@article(Alur1996, author = "R. Alur and T. Feder and T.A. Henzinger", year = "1996", title = "The benefits of relaxing punctuality", journal = "J. ACM", url = "http://doi.acm.org/10.1145/227595.227602", ) @inproceedings(Annapureddy2011, author = "Y. Annapureddy and C. Liu and G. Fainekos and S. Sankaranarayanan", year = "2011", title = "S-TaLiRo: A Tool for Temporal Logic Falsification for Hybrid Systems", booktitle = "Proceedings of TACAS", doi = "10.1007/978-3-642-19835-9\_21", ) @inproceedings(Baier1997, author = "C. Baier and E.M. Clarke and V. Hartonas-Garmhausen and M.Z. Kwiatkowska and M. Ryan", year = "1997", title = "Symbolic Model Checking for Probabilistic Processes", booktitle = "Proc. of ICALP '97, the 24th International Colloquium on Automata, Languages and Programming, Bologna, Italy, July 7Ð-11", series = "Lecture Notes in Computer Science", volume = "1256", publisher = "Springer Berlin Heidelberg", pages = "430--440", doi = "10.1007/3-540-63165-8\_199", ) @article(Baier2003, author = "C. Baier and B. Haverkort and H. Hermanns and J.-P. Katoen", year = "2003", title = "Model-Checking Algorithms for Continuous-Time Markov Chains", journal = "IEEE Trans. Softw. Eng.", volume = "29", number = "6", pages = "524--541", doi = "10.1109/TSE.2003.1205180", ) @inproceedings(Bartocci2013, author = "E. Bartocci and L. Bortolussi and L. Nenzi", year = "2013", title = "A temporal logic approach to modular design of synthetic biological circuits", booktitle = "In Proc. of CMSB 2013, the 11th International Conference on Computational Methods in Systems Biology, IST Austria, Klosterneuburg, Austria, September 23-25, 2013", series = "Lecture Notes in Computer Science", volume = "8130", address = "Springer-Verlag", pages = "164--178", doi = "10.1007/978-3-642-39176-7", ) @inproceedings(Bartocci2011, author = "E. Bartocci and R. Grosu and P. Katsaros and C. Ramakrishnan and S. A. Smolka", year = "2011", title = "Model Repair for Probabilistic Systems", booktitle = "Proceedings of TACAS 2011, the 17th International Conference on Tools and Algorithms for the Construction and Analysis of Systems", series = "Lecture Notes in Computer Science", volume = "6605", publisher = "Springer Berlin / Heidelberg", pages = "326--340", doi = "10.1007/978-3-642-19835-9\_30", ) @book(Bishop2006, author = "C. M. Bishop", year = "2006", title = "Pattern Recognition and Machine Learning", publisher = "Springer", ) @inproceedings(asmta10, author = "L. Bortolussi", year = "2010", title = "Limit behavior of the hybrid approximation of Stochastic Process Algebras", booktitle = "Proceedings of ASMTA 2010", doi = "10.1007/978-3-642-13568-2\_26", ) @article(tutorial, author = "L. Bortolussi and J. Hillston and D. Latella and M. Massink", year = "2013", title = "Continuous Approximation of Collective Systems Behaviour: a Tutorial", journal = "Performance Evaluation", volume = "70", number = "5", pages = "317--349", doi = "10.1016/j.peva.2013.01.001", ) @inproceedings(lucaIFAC07, author = "L. Bortolussi and A. Policriti", year = "2008", title = "Hybrid approximation of stochastic process algebras for systems biology", booktitle = "Proceedings of IFAC WC", doi = "10.3182/20080706-5-KR-1001.02132", ) @article(lucaTCS10, author = "L. Bortolussi and A. Policriti", year = "2010", title = "Hybrid Dynamics of Stochastic Programs", journal = "Theoretical Computer Science", volume = "411", number = "20", pages = "2052--2077", doi = "10.1016/j.tcs.2010.02.008", ) @article(JLC, author = "L. Bortolussi and A. Policriti", year = "in print", title = "({H}ybrid) Automata and (Stochastic) Programs. {T}he hybrid automata lattice of a stochastic program", journal = "Journal of Logic and Computation", ) @inproceedings(lucaQEST13, author = "L. Bortolussi and G. Sanguinetti", year = "2013", title = "{L}earning and {D}esigning {S}tochastic {P}rocesses from {L}ogical {C}onstraints", booktitle = "Proc. of QEST 2013, 10th International Conference on Quantitative Evaluation of Systems, Buenos Aires, Argentina, August 27-30, 2013", volume = "8054", pages = "89--105", doi = "10.1007/978-3-642-40196-1", ) @inproceedings(Bujorianu2005, author = "M. L. Bujorianu and J. Lygeros and M. C. Bujorianu", year = "2005", title = "Bisimulation for General Stochastic Hybrid Systems", booktitle = "Proceedings of HSCCl", pages = "198--214", doi = "10.1007/978-3-540-31954-2\_13", ) @article(biocham, author = "L. Calzone and F. Fages and S. Soliman", year = "2006", title = "BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge", journal = "Bioinformatics", volume = "22", pages = "1805--1807", doi = "10.1093/bioinformatics/btl172", ) @inproceedings(Chen2011a, author = "T. Chen and M. Diciolla and M. Kwiatkowska and A. Mereacre", year = "2011", title = "Time-bounded verification of CTMCs against real-time specifications", booktitle = "Proc. of FORMATS 2011, the 9th International Conference on Formal Modeling and Analysis of Timed Systems, Aalborg, Denmark, September 21--23", series = "Lecture Notes in Computer Science", volume = "6919", address = "Berlin, Heidelberg", pages = "26--42", doi = "10.1007/978-3-642-24310-3\_4", ) @book(davis, author = "M.H.A. Davis", year = "1993", title = "{M}arkov Models and Optimization", publisher = "Chapman \& Hall", ) @incollection(sensitivityCTMC, author = "Andrea Degasperi and Stephen Gilmore", year = "2008", title = "Sensitivity analysis of stochastic models of bistable biochemical reactions", booktitle = "Formal Methods for Computational Systems Biology", series = "Lecture Notes in Computer Science", volume = "5016", publisher = "Springer", pages = "1--20", doi = "10.1007/978-3-540-68894-5\_1", ) @incollection(Donze2010a, author = "A. Donz{\'e}", year = "2010", title = "Breach, A Toolbox for Verification and Parameter Synthesis of Hybrid Systems", booktitle = "Proceedings of CAV", url = "http://dx.doi.org/10.1007/978-3-642-14295-6_17", ) @article(Donze2010b, author = "A. Donz{\'e} and G. Clermont and C.J. Langmead", year = "2010", title = "Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology", journal = "Journal of Computational Biology", volume = "17", number = "3", pages = "325--336", doi = "10.1007/978-3-642-02008-7\_11", ) @article(Donze2011, author = "A. Donz{\'e} and E. Fanchon and L. M. Gattepaille and O. Maler and P. Tracqui", year = "2011", title = "Robustness analysis and behavior discrimination in enzymatic reaction networks", journal = "PLoS One", volume = "6", number = "9", pages = "e24246", doi = "10.1371/journal.pone.0024246", ) @inproceedings(Donze2013, author = "A. Donz{\'e} and T. Ferrer and O. Maler", year = "2013", title = "Efficient Robust Monitoring for STL", booktitle = "Proc. of CAV 2013, the 25th International Conference on Computer Aided Verification, Saint Petersburg, Russia, July 13-19", series = "Lecture Notes in Computer Science", volume = "8044", pages = "264--279", doi = "10.1007/978-3-642-39799-8\_19", ) @inproceedings(Donze2010, author = "A. Donz{\'e} and O. Maler", year = "2010", title = "Robust satisfaction of temporal logic over real-valued signals", booktitle = "Proc. of FORMATS 2010, the 8th International Conference on Formal Modeling and Analysis of Timed Systems, Klosterneuburg, Austria, September 8--10", volume = "6246", pages = "92--106", doi = "10.1007/978-3-642-15297-9\_9", ) @book(Durett2012, author = "R. Durett", year = "2012", title = "Essentials of stochastic processes", publisher = "Springer", doi = "10.1007/978-1-4614-3615-7", ) @article(elowitz00, author = "M.B. Elowitz and S. Leibler", year = "2000", title = "A synthetic oscillatory network of transcriptional regulators", journal = "Nature", volume = "403", pages = "335--338", doi = "10.1038/35002125", ) @incollection(Fainekos2007a, author = "G. Fainekos and G. Pappas", year = "2007", title = "Robust Sampling for MITL Specifications", booktitle = "Proc. of FORMATS 2007, the 5th International Conference on Formal Modeling and Analysis of Timed Systems", series = "Lecture Notes in Computer Science", volume = "8044", pages = "264--279", doi = "10.1007/978-3-540-75454-1\_12", ) @article(Fainekos2009, author = "G. E. Fainekos and G. J. Pappas", year = "2009", title = "Robustness of temporal logic specifications for continuous-time signals", journal = "Theor. Comput. Sci.", volume = "410", number = "42", pages = "4262--4291", doi = "10.1016/j.tcs.2009.06.021", ) @inproceedings(anastasisHSB12, author = "A. Georgoulas and A. Clark and A. Ocone and S. Gilmore and G. Sanguinetti", year = "2012", title = "A subsystems approach for parameter estimation of ODE models of hybrid systems", booktitle = "Proc. of HSB 2012, the 1st International Workshop on Hybrid Systems and Biology", series = "EPTCS", volume = "92", pages = "30--41", doi = "10.4204/EPTCS.92.3", ) @article(gillespie, author = "D.T. Gillespie", year = "1977", title = "Exact Stochastic Simulation of Coupled Chemical Reactions", journal = "J. of Physical Chemistry", volume = "81", number = "25", doi = "10.1021/j100540a008", ) @article(petzold05, author = "R. Gunawan and Y. Cao and L. Petzold and F.J. Doyle III", year = "2005", title = "Sensitivity analysis of discrete stochastic systems", journal = "Biophysical Journal", volume = "88", number = "4", pages = "2530", doi = "10.1529/biophysj.104.053405", ) @article(Jones2010, author = "K. D. Jones and Konrad V and D. Nickovic", year = "2010", title = "Analog property checkers: a DDR2 case study", journal = "Formal Methods in System Design", volume = "36", number = "2", pages = "114--130", doi = "10.1007/s10703-009-0085-x", ) @article(Kennedy2001, author = "M. Kennedy and A. O'Hagan", year = "2001", title = "Bayesian Calibration of Computer Models", journal = "Journal of the Royal Stat. Soc. Ser. B", volume = "63", number = "3", pages = "425--464", doi = "10.1111/1467-9868.00294", ) @article(komorowski2011, author = "M. Komorowski and M. J. Costa and D. A. Rand and M. PH Stumpf", year = "2011", title = "Sensitivity, robustness, and identifiability in stochastic chemical kinetics models", journal = "PNAS USA", volume = "108", number = "21", pages = "8645--8650", doi = "10.1073/pnas.1015814108", ) @article(Kwiatkowska2004, author = "Marta Kwiatkowska and Gethin Norman and David Parker", year = "2004", title = "Probabilistic symbolic model checking with PRISM: a hybrid approach", journal = "Int. J. Softw. Tools Technol. Transf.", volume = "6", number = "2", pages = "128--142", doi = "10.1007/s10009-004-0140-2", ) @inproceedings(davidCAV, author = "S. Drazan L. Brim, M. Ceska and D. {\v S}afr{\'a}nek", year = "2013", title = "Exploring Parameter Space of Stochastic Biochemical Systems using Quantitative Model Checking", booktitle = "Proc. of CAV 2013, the 25th International Conference on Computer Aided Verification, Saint Petersburg, Russia, July 13-19", series = "Lecture Notes in Computer Science", volume = "8044", pages = "107--123", doi = "10.1007/978-3-642-39799-8\_7", ) @inproceedings(Maler2004, author = "O. Maler and D. Nickovic", year = "2004", title = "Monitoring Temporal Properties of Continuous Signals", booktitle = "Proc. of Joint International Conferences on Formal Modeling and Analysis of Timed Systmes, FORMATS 2004, and Formal Techniques in Real-Time and Fault -Tolerant Systems, FTRTFT 2004, Grenoble, France, September 22-24", volume = "3253", pages = "152--166", doi = "10.1007/978-3-540-30206-3\_12", ) @article(Ocone:hybrid13, author = "A. Ocone and A. J. Millar and G. Sanguinetti", year = "2013", title = "Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics", journal = "Bioinformatics", volume = "29", number = "7", pages = "910--916", doi = "10.1093/bioinformatics/btt06", ) @inproceedings(Opper:approximate10, author = "M. Opper and A. Ruttor and G. Sanguinetti", year = "2010", title = "Approximate inference in continuous time Gaussian-Jump processes", booktitle = "Proceedings of NIPS 2010, the 4th Annual Conference on Neural Information Processing Systems, 6--9 December 2010, Vancouver, British Columbia, Canada", pages = "1831--1839", url = "http://books.nips.cc/papers/files/nips23/NIPS2010_1095.pdf", ) @article(Pnueli1977, author = "Amir Pnueli", year = "1977", title = "The temporal logic of programs", journal = "Foundations of Computer Science, IEEE Annual Symposium on", volume = "0", pages = "46--57", doi = "10.1109/SFCS.1977.32", ) @book(Rasmussen2007, author = "C. E. Rasmussen and C. K. I. Williams", year = "2006", title = "Gaussian Processes for Machine Learning", publisher = "MIT Press", ) @inproceedings(Rizk2008, author = "A. Rizk and G. Batt and F. Fages and S. Soliman", year = "2008", title = "On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology", booktitle = "Proc. of CMSB 2008, the 6th International Conference on Computational Methods in Systems Biology, Rostock, Germany, October 12--15", series = "Lecture Notes in Computer Science", volume = "5307", pages = "251--268", doi = "10.1007/978-3-540-88562-7\_19", ) @article(gpucb, author = "Niranjan Srinivas and Andreas Krause and Sham M. Kakade and Matthias W. Seeger", year = "2012", title = "Information-Theoretic Regret Bounds for Gaussian Process Optimization in the Bandit Setting", journal = "IEEE Transactions on Information Theory", volume = "58", number = "5", pages = "3250--3265", doi = "10.1109/TIT.2011.2182033", ) @inproceedings(Younes2004, author = "H. L. S. Younes and M. Z. Kwiatkowska and G. Norman and D. Parker", year = "2004", title = "Numerical vs. Statistical Probabilistic Model Checking: An Empirical Study", booktitle = "Proc. of 2004, the 10th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Barcelona, Spain, March 29 - April 2", doi = "10.1007/978-3-540-24730-2\_4", )