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