Paolo Zuliani - Publications
 

Work in progress

F. Shmarov, P. Zuliani. Probabilistic Bounded Reachability for Hybrid Systems with Continuous Nondeterministic and Probabilistic Parameters.


Journals

P. G. Jayathilake, P. Gupta, B. Li, C. Madsen, O. Oyebamiji, R. González-Cabaleiro, S. Rushton, B. Bridgens, D. Swailes, B. Allen, S. McGough, P. Zuliani, I. D. Ofiteru, D. Wilkinson, J. Chen, T. Curtis. A Mechanistic Individual-based Model of Microbial Communitiees. PLoS One, 2017. To appear.

G. Misirli, M. Cavaliere, W. Waites, M. Pocock, C. Madsen, O. Gilfellon, R. Honorato-Zimmer, P. Zuliani, V. Danos, and A. Wipat. Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation. Bioinformatics, 32(6):908-917, 2016.

P. Zuliani. Statistical Model Checking for Biological Applications. Software Tools for Technology Transfer, 17(4):527-536, 2015.

J. Rusakovica, J. Hallinan, A. Wipat, P. Zuliani. Probabilistic latent semantic analysis applied to whole bacterial genomes identifies common genomic features. Journal of Integrative Bioinformatics, 11(2):243, 2014.

P. Zuliani, A. Platzer, E. M. Clarke. Bayesian Statistical Model Checking with Application to Stateflow/Simulink Verification. Formal Methods in System Design, 43(2):338-367, 2013.

H. Gong, P. Zuliani, E. M. Clarke. Model checking of a synchronous diabetes-cancer logical network. Current Bioinformatics, 8(1):9-15, 2013.

H. Gong, P. Zuliani, A. Komuravelli, J. R. Faeder, E. M. Clarke. Analysis and Verification of the HMGB1 Signaling Pathway. BMC Bioinformatics 2010, 11(Suppl 7):S10. (Best Paper Award at InCoB 2010.)  Highly accessed

P. Zuliani. Reasoning about faulty quantum programs. Acta Informatica, 46(6):403-432, 2009.

P. Zuliani. Compiling quantum programs. Acta Informatica, 41(7-8):435–474, 2005.

G. Succi, W. Pedrycz, S. Djokic, P. Zuliani, and B. Russo. An empirical exploration of the distributions of the Chidamber and Kemerer object-oriented metrics suite. Empirical Software Engineering, 10(1):81–104, 2005.

P. Zuliani. Logical reversibility. IBM Journal of Research and Development, 45(6):807–818, 2001.


Tutorial Papers

E. M. Clarke, W. Klieber, M. Nováček, P. Zuliani. Model checking and the state explosion problem. In 8th LASER Summer School on Software Engineering, Sept. 4-10, 2011. LNCS volume 7682, pp. 1-30, 2012.


Conferences

F. Shmarov, P. Zuliani. Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques. In HVC 2016: 12th Haifa Verification Conference. LNCS volume 10028, pp. 152-168, 2016.

N. Miskov-Zivanov, P. Zuliani, Q. Wang, E. M. Clarke and J. R. Faeder. High-level modeling and verification of cellular signaling. In HLDVT 2016: 18th IEEE International High Level Design Validation and Test Workshop. IEEE, pp. 162-169, 2016.

L. Anticoli, C. Piazza, L. Taglialegne, P. Zuliani. Verifying Quantum Programs: From Quipper Circuits to QPMC. In RC 2016: 8th Conference on Reversible Computation. LNCS volume 9720, pp. 213-219, 2016.

F. Shmarov, P. Zuliani. SMT-Based Reasoning for Uncertain Hybrid Domains. In AAAI-16 Workshop on Planning for Hybrid Systems, 30th AAAI Conference on Artificial Intelligence, 2016.

C. Madsen, F. Shmarov, P. Zuliani. BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models. Download: [BioPSy]. In CMSB 2015: 13th Conference on Computational Methods in Systems Biology. LNCS volume 9308, pp. 182-194, 2015.

Q. Wang, P. Zuliani, S. Kong, S. Gao, E. M. Clarke. SReach: A Bounded Model Checker for Stochastic Hybrid Systems. Download: [SReach]. In CMSB 2015: 13th Conference on Computational Methods in Systems Biology. LNCS volume 9308, pp. 15-27, 2015.

F. Shmarov, P. Zuliani. ProbReach: Verified Probabilistic Delta-Reachability for Stochastic Hybrid Systems. Download: [ProbReach]. In HSCC 2015: 18th International Conference on Hybrid Systems: Computation and Control. ACM, pp. 134-139, 2015.

B. Liu, S. Kong, S. Gao, P. Zuliani, E. M. Clarke. Towards Personalized Prostate Cancer Therapy Using Delta-Reachability Analysis. In HSCC 2015: 18th International Conference on Hybrid Systems: Computation and Control. ACM, pp. 227-232, 2015.

B. Liu, S. Kong, S. Gao, P. Zuliani, E. M. Clarke. Parameter Synthesis for Cardiac Cell Hybrid Models Using Delta-Decisions.
In CMSB 2014: 12th Conference on Computational Methods in Systems Biology. LNCS volume 8859, pp. 99-113, 2014.

N. Miskov-Zivanov,
P. Zuliani, E. M. Clarke, J. R. Faeder. Studies of biological networks with statistical model checking: application to immune system cells. In ACM-BCB 2013: ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics. (Poster presentation, to appear.)

D. Henriques, J. Martins, P. Zuliani, A. Platzer, E. M. Clarke. Statistical model checking for Markov decision processes. In QEST 2012: 9th International Conference on Quantitative Evaluation of SysTems. IEEE, pp. 84-93.

P
. Zuliani, N. Miskov-Zivanov, J. R. Faeder, E. M. Clarke. Model checking for studying timing of events in T cell differentiation. In IWBDA 2012: 4th International Workshop on Bio-Design Automation, with 49th ACM/EDAC/IEEE Design Automation Conference (abstract, to appear).

P. Zuliani
, C. Baier, E.M. Clarke. Rare-Event Verification for Stochastic Hybrid Systems. In HSCC 2012: 15th ACM International Conference on Hybrid Systems: Computation and Control, pp. 217-226, 2012.

H. Gong, P. Zuliani, Q. Wang, E. M. Clarke.
Formal Analysis for Logical Models of Pancreatic Cancer. In CDC-ECC 2011: 50th IEEE Conference on Decision and Control and European Control Conference. IEEE, pp. 4855-4860, 2011.

E. M. Clarke and P. Zuliani. Statistical Model Checking for Cyber-Physical Systems. In ATVA 2011: 9th International Symposium on Automated Technology for Verification and Analysis. LNCS volume 6996,
pp. 1-12, 2011. (Invited paper.)

H. Gong, P. Zuliani, E. M. Clarke. Model Checking of a Diabetes-Cancer Model. In CMLS 2011: 3rd International Symposium on Computational Models for Life Sciences, AIP Conf. Proc. 1371, pp. 234-243, 2011.


H. Gong, Q. Wang, P. Zuliani, J. R. Faeder, M. T. Lotze, E. M. Clarke. Symbolic Model Checking of Signaling Pathways in Pancreatic Cancer. In BiCoB 2011: 3rd International Conference on Bioinformatics and Computational Biology, March 23-25, 2011, New Orleans, LA.

Y.-C. Wang, A. Komuravelli, P. Zuliani, E. M. Clarke. Analog Circuit Verification by Statistical Model Checking. In ASP-DAC 2011: 16th Asia and South Pacific Design Automation Conference. IEEE, pp. 1-6, 2011. (Best Paper Award nomination.)

H. L. S. Younes, E. M. Clarke, P. Zuliani. Statistical Verification of Probabilistic Properties with Unbounded Until. In SBMF 2010: 13th Brazilian Symposium on Formal Methods. LNCS volume 6527, pp. 144-160, 2011.

H. Gong, P. Zuliani, A. Komuravelli, J. R. Faeder, E. M. Clarke. Computational Modeling and Verification of Signaling Pathways in Cancer. In ANB 2010: 4th International Conference on Algebraic and Numeric Biology. LNCS volume 6479, pp. 117-135, 2010.

P. Zuliani, A. Platzer, E. M. Clarke. Bayesian Statistical Model Checking with Application to Stateflow/Simulink Verification. In HSCC 2010: 13th ACM International Conference on Hybrid Systems: Computation and Control, pp. 243-252, 2010.

S. K. Jha, E. M. Clarke, C. J. Langmead, A. Legay, A. Platzer, P. Zuliani. A Bayesian approach to model checking biological systems. In CMSB '09: 7th Conference on Computational Methods in Systems Biology. LNCS volume 5688, pp. 218-234, 2009.

P. Zuliani. A formal derivation of Grover’s quantum search algorithm. In TASE ’07: 1st IEEE & IFIP International Symposium on Theoretical Aspects of Software Engineering, pp. 67–74, 2007.

P. Zuliani. Quantum programming with mixed states. In QPL ’05: 3rd International Workshop on Quantum Programming Languages. Electronic Notes in Theoretical Computer Science, volume 170, pp. 185–199, 2007.

P. Zuliani. On counterfactual computation. In UC ’05: 4th International Conference on Unconventional Computation. LNCS, volume 3699, pp. 251–266, 2005.

P. Zuliani. Non-deterministic quantum programming. In QPL ’04: 2nd International Workshop on Quantum Programming Languages, pp. 179–195. TUCS Publication 33, Turku, Finland, 2004.

J. W. Sanders and P. Zuliani. Quantum programming. In MPC ’00: Mathematics of Program Construction. LNCS, volume 1837, pp. 80–99, 2000.

B. Rossi, B. Russo, P. Zuliani, and G. Succi. On the transition to an open source solution for desktop automation. In TCGOV ’05: ESF-TCD Conference on e-Government. LNCS, volume 3416, pp. 277–285, 2005.

A. Janes, B. Russo, P. Zuliani, and G. Succi. An empirical analysis on the discontinuous use of pair programming. In XP ’03: 4th International Conference on eXtreme Programming and Agile Processes in Software Engineering. LNCS, volume 2675, pp. 205–214, 2003. 


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