Selected Publications
From among the hundreds of papers annually published by scientists at FI, here is a brief overview of those published at the world's top CS conferences (A*), and in the top ten percent of scientific journals, as ranked by Journal Citation Reports.
“They’re not that hard to mitigate”: What Cryptographic Library Developers Think About Timing Attacks
Jančár, Ján — Fourné, Marcel — De Almeida Braga, Daniel — Sabt, Mohamed — Schwabe, Peter — Barthe, Gilles — Fouque, Pierre-Alain — Acar, Yasemin
Security and Privacy (S&P 2022), DOI
CombOptNet: Fit the Right NP-Hard Problem by Learning Integer Programming Constraints
Paulus, Anselm — Rolínek, Michal — Musil, Vít — Amos, Brandon — Martius, Georg
International Conference on Machine Learning (ICML 2021), URL
Computing Bottom SCCs Symbolically Using Transition Guided Reduction
Beneš, Nikola — Brim, Luboš — Pastva, Samuel — Šafránek, David
Computer Aided Verification (CAV 2021), DOI
Counting Maximal Satisfiable Subsets
Bendík, Jaroslav — Meel, Kuldeep S.
AAAI Conference on Artificial Intelligence (AAAI 2021), URL
Counting Minimal Unsatisfiable Subsets
Bendík, Jaroslav — Meel, Kuldeep S.
Computer Aided Verification (CAV 2021), DOI
Fast Computation of Strong Control Dependencies
Chalupa, Marek — Klaška, David — Strejček, Jan — Tomovič, Lukáš
Computer Aided Verification (CAV 2021), DOI
Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures
Hermosilla Casajús, Pedro — Schäfer, Marco — Lang, Matěj — Fackelmann, Gloria — Vázquez Alcocer, Pere-Pau — Kozlíková, Barbora — Krone, Michael — Ritschel, Tobias — Ropinski, Timo
International Conference on Learning Representations (ICLR 2021), URL
Proving non-termination by program reversal
Chatterjee, Krishnendu — Goharshady, Ehsan Kafshdar — Novotný, Petr — Žikelić, Djordje
Programming Language Design and Implementation (PLDI 2021), DOI
What Players Want: Information Needs of Players on Post-Game Visualizations
Wallner, Günter — Wijland, Marnix van — Bernhaupt, Regina — Kriglstein, Simone
Human Factors in Computing Systems (CHI 2021), DOI
Adversarial Patrolling with Drones
Klaška, David — Kučera, Antonín — Řehák, Vojtěch
Autonomous Agents and Multiagent Systems (AAMAS 2020), DOI
AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks
Beneš, Nikola — Brim, Luboš — Kadlecaj, Jakub — Pastva, Samuel — Šafránek, David
Computer Aided Verification (CAV 2020), DOI
Approximate Counting of Minimal Unsatisfiable Subsets
Bendík, Jaroslav — Meel, Kuldeep S.
Computer Aided Verification (CAV 2020), DOI
BIAS: Transparent reporting of biomedical image analysis challenges
Maier-Hein, Lena — Reinke, Annika — Kozubek, Michal — Martel, Anne L. — Arbel, Tal — Eisenmann, Matthias — Hanbury, Allan — Jannin, Pierre — Müller, Henning — Onogur, Sinan — Saez-Rodriguez, Julio — van Ginneken, Bram — Kopp-Schneider, Annette — Landman, Bennett A.
Medical Image Analysis, 2020, DOI
Checking Qualitative Liveness Properties of Replicated Systems with Stochastic Scheduling
Blondin, Michael — Esparza, Javier — Helfrich, Martin — Kučera, Antonín — Meyer, Philipp
Computer Aided Verification (CAV 2020), DOI
Efficient Analysis of VASS Termination Complexity
Kučera, Antonín — Leroux, Jérôme — Velan, Dominik
Logic in Computer Science (LICS 2020), DOI
Improved bounds for centered colorings
Debski, Michal Karol — Felsner, Stefan — Micek, Piotr — Schröder, Felix
Symposium on Discrete Algorithms (SODA 2020), DOI
Improving Orienteering-based Tourist Trip Planning with Social Sensing
Persia, Fabio — Pilato, Giovanni — Ge, Mouzhi — Bolzoni, Paolo — D'Auria, Daniela — Sven, Helmer
Future Generation Computer Systems, 2020, DOI
Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications
Chatterjee, Krishnendu — Chmelík, Martin — Karkhanis, Deep — Novotný, Petr — Royer, Amélie
Automated Planning and Scheduling (ICAPS 2020), URL
pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm
Labudová, Dominika — Hon, Jiří — Lexa, Matej
Bioinformatics, 2020, DOI
Qualitative Controller Synthesis for Consumption Markov Decision Processes
Blahoudek, František — Brázdil, Tomáš — Novotný, Petr — Ornik, Melkior — Thangeda, Pranay — Topcu, Ufuk
Computer Aided Verification (CAV 2020), DOI
Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes
Brázdil, Tomáš — Chatterjee, Krishnendu — Novotný, Petr — Vahala, Jiří
AAAI Conference on Artificial Intelligence (AAAI 2020), DOI
Seminator 2 Can Complement Generalized Büchi Automata via Improved Semi-determinization
Blahoudek, František — Duret-Lutz, Alexandre — Strejček, Jan
Computer Aided Verification (CAV 2020), DOI
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
Lexa, Matej — Jedlicka, Pavel — Vanát, Ivan — Červeňanský, Michal — Kejnovský, Eduard
Bioinformatics, 2020, DOI
What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?
Jedlicka, Pavel — Lexa, Matej — Kejnovský, Eduard
Frontiers in Plant Science, 2020, DOI
Would You Do It?: Enacting Moral Dilemmas in Virtual Reality for Understanding Ethical Decision-Making
Niforatos, Evangelos — Palma, Adam — Gluszny, Roman — Vourvopoulos, Athanasios — Liarokapis, Fotios
Human Factors in Computing Systems (CHI 2021), 2020, DOI
3-D Quantification of Filopodia in Motile Cancer Cells
Castilla, Carlos — Maška, Martin — Sorokin, Dmitry — Meijering, Erik — Ortiz-de-Solórzano, Carlos
IEEE Transactions on Medical Imaging, 2019, DOI
Compactness and finite forcibility of graphons
Glebov, Roman — Kráľ, Daniel — Volec, Jan
Journal of the European Mathematical Society, 2019, DOI
CytoPacq: A web-interface for simulating multi-dimensional cell imaging
Wiesner, David — Svoboda, David — Maška, Martin — Kozubek, Michal
Bioinformatics, 2019, DOI
Examining And Enhancing The Illusory Touch Perception In Virtual Reality Using Non-Invasive Brain Stimulation
Škola, Filip — Liarokapis, Fotis
Human Factors in Computing Systems (CHI 2019), DOI
Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments
Kouřil, David — Čmolík, Ladislav — Kozlíková, Barbora — Wu, Hsiang-Yun — Johnson, Graham — Goodsell, David S. — Olson, Arthur — Groeller, Eduard M. — Viola, Ivan
IEEE Transactions on Visualization and Computer Graphics, 2019, DOI
Mistakes in UML Diagrams: Analysis of Student Projects in a Software Engineering Course
Chren, Stanislav — Bühnová, Barbora — Macák, Martin — Daubner, Lukáš — Rossi, Bruno
Software Engineering (ICSE 2019), DOI
Optimal Probabilistic Storage and Retrieval of Unitary Channels
Sedlák, Michal — Bisio, Alessandro — Ziman, Mário
Physical Review Letters, 2019, DOI
PAC Statistical Model Checking for Markov Decision Processes and Stochastic Games
Ashok, Pranav — Křetínský, Jan — Weininger, Maximilian
Computer Aided Verification (CAV 2019), DOI
Postcards from the Post-HTTP World: Amplification of HTTPS Vulnerabilities in the Web Ecosystem
Calzavara, Stefano — Focardi, Riccardo — Nemec, Matúš — Rabitti, Alvise — Squarcina, Marco
Security and Privacy (S&P 2019), DOI
Q3B: An Efficient BDD-based SMT Solver for Quantified Bit-Vectors
Jonáš, Martin — Strejček, Jan
Computer Aided Verification (CAV 2019), DOI
Solving Integer Quadratic Programming via Explicit and Structural Restrictions
Eiben, Eduard — Ganian, Robert — Knop, Dusan — Ordyniak, Sebastian
AAAI Conference on Artificial Intelligence (AAAI 2019), DOI
The Parameterized Complexity of Cascading Portfolio Scheduling
Eiben, Eduard — Ganian, Robert — Kanj, Iyad — Szeider, Stefan
Advances in Neural Information Processing Systems (NIPS 2019), URL
Unbounded Orchestrations of Transducers for Manufacturing
Alechina, Natasha — Brázdil, Tomáš — De Giacomo, Giuseppe — Felli, Paolo — Logan, Brian — Vardi, Moshe
AAAI Conference on Artificial Intelligence (AAAI 2019), DOI
Visualization of Large Molecular Trajectories
Duran, David — Hermosilla, Pedro — Ropinski, Timo — Kozlíková, Barbora — Vinacua, Álvar — Vazquez, Pere-Pau
IEEE Transactions on Visualization and Computer Graphics, 2019, DOI
A large-scale comparative study of beta testers and regular users
Šťavová, Vlasta — Dědková, Lenka — Ukrop, Martin — Matyáš, Václav
Communications of the ACM, 2018, DOI
A Structural Approach to Activity Selection
Eiben, Eduard — Ganian, Robert — Ordyniak, Sebastian
Joint Conference on Artificial Intelligence (IJCAI 2018), DOI
Automatic Synthesis of Efficient Regular Strategies in Adversarial Patrolling Games
Klaška, David — Kučera, Antonín — Lamser, Tomáš — Řehák, Vojtěch
Autonomous Agents & Multiagent Systems (AAMAS 2018), DOI
CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories
Jurčík, Adam — Bednář, David — Byška, Jan — Marques, Sérgio Manuel — Furmanová, Katarína — Daniel, Lukáš — Kokkonen, Piia Pauliina — Brezovský, Jan — Strnad, Ondřej — Štourač, Jan — Pavelka, Antonín — Manak, Martin — Damborský, Jiří — Kozlíková, Barbora
Bioinformatics, 2018, DOI
Conditional Value-at-Risk for Reachability and Mean Payoff in Markov Decision Processes
Křetínský, Jan — Meggendorfer, Tobias
Logic in Computer Science (LICS 2018), DOI
Data-centric Dynamic Partial Order Reduction
Pavlogiannis, Andreas — Chalupa, Marek — Chatterjee, Krishnendu — Sinha, Nishant — Vaidya, Kapil
Principles of Programming Languages (POPL 2018), DOI
Detection of Advanced Persistent Threat Using Machine-Learning Correlation Analysis
Ghafir, Ibrahim — Hammoudeh, Mohammad — Přenosil, Václav — Han, Liangxiu — Hegarty, Robert — Rabie, Khaled — Aparicio-Navarro, Francisco J.
Future Generation Computer Systems, 2018, DOI
Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS
Brázdil, Tomáš — Chatterjee, Krishnendu — Kučera, Antonín — Novotný, Petr — Velan, Dominik — Zuleger, Florian
Logic in Computer Science (LICS 2018), DOI
FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia
Sorokin, Dmitry — Peterlík, Igor — Ulman, Vladimír — Svoboda, David — Nečasová, Tereza — Morgaenko, Katsiarina — Eiselleová, Lívia — Tesařová, Lenka — Maška, Martin
IEEE Transactions on Medical Imaging, 2018, DOI
Instant Construction and Visualization of Crowded Biological Environments
Klein, Tobias — Autin, Ludovic — Kozlíková, Barbora — Goodsell, David S. — Olson, Arthur — Gröller, Eduard M. — Viola, Ivan
IEEE Transactions on Visualization and Computer Graphics, 2018, DOI
Non-rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model
Sorokin, Dmitry — Peterlík, Igor — Tektonidis, Marco — Rohr, Karl — Matula, Pavel
IEEE Transactions on Medical Imaging, 2018, DOI
Parameterized Algorithms for the Matrix Completion Problem
Ganian, Robert — Kanj, Iyad — Ordyniak, Sebastian — Szeider, Stefan
Machine Learning (ICML 2018), URL
Polynomial-Time What-If Analysis for Prefix-Manipulating MPLS Networks
Schmid, Stefan — Srba, Jiří
Computer Communications (INFOCOM 2018), DOI
Practical device-independent quantum cryptography via entropy accumulation
Arnon-Friedman, Rotem — Dupont Dupuis, Frédéric — Fawzi, Omar — Renner, Renato — Vidick, Thomas
Nature Communications, 2018, DOI
Solving Patrolling Problems in the Internet Environment
Brázdil, Tomáš — Kučera, Antonín — Řehák, Vojtěch
Joint Conference on Artificial Intelligence (IJCAI 2018), DOI
Start Pruning When Time Gets Urgent: Partial Order Reduction for Timed Systems
Boenneland, Frederik M. — Jensen, Peter G. — Larsen, Kim G. — Muniz, Marco — Srba, Jiří
Computer Aided Verification (CAV 2018), DOI
The Broken Shield: Measuring Revocation Effectiveness in the Windows Code-Signing PKI
Kim, Doowon — Kwon, Bum Jun — Kozák, Kristián — Gates, Christopher — Dumitraș, Tudor
USENIX Security (USENIX 2018), URL
Unary Integer Linear Programming with Structural Restrictions
Eiben, Eduard — Ganian, Robert — Knop, Dusan — Ordyniak, Sebastian
Joint Conference on Artificial Intelligence (IJCAI 2018), DOI
Value Iteration for Simple Stochastic Games: Stopping Criterion and Learning Algorithm
Kelmendi, Edon — Krämer, Julia — Křetínský, Jan — Weininger, Maximilian
Computer Aided Verification (CAV 2018), DOI
Why rankings of biomedical image analysis competitions should be interpreted with care
Maier-Hein, Lena — Eisenmann, Matthias — Reinke, Annika — Onogur, Sinan — Stankovic, Marko — Scholz, Patrick — Arbel, Tal — Bogunovic, Hrvoje — Bradley, Andrew — Carass, Aaron — Feldmann, Carolin — Frangi, Alejandro — Full, Peter — van Ginneken, Bram — Hanbury, Allan — Honauer, Katrin — Kozubek, Michal — Landman, Bennett — März, Keno — Maier, Oskar — Maier-Hein, Klaus — Menze, Bjoern — Müller, Henning — Neher, Peter — Niessen, Wiro — Rajpoot, Nasir — Sharp, Gregory — Sirinukunwattana, Korsuk — Speidel, Stefanie — Stock, Christian — Stoyanov, Danail — Taha, Abdel Aziz — van der Sommen, Fons — Wang, Ching-Wei — Weber, Marc-André — Zheng, Guoyan — Jannin, Pierre — Kopp-Schneider, Annette
Nature Communications, 2018, DOI
A Touch of Evil: High-Assurance Cryptographic Hardware from Untrusted Components
Mavroudis, Vasilios — Cerulli, Andrea — Švenda, Petr — Cvrček, Daniel — Klinec, Dušan — Danezis, George
Computer and Communications Security (CCS 2017), DOI
Algorithm 970: Optimizing the NIST Statistical Test Suite and the Berlekamp-Massey Algorithm
Sýs, Marek — Říha, Zdeněk — Matyáš, Václav
ACM Transactions on Mathematical Software, 2017, DOI
An objective comparison of cell-tracking algorithms
Ulman, Vladimír — Maška, Martin — Magnusson, Klas E G — Ronneberger, Olaf — Haubold, Carsten — Harder, Nathalie — Matula, Pavel — Matula, Petr — Svoboda, David — Radojevic, Miroslav — Smal, Ihor — Rohr, Karl — Jaldén, Joakim — Blau, Helen M — Dzyubachyk, Oleh — Lelieveldt, Boudewijn — Xiao, Pengdong — Li, Yuexiang — Cho, Siu-Yeung — Dufour, Alexandre C — Olivo-Marin, Jean-Christophe — Reyes-Aldasoro, Constantino C — Solis-Lemus, Jose A — Bensch, Robert — Brox, Thomas — Stegmaier, Johannes — Mikut, Ralf — Wolf, Steffen — Hamprecht, Fred A — Esteves, Tiago — Quelhas, Pedro — Demirel, Ömer — Malmström, Lars — Jug, Florian — Tomancak, Pavel — Meijering, Erik — Muñoz-Barrutia, Arrate — Kozubek, Michal — Ortiz-de-Solorzano, Carlos
Nature Methods, 2017, DOI
Catalytic decoupling of quantum information
Majenz, Christian — Berta, Mario — Dupont Dupuis, Frédéric — Renner, Renato — Christandl, Matthias
Physical Review Letters, 2017, DOI
Going Beyond Primal Treewidth for {(M)ILP}
Ganian, Robert — Ramanujan, M.S. — Ordyniak, Sebastian
AAAI Conference on Artificial Intelligence (AAAI 2017), URL
MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy
Svoboda, David — Ulman, Vladimír
IEEE Transactions on Medical Imaging, 2017, DOI
Phosphorylation-Dependent Feedback Inhibition of RIG-I by DAPK1 Identified by Kinome-wide siRNA Screening
Willemsen, Joschka — Wicht, Oliver — Wolanski, Julia — Baur, Nina — Bastian, Sandra — Haas, Darya — Matula, Petr — Knapp, Bettina — Meyniel-Schicklin, Laurene — Wang, Chen — Bartenschlager, Ralf — Lohmann, Volker — Rohr, Karl — Erfle, Holger — Kaderali, Lars — Marcotrigiano, Joseph — Pichlmair, Andreas — Binder, Marco
Molecular Cell, 2017, DOI
Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-Affine Dynamical Systems
Beneš, Nikola — Brim, Luboš — Demko, Martin — Pastva, Samuel — Šafránek, David
Computer Aided Verification (CAV 2017), DOI
pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R
Hon, Jiří — Martínek, Tomáš — Zendulka, Jaroslav — Lexa, Matej
Bioinformatics, 2017, DOI
Solving Integer Linear Programs with a Small Number of Global Variables and Constraints
Dvorak, Pavel — Eiben, Eduard — Ganian, Robert — Knop, Dusan — Ordyniak, Sebastian
Joint Conference on Artificial Intelligence (IJCAI 2017), DOI
Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games
Svoreňová, Mária — Křetínský, Jan — Chmelík, Martin — Chatterjee, Krishnendu — Černá, Ivana — Belta, Calin
Nonlinear Analysis: Hybrid Systems, 2017, DOI
The Return of Coppersmith's Attack: Practical Factorization of Widely Used RSA Moduli
Nemec, Matúš — Sýs, Marek — Švenda, Petr — Klinec, Dušan — Matyáš, Václav
Computer and Communications Security (CCS 2017), DOI
Data updated on 2022/2/24.