1376, pp. 18–61. Springer, Heidelberg (1998)Meseguer, J., Thati, P.: Symbolic reachability analysis using narrowing and its application to verification of cryptographic protocols. Higher-Order and Symbolic Computation 20(1–2), 123–160 (2007)Ohlebusch, E.: Advanced Topics in Term Rewriting. Springer, Heidelberg (2002)Santiago, S., Talcott, C.L., Escobar, S., Meadows, C., Meseguer, J.: A graphical user interface for Maude-NPA. Electr. Notes Theor. Comput. Sci. 258(1), 3–20 (2009)Schmidt-Schauß, M.: Unification in a combination of arbitrary disjoint equational theories. J. Symb. Comput. 8(1/2), 51–99 (1989)Terese (ed.): Term Rewriting Systems. Cambridge University Press, Cambridge (2003)Turuani, M.: The CL-atse protocol analyser. In: Pfenning, F. (ed.) RTA 2006. LNCS, vol. 4098, pp. 277–286. Springer, Heidelberg (2006

Vandetanib (ZD6474), an inhibitor of VEGFR and EGFR signalling, as a novel molecular-targeted therapy against cholangiocarcinoma

Cholangiocarcinoma is an intractable cancer, with no effective therapy other than surgical resection. Elevated vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR) expressions are associated with the progression of cholangiocarcinoma. We therefore examined whether inhibition of VEGFR and EGFR could be a potential therapeutic target for cholangiocarcinoma. Vandetanib (ZD6474, ZACTIMA), a VEGFR-2/EGFR inhibitor, was evaluated. Four human cholangiocarcinoma cell lines were molecularly characterised and investigated for their response to vandetanib. In vitro, two cell lines (OZ and HuCCT1), both of which harboured KRAS mutation, were refractory to vandetanib, one cell line (TGBC24TKB) was somewhat resistant, and another cell line (TKKK) was sensitive. The most sensitive cell line (TKKK) had EGFR amplification. Vandetanib significantly inhibited the growth of TKKK xenografts at doses ⩾12.5 mg kg−1 day−1 (P<0.05), but higher doses (50 mg kg−1 day−1, P<0.05) of vandetanib were required to inhibit the growth of OZ xenografts. Vandetanib (25 mg kg−1 day−1) also significantly (P=0.006) prolonged the time to metastasis in an intravenous model of TKKK metastasis. Inhibiting both VEGFR and EGFR signalling appears a promising therapeutic approach for cholangiocarcinoma. The absence of KRAS mutation and the presence of EGFR amplification may be potential predictive molecular marker of sensitivity to EGFR-targeted therapy in cholangiocarcinoma

SCALA: In situ calibration for integral field spectrographs

International audienceThe scientific yield of current and future optical surveys is increasingly limited by systematic uncertainties in the flux calibration. This is the case for Type Ia supernova (SN Ia) cosmology programs, where an improved calibration directly translates into improved cosmological constraints. Current methodology rests on models of stars. Here we aim to obtain flux calibration that is traceable to state-of-the-art detector-based calibration. We present the SNIFS Calibration Apparatus (SCALA), a color (relative) flux calibration system developed for the SuperNova Integral Field Spectrograph (SNIFS), operating at the University of Hawaii 2.2 m (UH 88) telescope. By comparing the color trend of the illumination generated by SCALA during two commissioning runs, and to previous laboratory measurements, we show that we can determine the light emitted by SCALA with a long-term repeatability better than 1%. We describe the calibration procedure necessary to control for system aging. We present measurements of the SNIFS throughput as estimated by SCALA observations. The SCALA calibration unit is now fully deployed at the UH\,88 telescope, and with it color-calibration between 4000 {\AA} and 9000 {\AA} is stable at the percent level over a one-year baseline