Selected Publications

Generative modeling of living cells with SO(3)-equivariant implicit neural representations

Wiesner, David — Suk, Julian — Dummer, Sven — Nečasová, Tereza — Vladimír, Ulman — Svoboda, David — Wolterink, Jelmer
Medical Image Analysis, 2024, DOI

Machine learning estimated probability of relapse in early-stage non-small-cell lung cancer patients with aneuploidy imputation scores and knowledge graph embeddings

Buosi, Samuele — Timilsina, Mohan — Janik, Adriann — Costabello, Luca — Torrente, Maria — Provencio, Mariano — Fey, Dirk — Nováček, Vít
Expert Systems with Applications, 2024, DOI

Using data clustering to reveal trainees’ behavior in cybersecurity education

Dočkalová Burská, Karolína — Mlynárik, Jakub Rudolf — Ošlejšek, Radek
Education and Information Technologies, 2024, DOI

Applications of deep language models for reflective writings

Nehyba, Jan — Štefánik, Michal
EDUCATION AND INFORMATION TECHNOLOGIES, 2023, DOI

Automated Feedback for Participants of Hands-on Cybersecurity Training

Švábenský, Valdemar — Vykopal, Jan — Čeleda, Pavel — Dovjak, Ján
Education and Information Technologies, 2023, DOI

Calc-X and Calcformers: Empowering Arithmetical Chain-of-Thought through Interaction with Symbolic Systems

Kadlčík, Marek — Štefánik, Michal — Sotolář, Ondřej — Martinek, Vlastimil
Empirical Methods in Natural Language Processing (EMNLP 2023), DOI

Guessing Winning Policies in LTL Synthesis by Semantic Learning

Křetínský, Jan — Meggendorfer, Tobias — Prokop, Maximilian — Rieder, Sabine
Computer Aided Verification (CAV 2023), DOI

Kratos2: An SMT-Based Model Checker for Imperative Programs

Griggio, Alberto — Jonáš, Martin
Computer Aided Verification (CAV 2023), DOI

Mean Payoff Optimization for Systems of Periodic Service and Maintenance

Klaška, David — Kučera, Antonín — Musil, Vít — Řehák, Vojtěch
International Joint Conference on Artificial Intelligence (IJCAI 2023), DOI

Optical Cryptanalysis: Recovering Cryptographic Keys from Power LED Light Fluctuations

Nassi, Ben — Vayner, Ofek — Iluz, Etay — Nassi, Dudi — Cohen, Or Hai — Jančár, Ján — Genkin, Daniel — Tromer, Eran — Zadov, Boris — Elovici, Yuval
Computer and Communications Security (CCS 2023), DOI

Optimal Sobolev embeddings for the Ornstein-Uhlenbeck operator

Cianchi, Andrea — Musil, Vít — Pick, Luboš
Journal of Differential Equations, 2023, DOI

Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy

Hradecká, Lucia — Wiesner, David — Sumbal, Jakub — Sumbalová Koledová, Zuzana — Maška, Martin
IEEE Transactions on Medical Imaging, 2023, DOI

Shielding in Resource-Constrained Goal POMDPs

Ajdarów, Michal — Brlej, Šimon — Novotný, Petr
AAAI Conference on Artificial Intelligence (AAAI 2023), DOI

Soft Alignment Objectives for Robust Adaptation of Language Generation

Štefánik, Michal — Kadlčík, Marek — Sojka, Petr
Annual Meeting of the Association for Computational Linguistics (ACL 2023), DOI

Synthesizing Resilient Strategies for Infinite-Horizon Objectives in Multi-Agent Systems

Klaška, David — Kučera, Antonín — Kurečka, Martin — Musil, Vít — Novotný, Petr — Řehák, Vojtěch
International Joint Conference on Artificial Intelligence (IJCAI 2023), DOI

Tentacle-Based Shape Shifting of Metamorphic Robots Using Fast Inverse Kinematics

Mrázek, Jan — Ondika, Patrick — Černá, Ivana — Barnat, Jiří
International Conference on Robotics and Automation (ICRA 2023), DOI

The Cell Tracking Challenge: 10 years of objective benchmarking

Maška, Martin — Ulman, Vladimír — Delgado-Rodriguez, Pablo — Gómez-de-Mariscal, Estibaliz — Nečasová, Tereza — Peña, Fidel A Guerrero — Ren, Tsang Ing — Meyerowitz, Elliot M — Scherr, Tim — Löffler, Katharina — Mikut, Ralf — Guo, Tianqi — Wang, Yin — Allebach, Jan P — Bao, Rina — Al-Shakarji, Noor M — Rahmon, Gani — Toubal, Imad Eddine — Palaniappan, Kannappan — Lux, Filip — Matula, Petr — Sugawara, Ko — Magnusson, Klas E G — Aho, Layton — Cohen, Andrew R — Arbelle, Assaf — Ben-Haim, Tal — Raviv, Tammy Riklin — Isensee, Fabian — Jäger, Paul F — Maier-Hein, Klaus H — Zhu, Yanming — Ederra, Cristina — Urbiola, Ainhoa — Meijering, Erik — Cunha, Alexandre — Muñoz-Barrutia, Arrate — Kozubek, Michal — Ortiz-de-Solórzano, Carlos
Nature Methods, 2023, DOI

CATANA: an online modelling environment for proteins and nucleic acid nanostructures

Kuťák, David — Melo, Lucas — Schroeder, Fabian — Jelic-Matošević, Zoe — Mutter, Natalie — Bertoša, Branimir — Barišić, Ivan
Nucleic acids research, 2022, DOI

Even if users do not read security directives, their behavior is not so catastrophic

Matyáš, Václav — Malinka, Kamil — Kraus, Lydia — Knapová, Lenka — Kružíková, Agáta
Communications of the ACM, 2022, DOI

Federated learning enables big data for rare cancer boundary detection

Pati, Sarthak — Baid, Ujjwal — Edwards, Brandon — Sheller, Micah — Wang, Shih-Han — Reina, G Anthony — Foley, Patrick — Gruzdev, Alexey — Karkada, Deepthi — Davatzikos, Christos — Sako, Chiharu — Ghodasara, Satyam — Bilello, Michel — Mohan, Suyash — Vollmuth, Philipp — Brugnara, Gianluca — Preetha, Chandrakanth J — Sahm, Felix — Maier-Hein, Klaus — Zenk, Maximilian — Bendszus, Martin — Wick, Wolfgang — Calabrese, Evan — Rudie, Jeffrey — Villanueva-Meyer, Javier — Cha, Soonmee — Ingalhalikar, Madhura — Jadhav, Manali — Pandey, Umang — Saini, Jitender — Garrett, John — Larson, Matthew — Jeraj, Robert — Currie, Stuart — Frood, Russell — Fatania, Kavi — Huang, Raymond Y — Chang, Ken — Quintero, Carmen Balaña — Capellades, Jaume — Puig, Josep — Trenkler, Johannes — Pichler, Josef — Necker, Georg — Haunschmidt, Andreas — Meckel, Stephan — Shukla, Gaurav — Liem, Spencer — Alexander, Gregory S — Lombardo, Joseph — Palmer, Joshua D — Flanders, Adam E — Dicker, Adam P — Sair, Haris I — Jones, Craig K — Venkataraman, Archana — Jiang, Meirui — So, Tiffany Y — Chen, Cheng — Heng, Pheng Ann — Dou, Qi — Kozubek, Michal — Lux, Filip — Michálek, Jan — Matula, Petr — Keřkovský, Miloš — Kopřivová, Tereza — Dostál, Marek — Vybíhal, Václav — Vogelbaum, Michael A — Mitchell, J Ross — Farinhas, Joaquim — Maldjian, Joseph A — Yogananda, Chandan Ganesh Bangalore — Pinho, Marco C — Reddy, Divya — Holcomb, James — Wagner, Benjamin C — Ellingson, Benjamin M — Cloughesy, Timothy F — Raymond, Catalina — Oughourlian, Talia — Hagiwara, Akifumi — Wang, Chencai — To, Minh-Son — Bhardwaj, Sargam — Chong, Chee — Agzarian, Marc — Falcão, Alexandre Xavier — Martins, Samuel B — Teixeira, Bernardo C A — Sprenger, Flávia — Menotti, David — Lucio, Diego R — LaMontagne, Pamela — Marcus, Daniel — Wiestler, Benedikt — Kofler, Florian — Ezhov, Ivan — Metz, Marie — Jain, Rajan
Nature Communications, 2022, DOI

General Optimization Framework for Recurrent Reachability Objectives

Klaška, David — Kučera, Antonín — Musil, Vít — Řehák, Vojtěch
International Joint Conference on Artificial Intelligence (IJCAI 2022), DOI

“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

Biological applications of knowledge graph embedding models

Mohamed, Sameh K — Nounu, Ayah — Nováček, Vít
Briefings in Bioinformatics, 2021, 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

Proving non-termination by program reversal

Chatterjee, Krishnendu — Goharshady, Ehsan Kafshdar — Novotný, Petr — Žikelić, Djordje
Programming Language Design and Implementation (PLDI 2021), DOI

Semantic-driven Watermarking of Relational Textual Databases

Làzaro Pèrez Gort, Maikel — Olliaro, Martina — Cortesi, Agostino — Feregrino Uribe, Claudia
Expert Systems with Applications, 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

Who Is Smart with Their Smartphones? Determinants of Smartphone Security Behavior

Knapová, Lenka — Kružíková, Agáta — Dědková, Lenka — Šmahel, David
Cyberpsychology, Behavior, and Social Networking, 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

Dębski, Michał 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