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2020 – today
- 2023
[j30]Nikola Benes
, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek:
Boolean network sketches: a unifying framework for logical model inference. Bioinform. 39(4) (2023)- [j29]Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková:
Temporary and permanent control of partially specified Boolean networks. Biosyst. 223: 104795 (2023) - [j28]Matej Troják, David Safránek, Samuel Pastva, Lubos Brim:
Rule-based modelling of biological systems using regulated rewriting. Biosyst. 225: 104843 (2023) - [c97]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková:
Phenotype Control of Partially Specified Boolean Networks. CMSB 2023: 18-35 - 2022
- [j27]Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek, Eva Smijáková:
AEON.py: Python library for attractor analysis in asynchronous Boolean networks. Bioinform. 38(21): 4978-4980 (2022) - [j26]Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek:
Exploring attractor bifurcations in Boolean networks. BMC Bioinform. 23(1): 173 (2022) - [j25]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. Log. Methods Comput. Sci. 18(1) (2022) - [c96]Matej Troják, David Safránek, Branislav Brozmann, Lubos Brim:
eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. CMSB 2022: 302-309 - [i14]Matej Troják, David Safránek, Lubos Brim:
Biochemical Space Language in Relation to Multiset Rewriting Systems. CoRR abs/2201.08817 (2022) - [i13]Lubos Brim, Samuel Pastva, David Safránek, Eva Smijáková:
Robust Control of Partially Specified Boolean Networks. CoRR abs/2202.13440 (2022) - 2021
- [c95]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Computing Bottom SCCs Symbolically Using Transition Guided Reduction. CAV (1) 2021: 505-528 - [c94]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Aeon 2021: Bifurcation Decision Trees in Boolean Networks. CMSB 2021: 230-237 - [c93]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Symbolic Coloured SCC Decomposition. TACAS (2) 2021: 64-83 - [i12]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. CoRR abs/2108.13113 (2021) - [i11]Matej Troják, Samuel Pastva, David Safránek, Lubos Brim:
Regulated Multiset Rewriting Systems. CoRR abs/2111.13036 (2021) - 2020
- [j24]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Digital Bifurcation Analysis of Internet Congestion Control Protocols. Int. J. Bifurc. Chaos 30(13): 2030038:1-2030038:18 (2020) - [j23]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Parallel parameter synthesis algorithm for hybrid CTL. Sci. Comput. Program. 185 (2020) - [c92]Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek:
AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. CAV (1) 2020: 569-581 - [c91]Eva Smijáková, Samuel Pastva, David Safránek, Lubos Brim:
Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. CMSB 2020: 280-297 - [c90]Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim:
eBCSgen: A Software Tool for Biochemical Space Language. CMSB 2020: 356-361 - [c89]Matej Troják, David Safránek, Lukrécia Mertová, Lubos Brim:
Parameter Synthesis and Robustness Analysis of Rule-Based Models. NFM 2020: 41-59 - [c88]Matej Troják, David Safránek, Lubos Brim, Jakub Salagovic, Jan Cervený:
Executable Biochemical Space for Specification and Analysis of Biochemical Systems. SASB 2020: 91-116 - [i10]Matej Troják, David Safránek, Lubos Brim:
Executable Biochemical Space for Specification and Analysis of Biochemical Systems. CoRR abs/2002.00731 (2020) - [i9]Lubos Brim, Samuel Pastva, David Safránek, Eva Smijakova:
Parallel One-Step Control of Parametrised Boolean Networks. CoRR abs/2009.00359 (2020)
2010 – 2019
- 2019
- [c87]David Safránek, Matej Troják, Vojtech Bruza, Tomás Vejpustek, Jan Papousek, Martin Demko, Samuel Pastva, Ales Pejznoch, Lubos Brim:
Barbaric Robustness Monitoring Revisited for STL* in Parasim. CMSB 2019: 356-359 - [c86]Nikola Benes, Lubos Brim, Jana Drazanová, Samuel Pastva, David Safránek:
Facetal abstraction for non-linear dynamical systems based on δ-decidable SMT. HSCC 2019: 99-108 - [c85]Nikola Benes, Lubos Brim, Samuel Pastva, Jakub Polácek, David Safránek:
Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks. ICFEM 2019: 353-369 - [c84]Nikola Benes, Lubos Brim, Martin Geletka, Samuel Pastva, David Safránek:
Accelerating Parameter Synthesis Using Semi-algebraic Constraints. IFM 2019: 27-45 - [c83]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Digital Bifurcation Analysis of TCP Dynamics. TACAS (2) 2019: 339-356 - [p1]Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
Model Checking Approach to the Analysis of Biological Systems. Automated Reasoning for Systems Biology and Medicine 2019: 3-35 - 2017
- [j22]Milan Ceska, Frits Dannenberg, Nicola Paoletti, Marta Kwiatkowska, Lubos Brim:
Precise parameter synthesis for stochastic biochemical systems. Acta Informatica 54(6): 589-623 (2017) - [c82]Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek:
Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-affine Dynamical Systems. CAV (1) 2017: 591-598 - [c81]Jiri Barnat, Nikola Benes, Lubos Brim, Martin Demko, Matej Hajnal, Samuel Pastva, David Safránek:
Detecting Attractors in Biological Models with Uncertain Parameters. CMSB 2017: 40-56 - 2016
- [j21]Jiri Barnat, Petr Bauch, Nikola Benes, Lubos Brim, Jan Beran, Tomas Kratochvila:
Analysing sanity of requirements for avionics systems. Formal Aspects Comput. 28(1): 45-63 (2016) - [j20]Petr Rockai, Jiri Barnat, Lubos Brim:
Model checking C++ programs with exceptions. Sci. Comput. Program. 128: 68-85 (2016) - [c80]Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek:
Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-affine Systems. ATVA 2016: 192-208 - [c79]Martin Demko, Nikola Benes, Lubos Brim, Samuel Pastva, David Safránek:
High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. CMSB 2016: 82-97 - [c78]Nikola Benes, Lubos Brim, Martin Demko, Samuel Pastva, David Safránek:
A Model Checking Approach to Discrete Bifurcation Analysis. FM 2016: 85-101 - [c77]Matej Hajnal, David Safránek, Martin Demko, Samuel Pastva, Pavel Krejcí, Lubos Brim:
Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways. HSB 2016: 57-66 - [c76]Milan Ceska, Petr Pilar, Nicola Paoletti, Lubos Brim, Marta Z. Kwiatkowska:
PRISM-PSY: Precise GPU-Accelerated Parameter Synthesis for Stochastic Systems. TACAS 2016: 367-384 - 2015
- [c75]Alessandro Abate, Lubos Brim, Milan Ceska, Marta Z. Kwiatkowska:
Adaptive Aggregation of Markov Chains: Quantitative Analysis of Chemical Reaction Networks. CAV (1) 2015: 195-213 - [c74]Lubos Brim, Milan Ceska, Martin Demko, Samuel Pastva, David Safránek:
Parameter Synthesis by Parallel Coloured CTL Model Checking. CMSB 2015: 251-263 - [c73]Lubos Brim, Martin Demko, Samuel Pastva, David Safránek:
High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. HSB 2015: 58-74 - [c72]T. Ded, David Safránek, Matej Troják, Matej Klement, Jakub Salagovic, Lubos Brim:
Formal Biochemical Space with Semantics in Kappa and BNGL. SASB 2015: 27-49 - [i8]Jiri Barnat, Petr Bauch, Nikola Benes, Lubos Brim, Jan Beran, Tomas Kratochvila:
Analysing Sanity of Requirements for Avionics Systems (Preliminary Version). CoRR abs/1510.02669 (2015) - 2014
- [j19]Petr Rockai, Jiri Barnat, Lubos Brim:
Model Checking C++ with Exceptions. Electron. Commun. Eur. Assoc. Softw. Sci. Technol. 70 (2014) - [j18]Lubos Brim, Petr Dluhos, David Safránek, Tomas Vejpustek:
STL⁎: Extending signal temporal logic with signal-value freezing operator. Inf. Comput. 236: 52-67 (2014) - [c71]Lubos Brim, J. Niznan, David Safránek:
Compact Representation of Photosynthesis Dynamics by Rule-based Models. SASB 2014: 17-27 - [i7]Lubos Brim, J. Niznan, David Safránek:
Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version). CoRR abs/1410.3632 (2014) - 2013
- [c70]Jiri Barnat, Lubos Brim, Vojtech Havel:
LTL Model Checking of Parallel Programs with Under-Approximated TSO Memory Model. ACSD 2013: 51-59 - [c69]Lubos Brim, Vilém Ded, David Safránek:
Qualitative modelling and analysis of Photosystem II. BioPPN@Petri Nets 2013: 17-29 - [c68]Lubos Brim, Milan Ceska, Sven Drazan, David Safránek:
Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. CAV 2013: 107-123 - [c67]Jiri Barnat, Lubos Brim, Vojtech Havel, Jan Havlícek, Jan Kriho, Milan Lenco, Petr Rockai, Vladimír Still, Jirí Weiser:
DiVinE 3.0 - An Explicit-State Model Checker for Multithreaded C & C++ Programs. CAV 2013: 863-868 - [c66]Petr Rockai, Jiri Barnat, Lubos Brim:
Improved State Space Reductions for LTL Model Checking of C and C++ Programs. NASA Formal Methods 2013: 1-15 - [c65]Lubos Brim, Milan Ceska, David Safránek:
Model Checking of Biological Systems. SFM 2013: 63-112 - [c64]Lubos Brim, Tomas Vejpustek, David Safránek, Jana Fabriková:
Robustness Analysis for Value-Freezing Signal Temporal Logic. HSB 2013: 20-36 - [i6]Lubos Brim, Milan Ceska, Sven Drazan, David Safránek:
On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking. CoRR abs/1310.4734 (2013) - 2012
- [j17]Lubos Brim, Jakub Chaloupka:
Using Strategy Improvement to Stay Alive. Int. J. Found. Comput. Sci. 23(3): 585-608 (2012) - [j16]Jiri Barnat, Petr Bauch, Lubos Brim, Milan Ceska:
Designing fast LTL model checking algorithms for many-core GPUs. J. Parallel Distributed Comput. 72(9): 1083-1097 (2012) - [j15]Jiri Barnat, Lubos Brim, Petr Rockai:
On-the-fly parallel model checking algorithm that is optimal for verification of weak LTL properties. Sci. Comput. Program. 77(12): 1272-1288 (2012) - [j14]Jiri Barnat, Lubos Brim, Adam Krejci, Adam Streck, David Safránek, Martin Vejnar, Tomas Vejpustek:
On Parameter Synthesis by Parallel Model Checking. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 693-705 (2012) - [j13]Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek:
On Approximative Reachability Analysis of Biochemical Dynamical Systems. Trans. Comp. Sys. Biology 14: 77-101 (2012) - [c63]Jiri Barnat, Jan Beran, Lubos Brim, Tomas Kratochvila, Petr Rockai:
Tool Chain to Support Automated Formal Verification of Avionics Simulink Designs. FMICS 2012: 78-92 - [c62]Jiri Barnat, Lubos Brim, Petr Rockai:
Towards LTL Model Checking of Unmodified Thread-Based C & C++ Programs. NASA Formal Methods 2012: 252-266 - [c61]Jiri Barnat, Petr Bauch, Lubos Brim:
Checking Sanity of Software Requirements. SEFM 2012: 48-62 - [c60]Jiri Barnat, Lubos Brim, Jan Beran, Tomas Kratochvila, Italo R. Oliveira:
Executing Model Checking Counterexamples in Simulink. TASE 2012: 245-248 - [c59]Petr Dluhos, Lubos Brim, David Safránek:
On Expressing and Monitoring Oscillatory Dynamics. HSB 2012: 73-87 - [c58]S. Van Goethem, Jean-Marie Jacquet, Lubos Brim, David Safránek:
Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization. CS2Bio 2012: 67-81 - 2011
- [j12]David Safránek, Jan Cervený, Matej Klement, Jana Pospísilová, Lubos Brim, Dusan Lazar, Ladislav Nedbal:
E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. Biosyst. 103(2): 115-124 (2011) - [j11]Lubos Brim, Jakub Chaloupka, Laurent Doyen, Raffaella Gentilini, Jean-François Raskin:
Faster algorithms for mean-payoff games. Formal Methods Syst. Des. 38(2): 97-118 (2011) - [j10]Stefan Edelkamp, Damian Sulewski, Jiri Barnat, Lubos Brim, Pavel Simecek:
Flash memory efficient LTL model checking. Sci. Comput. Program. 76(2): 136-157 (2011) - [j9]Nikola Benes, Lubos Brim, Barbora Buhnova, Ivana Cerná, Jiri Sochor, Pavlína Vareková:
Partial order reduction for state/event LTL with application to component-interaction automata. Sci. Comput. Program. 76(10): 877-890 (2011) - [c57]Jiri Barnat, Petr Bauch, Lubos Brim, Milan Ceska:
Computing Strongly Connected Components in Parallel on CUDA. IPDPS 2011: 544-555 - [c56]Lubos Brim, Jiri Barnat:
Platform Dependent Verification: On Engineering Verification Tools for 21st Century. PDMC 2011: 1-12 - [c55]Jiri Barnat, Petr Bauch, Lubos Brim, Milan Ceska:
Computing Optimal Cycle Mean in Parallel on CUDA. PDMC 2011: 68-83 - [c54]Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek:
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract). CompMod 2011: 97-112 - [i5]Lubos Brim, Jana Fabriková, Sven Drazan, David Safránek:
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation. CoRR abs/1107.5924 (2011) - 2010
- [j8]Jiri Barnat, Lubos Brim, David Safránek:
High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings Bioinform. 11(3): 301-312 (2010) - [j7]Jiri Barnat, Lubos Brim, Petr Rockai:
Scalable shared memory LTL model checking. Int. J. Softw. Tools Technol. Transf. 12(2): 139-153 (2010) - [c53]Jiri Barnat, Petr Bauch, Lubos Brim, Milan Ceska:
Employing Multiple CUDA Devices to Accelerate LTL Model Checking. ICPADS 2010: 259-266 - [c52]Jiri Barnat, Lubos Brim, Petr Rockai:
Parallel Partial Order Reduction with Topological Sort Proviso. SEFM 2010: 222-231 - [c51]Lubos Brim, Jakub Chaloupka:
Using Strategy Improvement to Stay Alive. GANDALF 2010: 40-54
2000 – 2009
- 2009
- [j6]Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, Jana Fabriková, David Safránek:
On algorithmic analysis of transcriptional regulation by LTL model checking. Theor. Comput. Sci. 410(33-34): 3128-3148 (2009) - [c50]Jiri Barnat, Lubos Brim, Petr Rockai:
A Time-Optimal On-the-Fly Parallel Algorithm for Model Checking of Weak LTL Properties. ICFEM 2009: 407-425 - [c49]Jiri Barnat, Lubos Brim, Milan Ceska, Tomas Lamr:
CUDA Accelerated LTL Model Checking. ICPADS 2009: 34-41 - [c48]Nikola Benes, Lubos Brim, Ivana Cerná, Jiri Sochor, Pavlína Vareková, Barbora Zimmerová:
Partial Order Reduction for State/Event LTL. IFM 2009: 307-321 - [c47]Kees Verstoep, Henri E. Bal, Jiri Barnat, Lubos Brim:
Efficient large-scale model checking. IPDPS 2009: 1-12 - [c46]Jiri Barnat, Lubos Brim, Pavel Simecek:
Cluster-Based I/O-Efficient LTL Model Checking. ASE 2009: 635-639 - [c45]Jakub Chaloupka, Lubos Brim:
Faster Algorithm for Mean-Payoff Games. MEMICS 2009 - [c44]Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, Jana Fabriková, Jan Láník, David Safránek, Hongwu Ma:
BioDiVinE: A Framework for Parallel Analysis of Biological Models. COMPMOD 2009: 31-45 - [c43]Jiri Barnat, Lubos Brim, Milan Ceska:
DiVinE-CUDA - A Tool for GPU Accelerated LTL Model Checking. PDMC 2009: 107-111 - [e11]Lubos Brim, Stefan Edelkamp, Eric A. Hansen, Peter Sanders:
Graph Search Engineering, 29.11. - 04.12.2009. Dagstuhl Seminar Proceedings 09491, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Germany 2009 [contents] - [e10]Lubos Brim, Jaco van de Pol:
Proceedings 8th International Workshop on Parallel and Distributed Methods in verifiCation, PDMC 2009, Eindhoven, The Netherlands, 4th November 2009. EPTCS 14, 2009 [contents] - [i4]Lubos Brim, Stefan Edelkamp, Eric A. Hansen, Peter Sanders:
09491 Abstracts Collection - Graph Search Engineering. Graph Search Engineering 2009 - 2008
- [c42]Jiri Barnat, Lubos Brim, Petr Rockai:
DiVinE Multi-Core - A Parallel LTL Model-Checker. ATVA 2008: 234-239 - [c41]Jiri Barnat, Lubos Brim, Ivana Cerná, Milan Ceska, Jana Tumova:
Local Quantitative LTL Model Checking. FMICS 2008: 53-68 - [c40]Jiri Barnat, Lubos Brim, Stefan Edelkamp, Damian Sulewski, Pavel Simecek:
Can Flash Memory Help in Model Checking? FMICS 2008: 150-165 - [c39]Jiri Barnat, Lubos Brim:
Squeeze All the Power Out of Your Hardware to Verify Your Software!. ISoLA 2008: 604-618 - [c38]Jiri Barnat, Lubos Brim, Ivana Cerná, Milan Ceska, Jana Tumova:
ProbDiVinE-MC: Multi-core LTL Model Checker for Probabilistic Systems. QEST 2008: 77-78 - [c37]Jiri Barnat, Lubos Brim, Pavel Simecek, M. Weber:
Revisiting Resistance Speeds Up I/O-Efficient LTL Model Checking. TACAS 2008: 48-62 - [e9]Henri E. Bal, Lubos Brim, Martin Leucker:
Distributed Verification and Grid Computing, 10.08. - 14.08.2008. Dagstuhl Seminar Proceedings 08332, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Germany 2008 [contents] - [i3]Henri E. Bal, Lubos Brim, Martin Leucker:
08332 Abstracts Collection - Distributed Verification and Grid Computing. Distributed Verification and Grid Computing 2008 - [i2]Henri E. Bal, Lubos Brim, Martin Leucker:
08332 Executive Summary - Distributed Verification and Grid Computing. Distributed Verification and Grid Computing 2008 - [i1]Kees Verstoep, Henri E. Bal, Jiri Barnat, Lubos Brim:
Efficient Large-Scale Model Checking. Distributed Verification and Grid Computing 2008 - 2007
- [c36]Jiri Barnat, Lubos Brim, Pavel Simecek:
I/O Efficient Accepting Cycle Detection. CAV 2007: 281-293 - [c35]Barbora Zimmerová, Pavlína Vareková, Nikola Benes, Ivana Cerná, Lubos Brim, Jiri Sochor:
Component-Interaction Automata Approach (CoIn). CoCoME 2007: 146-176 - [c34]Jiri Barnat, Lubos Brim, Martin Leucker:
Parallel Model Checking and the FMICS-jETI Platform. ICECCS 2007: 330-339 - [c33]Jiri Barnat, Lubos Brim, Ivana Cerná, Milan Ceska, Jana Tumova:
ProbDiVinE: A Parallel Qualitative LTL Model Checker. QEST 2007: 215-216 - [c32]Lubos Brim, Mojmír Kretínský:
Model-Checking Large Finite-State Systems and Beyond. SOFSEM (1) 2007: 9-28 - [c31]Lubos Brim, Jiri Barnat:
Tutorial: Parallel Model Checking. SPIN 2007: 2-3 - [c30]Jiri Barnat, Lubos Brim, Petr Rockai:
Scalable Multi-core LTL Model-Checking. SPIN 2007: 187-203 - [c29]Jiri Barnat, Lubos Brim, Ivana Cerná, Sven Drazan, David Safránek:
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. FBTC@CONCUR 2007: 35-50 - [e8]Lubos Brim, Boudewijn R. Haverkort, Martin Leucker, Jaco van de Pol:
Formal Methods: Applications and Technology, 11th International Workshop, FMICS 2006 and 5th International Workshop PDMC 2006, Bonn, Germany, August 26-27, and August 31, 2006, Revised Selected Papers. Lecture Notes in Computer Science 4346, Springer 2007, ISBN 978-3-540-70951-0 [contents] - 2006
- [j5]Lubos Brim, Martin Leucker:
Foreword. Formal Methods Syst. Des. 29(2): 115-116 (2006) - [j4]Lubos Brim, Ivana Cerná, Pavlína Vareková, Barbora Zimmerová:
Component-interaction automata as a verification-oriented component-based system specification. ACM SIGSOFT Softw. Eng. Notes 31(2) (2006) - [c28]Jiri Barnat, Lubos Brim, Ivana Cerná,